Links to Exploration step
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification of genetic relationships and subspecies signatures in <italic>Xylella fastidiosa</italic></title><author><name sortKey="Denance, Nicolas" sort="Denance, Nicolas" uniqKey="Denance N" first="Nicolas" last="Denancé">Nicolas Denancé</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Briand, Martial" sort="Briand, Martial" uniqKey="Briand M" first="Martial" last="Briand">Martial Briand</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Gaborieau, Romain" sort="Gaborieau, Romain" uniqKey="Gaborieau R" first="Romain" last="Gaborieau">Romain Gaborieau</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Gaillard, Sylvain" sort="Gaillard, Sylvain" uniqKey="Gaillard S" first="Sylvain" last="Gaillard">Sylvain Gaillard</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Jacques, Marie Agnes" sort="Jacques, Marie Agnes" uniqKey="Jacques M" first="Marie-Agnès" last="Jacques">Marie-Agnès Jacques</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">30909861</idno><idno type="pmc">6434890</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434890</idno><idno type="RBID">PMC:6434890</idno><idno type="doi">10.1186/s12864-019-5565-9</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000301</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000301</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of genetic relationships and subspecies signatures in <italic>Xylella fastidiosa</italic></title><author><name sortKey="Denance, Nicolas" sort="Denance, Nicolas" uniqKey="Denance N" first="Nicolas" last="Denancé">Nicolas Denancé</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Briand, Martial" sort="Briand, Martial" uniqKey="Briand M" first="Martial" last="Briand">Martial Briand</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Gaborieau, Romain" sort="Gaborieau, Romain" uniqKey="Gaborieau R" first="Romain" last="Gaborieau">Romain Gaborieau</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Gaillard, Sylvain" sort="Gaillard, Sylvain" uniqKey="Gaillard S" first="Sylvain" last="Gaillard">Sylvain Gaillard</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author><author><name sortKey="Jacques, Marie Agnes" sort="Jacques, Marie Agnes" uniqKey="Jacques M" first="Marie-Agnès" last="Jacques">Marie-Agnès Jacques</name><affiliation><nlm:aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</nlm:aff></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p id="Par1">The phytopathogenic bacterium <italic>Xylella fastidiosa</italic> was thought to be restricted to the Americas where it infects and kills numerous hosts. Its detection worldwide has been blooming since 2013 in Europe and Asia. Genetically diverse, this species is divided into six subspecies but genetic traits governing this classification are poorly understood.</p></sec><sec><title>Results</title><p id="Par2">SkIf (Specific k-mers Identification) was designed and exploited for comparative genomics on a dataset of 46 <italic>X. fastidiosa</italic> genomes, including seven newly sequenced individuals. It was helpful to quickly check the synonymy between strains from different collections. SkIf identified specific SNPs within 16S rRNA sequences that can be employed for predicting the distribution of <italic>Xylella</italic> through data mining. Applied to inter- and intra-subspecies analyses, it identified specific k-mers in genes affiliated to differential gene ontologies. Chemotaxis-related genes more prevalently possess specific k-mers in genomes from subspecies <italic>fastidiosa, morus</italic> and <italic>sandyi</italic> taken as a whole group. In the subspecies <italic>pauca</italic> increased abundance of specific k-mers was found in genes associated with the bacterial cell wall/envelope/plasma membrane. Most often, the k-mer specificity occurred in core genes with non-synonymous SNPs in their sequences in genomes of the other subspecies, suggesting putative impact in the protein functions. The presence of two integrative and conjugative elements (ICEs) was identified, one chromosomic and an entire plasmid in a single strain of <italic>X. fastidiosa</italic> subsp. <italic>pauca</italic>. Finally, a revised taxonomy of <italic>X. fastidiosa</italic> into three major clades defined by the subspecies <italic>pauca</italic> (clade I), <italic>multiplex</italic> (clade II) and the combination of <italic>fastidiosa, morus</italic> and <italic>sandyi</italic> (clade III) was strongly supported by k-mers specifically associated with these subspecies.</p></sec><sec><title>Conclusions</title><p id="Par3">SkIf is a robust and rapid software, freely available, that can be dedicated to the comparison of sequence datasets and is applicable to any field of research. Applied to <italic>X. fastidiosa</italic>, an emerging pathogen in Europe<italic>,</italic> it provided an important resource to mine for identifying genetic markers of subspecies to optimize the strategies attempted to limit the pathogen dissemination in novel areas.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12864-019-5565-9) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Saponari, M" uniqKey="Saponari M">M Saponari</name></author><author><name sortKey="Boscia, D" uniqKey="Boscia D">D Boscia</name></author><author><name sortKey="Nigro, F" uniqKey="Nigro F">F Nigro</name></author><author><name sortKey="Martelli, Gp" uniqKey="Martelli G">GP Martelli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Denance, N" uniqKey="Denance N">N Denancé</name></author><author><name sortKey="Legendre, B" uniqKey="Legendre B">B Legendre</name></author><author><name sortKey="Briand, M" uniqKey="Briand M">M Briand</name></author><author><name sortKey="Olivier, V" uniqKey="Olivier V">V Olivier</name></author><author><name sortKey="De Boisseson, C" uniqKey="De Boisseson C">C de Boisséson</name></author><author><name sortKey="Poliakoff, F" uniqKey="Poliakoff F">F Poliakoff</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Strona, G" uniqKey="Strona G">G Strona</name></author><author><name sortKey="Carstens, Cj" uniqKey="Carstens C">CJ Carstens</name></author><author><name sortKey="Beck, Psa" uniqKey="Beck P">PSA Beck</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soubeyrand, S" uniqKey="Soubeyrand S">S Soubeyrand</name></author><author><name sortKey="De Jerphanion, P" uniqKey="De Jerphanion P">P de Jerphanion</name></author><author><name sortKey="Martin, O" uniqKey="Martin O">O Martin</name></author><author><name sortKey="Saussac, M" uniqKey="Saussac M">M Saussac</name></author><author><name sortKey="Manceau, C" uniqKey="Manceau C">C Manceau</name></author><author><name sortKey="Hendrikx, P" uniqKey="Hendrikx P">P Hendrikx</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Bergsma Vlami, M" uniqKey="Bergsma Vlami M">M Bergsma-Vlami</name></author><author><name sortKey="Van De Bilt, Jlj" uniqKey="Van De Bilt J">JLJ van de Bilt</name></author><author><name sortKey="Tjou Tam Sin, Nna" uniqKey="Tjou Tam Sin N">NNA Tjou-Tam-Sin</name></author><author><name sortKey="Helderman, Cm" uniqKey="Helderman C">CM Helderman</name></author><author><name sortKey="Gorkink Smits, Ppma" uniqKey="Gorkink Smits P">PPMA Gorkink-Smits</name></author><author><name sortKey="Landman, Nm" uniqKey="Landman N">NM Landman</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Jacques, Ma" uniqKey="Jacques M">MA Jacques</name></author><author><name sortKey="Denance, N" uniqKey="Denance N">N Denancé</name></author><author><name sortKey="Legendre, B" uniqKey="Legendre B">B Legendre</name></author><author><name sortKey="Morel, E" uniqKey="Morel E">E Morel</name></author><author><name sortKey="Briand, M" uniqKey="Briand M">M Briand</name></author><author><name sortKey="Mississipi, S" uniqKey="Mississipi S">S Mississipi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bergsma Vlami, M" uniqKey="Bergsma Vlami M">M Bergsma-Vlami</name></author><author><name sortKey="Van De Bilt, Jlj" uniqKey="Van De Bilt J">JLJ van de Bilt</name></author><author><name sortKey="Tjou Tam Sin, Nna" uniqKey="Tjou Tam Sin N">NNA Tjou-Tam-Sin</name></author><author><name sortKey="Van De Vossenberg, Btlh" uniqKey="Van De Vossenberg B">BTLH van de Vossenberg</name></author><author><name sortKey="Westenberg, M" uniqKey="Westenberg M">M Westenberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Su, Cc" uniqKey="Su C">CC Su</name></author><author><name sortKey="Deng, Wl" uniqKey="Deng W">WL Deng</name></author><author><name sortKey="Jan, Fj" uniqKey="Jan F">FJ Jan</name></author><author><name sortKey="Chang, Cj" uniqKey="Chang C">CJ Chang</name></author><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Shih, Ht" uniqKey="Shih H">HT Shih</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nunney, L" uniqKey="Nunney L">L Nunney</name></author><author><name sortKey="Yuan, X" uniqKey="Yuan X">X Yuan</name></author><author><name sortKey="Bromley, Re" uniqKey="Bromley R">RE Bromley</name></author><author><name sortKey="Stouthamer, R" uniqKey="Stouthamer R">R Stouthamer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nunney, L" uniqKey="Nunney L">L Nunney</name></author><author><name sortKey="Ortiz, B" uniqKey="Ortiz B">B Ortiz</name></author><author><name sortKey="Russell, Sa" uniqKey="Russell S">SA Russell</name></author><author><name sortKey="Ruiz Sanchez, R" uniqKey="Ruiz Sanchez R">R Ruiz-Sanchez</name></author><author><name sortKey="Stouthamer, R" uniqKey="Stouthamer R">R Stouthamer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nunney, L" uniqKey="Nunney L">L Nunney</name></author><author><name sortKey="Schuenzel, El" uniqKey="Schuenzel E">EL Schuenzel</name></author><author><name sortKey="Scally, M" uniqKey="Scally M">M Scally</name></author><author><name sortKey="Bromley, Re" uniqKey="Bromley R">RE Bromley</name></author><author><name sortKey="Stouthamer, R" uniqKey="Stouthamer R">R Stouthamer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Loconsole, G" uniqKey="Loconsole G">G Loconsole</name></author><author><name sortKey="Saponari, M" uniqKey="Saponari M">M Saponari</name></author><author><name sortKey="Boscia, D" uniqKey="Boscia D">D Boscia</name></author><author><name sortKey="D Ttoma, G" uniqKey="D Ttoma G">G D’Attoma</name></author><author><name sortKey="Morelli, M" uniqKey="Morelli M">M Morelli</name></author><author><name sortKey="Martelli, Gp" uniqKey="Martelli G">GP Martelli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Coletta Filho, Hd" uniqKey="Coletta Filho H">HD Coletta-Filho</name></author><author><name sortKey="Francisco, Cs" uniqKey="Francisco C">CS Francisco</name></author><author><name sortKey="Lopes, Jrs" uniqKey="Lopes J">JRS Lopes</name></author><author><name sortKey="Muller, C" uniqKey="Muller C">C Muller</name></author><author><name sortKey="Almeida, Rpp" uniqKey="Almeida R">RPP Almeida</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rizk, G" uniqKey="Rizk G">G Rizk</name></author><author><name sortKey="Lavenier, D" uniqKey="Lavenier D">D Lavenier</name></author><author><name sortKey="Chikhi, R" uniqKey="Chikhi R">R Chikhi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ghandi, M" uniqKey="Ghandi M">M Ghandi</name></author><author><name sortKey="Lee, D" uniqKey="Lee D">D Lee</name></author><author><name sortKey="Mohammad Noori, M" uniqKey="Mohammad Noori M">M Mohammad-Noori</name></author><author><name sortKey="Beer, Ma" uniqKey="Beer M">MA Beer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Melsted, P" uniqKey="Melsted P">P Melsted</name></author><author><name sortKey="Halld Rsson, Bv" uniqKey="Halld Rsson B">BV Halldórsson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abo, Rp" uniqKey="Abo R">RP Abo</name></author><author><name sortKey="Ducar, M" uniqKey="Ducar M">M Ducar</name></author><author><name sortKey="Garcia, Ep" uniqKey="Garcia E">EP Garcia</name></author><author><name sortKey="Thorner, Ar" uniqKey="Thorner A">AR Thorner</name></author><author><name sortKey="Rojas Rudilla, V" uniqKey="Rojas Rudilla V">V Rojas-Rudilla</name></author><author><name sortKey="Lin, L" uniqKey="Lin L">L Lin</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Mapleson, D" uniqKey="Mapleson D">D Mapleson</name></author><author><name sortKey="Garcia Accinelli, G" uniqKey="Garcia Accinelli G">G Garcia Accinelli</name></author><author><name sortKey="Kettleborough, G" uniqKey="Kettleborough G">G Kettleborough</name></author><author><name sortKey="Wright, J" uniqKey="Wright J">J Wright</name></author><author><name sortKey="Clavijo, Bj" uniqKey="Clavijo B">BJ Clavijo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marinier, E" uniqKey="Marinier E">E Marinier</name></author><author><name sortKey="Zaheer, R" uniqKey="Zaheer R">R Zaheer</name></author><author><name sortKey="Berry, C" uniqKey="Berry C">C Berry</name></author><author><name sortKey="Weedmark, Ka" uniqKey="Weedmark K">KA Weedmark</name></author><author><name sortKey="Domaratzki, M" uniqKey="Domaratzki M">M Domaratzki</name></author><author><name sortKey="Mabon, P" uniqKey="Mabon P">P Mabon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pandey, P" uniqKey="Pandey P">P Pandey</name></author><author><name sortKey="Bender, Ma" uniqKey="Bender M">MA Bender</name></author><author><name sortKey="Johnson, R" uniqKey="Johnson R">R Johnson</name></author><author><name sortKey="Patro, R" uniqKey="Patro R">R Patro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hasman, H" uniqKey="Hasman H">H Hasman</name></author><author><name sortKey="Saputra, D" uniqKey="Saputra D">D Saputra</name></author><author><name sortKey="Sicheritz Ponten, T" uniqKey="Sicheritz Ponten T">T Sicheritz-Ponten</name></author><author><name sortKey="Lund, O" uniqKey="Lund O">O Lund</name></author><author><name sortKey="Svendsen, Ca" uniqKey="Svendsen C">CA Svendsen</name></author><author><name sortKey="Frimodt M Ller, N" uniqKey="Frimodt M Ller N">N Frimodt-Møller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chattaway, Ma" uniqKey="Chattaway M">MA Chattaway</name></author><author><name sortKey="Schaefer, U" uniqKey="Schaefer U">U Schaefer</name></author><author><name sortKey="Tewolde, R" uniqKey="Tewolde R">R Tewolde</name></author><author><name sortKey="Dallman, Tj" uniqKey="Dallman T">TJ Dallman</name></author><author><name sortKey="Jenkins, C" uniqKey="Jenkins C">C Jenkins</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Richter, M" uniqKey="Richter M">M Richter</name></author><author><name sortKey="Rossell M Ra, R" uniqKey="Rossell M Ra R">R Rosselló-Móra</name></author><author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glöckner</name></author><author><name sortKey="Peplies, J" uniqKey="Peplies J">J Peplies</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pritchard, L" uniqKey="Pritchard L">L Pritchard</name></author><author><name sortKey="Glover, Rh" uniqKey="Glover R">RH Glover</name></author><author><name sortKey="Humphris, S" uniqKey="Humphris S">S Humphris</name></author><author><name sortKey="Elphinstone, Jg" uniqKey="Elphinstone J">JG Elphinstone</name></author><author><name sortKey="Toth, Ik" uniqKey="Toth I">IK Toth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schaad, Nw" uniqKey="Schaad N">NW Schaad</name></author><author><name sortKey="Postnikova, E" uniqKey="Postnikova E">E Postnikova</name></author><author><name sortKey="Lacy, G" uniqKey="Lacy G">G Lacy</name></author><author><name sortKey="Fatmi, M" uniqKey="Fatmi M">M Fatmi</name></author><author><name sortKey="Chang, Cj" uniqKey="Chang C">CJ Chang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Verslyppe, B" uniqKey="Verslyppe B">B Verslyppe</name></author><author><name sortKey="De Smet, W" uniqKey="De Smet W">W De Smet</name></author><author><name sortKey="De Baets, B" uniqKey="De Baets B">B De Baets</name></author><author><name sortKey="De Vos, P" uniqKey="De Vos P">P De Vos</name></author><author><name sortKey="Dawyndt, D" uniqKey="Dawyndt D">D Dawyndt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giampetruzzi, A" uniqKey="Giampetruzzi A">A Giampetruzzi</name></author><author><name sortKey="Chiumenti, M" uniqKey="Chiumenti M">M Chiumenti</name></author><author><name sortKey="Saponari, M" uniqKey="Saponari M">M Saponari</name></author><author><name sortKey="Donvito, G" uniqKey="Donvito G">G Donvito</name></author><author><name sortKey="Italiano, A" uniqKey="Italiano A">A Italiano</name></author><author><name sortKey="Loconsole, G" uniqKey="Loconsole G">G Loconsole</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rogers, Ee" uniqKey="Rogers E">EE Rogers</name></author><author><name sortKey="Stenger, Dc" uniqKey="Stenger D">DC Stenger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giampetruzzi, A" uniqKey="Giampetruzzi A">A Giampetruzzi</name></author><author><name sortKey="Saponari, M" uniqKey="Saponari M">M Saponari</name></author><author><name sortKey="Almeida, Rpp" uniqKey="Almeida R">RPP Almeida</name></author><author><name sortKey="Essakhi, S" uniqKey="Essakhi S">S Essakhi</name></author><author><name sortKey="Boscia, D" uniqKey="Boscia D">D Boscia</name></author><author><name sortKey="Loconsole, G" uniqKey="Loconsole G">G Loconsole</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Al Okaily, A" uniqKey="Al Okaily A">A Al-Okaily</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Powers, Jg" uniqKey="Powers J">JG Powers</name></author><author><name sortKey="Weigman, Vj" uniqKey="Weigman V">VJ Weigman</name></author><author><name sortKey="Shu, J" uniqKey="Shu J">J Shu</name></author><author><name sortKey="Pufky, Jm" uniqKey="Pufky J">JM Pufky</name></author><author><name sortKey="Cox, D" uniqKey="Cox D">D Cox</name></author><author><name sortKey="Hurban, P" uniqKey="Hurban P">P Hurban</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Konstantinidis, Kt" uniqKey="Konstantinidis K">KT Konstantinidis</name></author><author><name sortKey="Tiedje, Jm" uniqKey="Tiedje J">JM Tiedje</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Richter, M" uniqKey="Richter M">M Richter</name></author><author><name sortKey="Rossello Mora, R" uniqKey="Rossello Mora R">R Rossello-Mora</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name></author><author><name sortKey="Kasif, S" uniqKey="Kasif S">S Kasif</name></author><author><name sortKey="Fleischmann, Rd" uniqKey="Fleischmann R">RD Fleischmann</name></author><author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name></author><author><name sortKey="White, O" uniqKey="White O">O White</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Teeling, H" uniqKey="Teeling H">H Teeling</name></author><author><name sortKey="Waldmann, J" uniqKey="Waldmann J">J Waldmann</name></author><author><name sortKey="Lombardot, T" uniqKey="Lombardot T">T Lombardot</name></author><author><name sortKey="Bauer, M" uniqKey="Bauer M">M Bauer</name></author><author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glöckner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goris, J" uniqKey="Goris J">J Goris</name></author><author><name sortKey="Konstantinidis, Kt" uniqKey="Konstantinidis K">KT Konstantinidis</name></author><author><name sortKey="Klappenbach, Ja" uniqKey="Klappenbach J">JA Klappenbach</name></author><author><name sortKey="Coenye, T" uniqKey="Coenye T">T Coenye</name></author><author><name sortKey="Vandamme, P" uniqKey="Vandamme P">P Vandamme</name></author><author><name sortKey="Tiedje, Jm" uniqKey="Tiedje J">JM Tiedje</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marcelletti, S" uniqKey="Marcelletti S">S Marcelletti</name></author><author><name sortKey="Scortichini, M" uniqKey="Scortichini M">M Scortichini</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goris, J" uniqKey="Goris J">J Goris</name></author><author><name sortKey="Dejonghe, W" uniqKey="Dejonghe W">W Dejonghe</name></author><author><name sortKey="Falsen, E" uniqKey="Falsen E">E Falsen</name></author><author><name sortKey="De Clerck, E" uniqKey="De Clerck E">E De Clerck</name></author><author><name sortKey="Geeraerts, B" uniqKey="Geeraerts B">B Geeraerts</name></author><author><name sortKey="Willems, A" uniqKey="Willems A">A Willems</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Y" uniqKey="Lee Y">Y Lee</name></author><author><name sortKey="Jeon, Co" uniqKey="Jeon C">CO Jeon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nelson, Mjk" uniqKey="Nelson M">MJK Nelson</name></author><author><name sortKey="Montgomery, So" uniqKey="Montgomery S">SO Montgomery</name></author><author><name sortKey="O Eill, Ej" uniqKey="O Eill E">EJ O’Neill</name></author><author><name sortKey="Pritchard, Ph" uniqKey="Pritchard P">PH Pritchard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jones, Jb" uniqKey="Jones J">JB Jones</name></author><author><name sortKey="Lacy, Gh" uniqKey="Lacy G">GH Lacy</name></author><author><name sortKey="Bouzar, H" uniqKey="Bouzar H">H Bouzar</name></author><author><name sortKey="Stall, Re" uniqKey="Stall R">RE Stall</name></author><author><name sortKey="Schaad, Nw" uniqKey="Schaad N">NW Schaad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Albuquerque, P" uniqKey="Albuquerque P">P Albuquerque</name></author><author><name sortKey="Caridade, Cmr" uniqKey="Caridade C">CMR Caridade</name></author><author><name sortKey="Rodrigues, As" uniqKey="Rodrigues A">AS Rodrigues</name></author><author><name sortKey="Marcal, Ars" uniqKey="Marcal A">ARS Marcal</name></author><author><name sortKey="Cruz, J" uniqKey="Cruz J">J Cruz</name></author><author><name sortKey="Cruz, L" uniqKey="Cruz L">L Cruz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Estrada De Los Santos, P" uniqKey="Estrada De Los Santos P">P Estrada-De Los Santos</name></author><author><name sortKey="Bustillos Cristales, R" uniqKey="Bustillos Cristales R">R Bustillos-Cristales</name></author><author><name sortKey="Caballero Mellado, J" uniqKey="Caballero Mellado J">J Caballero-Mellado</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carvalho, Gm" uniqKey="Carvalho G">GM Carvalho</name></author><author><name sortKey="Carvalho, Ap" uniqKey="Carvalho A">AP Carvalho</name></author><author><name sortKey="Folescu, Tw" uniqKey="Folescu T">TW Folescu</name></author><author><name sortKey="Higa, L" uniqKey="Higa L">L Higa</name></author><author><name sortKey="Teixeira, Lm" uniqKey="Teixeira L">LM Teixeira</name></author><author><name sortKey="Plotkowski, Mc" uniqKey="Plotkowski M">MC Plotkowski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nunney, L" uniqKey="Nunney L">L Nunney</name></author><author><name sortKey="Elfekih, S" uniqKey="Elfekih S">S Elfekih</name></author><author><name sortKey="Stouthamer, R" uniqKey="Stouthamer R">R Stouthamer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yuan, X" uniqKey="Yuan X">X Yuan</name></author><author><name sortKey="Morano, L" uniqKey="Morano L">L Morano</name></author><author><name sortKey="Bromley, R" uniqKey="Bromley R">R Bromley</name></author><author><name sortKey="Spring Pearson, S" uniqKey="Spring Pearson S">S Spring-Pearson</name></author><author><name sortKey="Stouthamer, R" uniqKey="Stouthamer R">R Stouthamer</name></author><author><name sortKey="Nunney, L" uniqKey="Nunney L">L Nunney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wells, Jm" uniqKey="Wells J">JM Wells</name></author><author><name sortKey="Raju, Bc" uniqKey="Raju B">BC Raju</name></author><author><name sortKey="Nyland, G" uniqKey="Nyland G">G Nyland</name></author><author><name sortKey="Lowe, Sk" uniqKey="Lowe S">SK Lowe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Sallet, E" uniqKey="Sallet E">E Sallet</name></author><author><name sortKey="Gouzy, J" uniqKey="Gouzy J">J Gouzy</name></author><author><name sortKey="Schiex, T" uniqKey="Schiex T">T Schiex</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simpson, Aj" uniqKey="Simpson A">AJ Simpson</name></author><author><name sortKey="Reinach, Fc" uniqKey="Reinach F">FC Reinach</name></author><author><name sortKey="Arruda, P" uniqKey="Arruda P">P Arruda</name></author><author><name sortKey="Abreu, Fa" uniqKey="Abreu F">FA Abreu</name></author><author><name sortKey="Acencio, M" uniqKey="Acencio M">M Acencio</name></author><author><name sortKey="Alvarenga, R" uniqKey="Alvarenga R">R Alvarenga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Sluys, Ma" uniqKey="Van Sluys M">MA Van Sluys</name></author><author><name sortKey="De Oliveira, Mc" uniqKey="De Oliveira M">MC de Oliveira</name></author><author><name sortKey="Monteiro Vitorello, Cb" uniqKey="Monteiro Vitorello C">CB Monteiro-Vitorello</name></author><author><name sortKey="Miyaki, Cy" uniqKey="Miyaki C">CY Miyaki</name></author><author><name sortKey="Furlan, Lr" uniqKey="Furlan L">LR Furlan</name></author><author><name sortKey="Camargo, Le" uniqKey="Camargo L">LE Camargo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gueguen, L" uniqKey="Gueguen L">L Guéguen</name></author><author><name sortKey="Gaillard, S" uniqKey="Gaillard S">S Gaillard</name></author><author><name sortKey="Boussau, B" uniqKey="Boussau B">B Boussau</name></author><author><name sortKey="Gouy, M" uniqKey="Gouy M">M Gouy</name></author><author><name sortKey="Groussin, M" uniqKey="Groussin M">M Groussin</name></author><author><name sortKey="Rochette, Nc" uniqKey="Rochette N">NC Rochette</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kearse, M" uniqKey="Kearse M">M Kearse</name></author><author><name sortKey="Moir, R" uniqKey="Moir R">R Moir</name></author><author><name sortKey="Wilson, A" uniqKey="Wilson A">A Wilson</name></author><author><name sortKey="Stones Havas, S" uniqKey="Stones Havas S">S Stones-Havas</name></author><author><name sortKey="Cheung, M" uniqKey="Cheung M">M Cheung</name></author><author><name sortKey="Sturrock, S" uniqKey="Sturrock S">S Sturrock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ward, Jh" uniqKey="Ward J">JH Ward</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paradis, E" uniqKey="Paradis E">E Paradis</name></author><author><name sortKey="Claude, J" uniqKey="Claude J">J Claude</name></author><author><name sortKey="Strimmer, K" uniqKey="Strimmer K">K Strimmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Schwartz, S" uniqKey="Schwartz S">S Schwartz</name></author><author><name sortKey="Wagner, L" uniqKey="Wagner L">L Wagner</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gotz, S" uniqKey="Gotz S">S Götz</name></author><author><name sortKey="Garcia G Mez, Jm" uniqKey="Garcia G Mez J">JM García-Gómez</name></author><author><name sortKey="Terol, J" uniqKey="Terol J">J Terol</name></author><author><name sortKey="Williams, Td" uniqKey="Williams T">TD Williams</name></author><author><name sortKey="Nagaraj, Sh" uniqKey="Nagaraj S">SH Nagaraj</name></author><author><name sortKey="Nueda, Mj" uniqKey="Nueda M">MJ Nueda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bardou, P" uniqKey="Bardou P">P Bardou</name></author><author><name sortKey="Mariette, J" uniqKey="Mariette J">J Mariette</name></author><author><name sortKey="Escudie, F" uniqKey="Escudie F">F Escudié</name></author><author><name sortKey="Djemiel, C" uniqKey="Djemiel C">C Djemiel</name></author><author><name sortKey="Klopp, C" uniqKey="Klopp C">C Klopp</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quast, C" uniqKey="Quast C">C Quast</name></author><author><name sortKey="Pruesse, E" uniqKey="Pruesse E">E Pruesse</name></author><author><name sortKey="Yilmaz, P" uniqKey="Yilmaz P">P Yilmaz</name></author><author><name sortKey="Gerken, J" uniqKey="Gerken J">J Gerken</name></author><author><name sortKey="Schweer, T" uniqKey="Schweer T">T Schweer</name></author><author><name sortKey="Yarza, P" uniqKey="Yarza P">P Yarza</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, S" uniqKey="Zhang S">S Zhang</name></author><author><name sortKey="Flores Cruz, Z" uniqKey="Flores Cruz Z">Z Flores-Cruz</name></author><author><name sortKey="Kumar, D" uniqKey="Kumar D">D Kumar</name></author><author><name sortKey="Chakrabarty, P" uniqKey="Chakrabarty P">P Chakrabarty</name></author><author><name sortKey="Hopkins, Dl" uniqKey="Hopkins D">DL Hopkins</name></author><author><name sortKey="Gabriel, Dw" uniqKey="Gabriel D">DW Gabriel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schreiber, Hl" uniqKey="Schreiber H">HL Schreiber</name></author><author><name sortKey="Koirala, M" uniqKey="Koirala M">M Koirala</name></author><author><name sortKey="Lara, A" uniqKey="Lara A">A Lara</name></author><author><name sortKey="Ojeda, M" uniqKey="Ojeda M">M Ojeda</name></author><author><name sortKey="Dowd, Se" uniqKey="Dowd S">SE Dowd</name></author><author><name sortKey="Bextine, B" uniqKey="Bextine B">B Bextine</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Xie, G" uniqKey="Xie G">G Xie</name></author><author><name sortKey="Han, S" uniqKey="Han S">S Han</name></author><author><name sortKey="Chertkov, O" uniqKey="Chertkov O">O Chertkov</name></author><author><name sortKey="Sims, D" uniqKey="Sims D">D Sims</name></author><author><name sortKey="Civerolo, El" uniqKey="Civerolo E">EL Civerolo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Wu, F" uniqKey="Wu F">F Wu</name></author><author><name sortKey="Zheng, Z" uniqKey="Zheng Z">Z Zheng</name></author><author><name sortKey="Deng, X" uniqKey="Deng X">X Deng</name></author><author><name sortKey="Burbank, Lp" uniqKey="Burbank L">LP Burbank</name></author><author><name sortKey="Stenger, Dc" uniqKey="Stenger D">DC Stenger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Horn, C" uniqKey="Van Horn C">C Van Horn</name></author><author><name sortKey="Chang, Cj" uniqKey="Chang C">CJ Chang</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bhattacharyya, A" uniqKey="Bhattacharyya A">A Bhattacharyya</name></author><author><name sortKey="Stilwagen, S" uniqKey="Stilwagen S">S Stilwagen</name></author><author><name sortKey="Ivanova, N" uniqKey="Ivanova N">N Ivanova</name></author><author><name sortKey="D Souza, M" uniqKey="D Souza M">M D'Souza</name></author><author><name sortKey="Bernal, A" uniqKey="Bernal A">A Bernal</name></author><author><name sortKey="Lykidis, A" uniqKey="Lykidis A">A Lykidis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Chang, C J" uniqKey="Chang C">C-J Chang</name></author><author><name sortKey="Stenger, Dc" uniqKey="Stenger D">DC Stenger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guan, W" uniqKey="Guan W">W Guan</name></author><author><name sortKey="Shao, J" uniqKey="Shao J">J Shao</name></author><author><name sortKey="Davis, Re" uniqKey="Davis R">RE Davis</name></author><author><name sortKey="Zhao, T" uniqKey="Zhao T">T Zhao</name></author><author><name sortKey="Huang, Q" uniqKey="Huang Q">Q Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schuenzel, El" uniqKey="Schuenzel E">EL Schuenzel</name></author><author><name sortKey="Scally, M" uniqKey="Scally M">M Scally</name></author><author><name sortKey="Stouthamer, R" uniqKey="Stouthamer R">R Stouthamer</name></author><author><name sortKey="Nunney, L" uniqKey="Nunney L">L Nunney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giampetruzzi, A" uniqKey="Giampetruzzi A">A Giampetruzzi</name></author><author><name sortKey="Loconsole, G" uniqKey="Loconsole G">G Loconsole</name></author><author><name sortKey="Boscia, D" uniqKey="Boscia D">D Boscia</name></author><author><name sortKey="Calzolari, A" uniqKey="Calzolari A">A Calzolari</name></author><author><name sortKey="Chiumenti, M" uniqKey="Chiumenti M">M Chiumenti</name></author><author><name sortKey="Martelli, Gp" uniqKey="Martelli G">GP Martelli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guan, W" uniqKey="Guan W">W Guan</name></author><author><name sortKey="Shao, J" uniqKey="Shao J">J Shao</name></author><author><name sortKey="Zhao, T" uniqKey="Zhao T">T Zhao</name></author><author><name sortKey="Huang, Q" uniqKey="Huang Q">Q Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alencar, Vc" uniqKey="Alencar V">VC Alencar</name></author><author><name sortKey="Barbosa, D" uniqKey="Barbosa D">D Barbosa</name></author><author><name sortKey="Santos, Ds" uniqKey="Santos D">DS Santos</name></author><author><name sortKey="Oliveira, Acf" uniqKey="Oliveira A">ACF Oliveira</name></author><author><name sortKey="De Oliveira, Rc" uniqKey="De Oliveira R">RC de Oliveira</name></author><author><name sortKey="Nunes, Lr" uniqKey="Nunes L">LR Nunes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Niza, B" uniqKey="Niza B">B Niza</name></author><author><name sortKey="Merfa, Mv" uniqKey="Merfa M">MV Merfa</name></author><author><name sortKey="Alencar, Vc" uniqKey="Alencar V">VC Alencar</name></author><author><name sortKey="Menegidio, Fb" uniqKey="Menegidio F">FB Menegidio</name></author><author><name sortKey="Nunes, Lr" uniqKey="Nunes L">LR Nunes</name></author><author><name sortKey="Machado, Ma" uniqKey="Machado M">MA Machado</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Su, Cc" uniqKey="Su C">CC Su</name></author><author><name sortKey="Deng, Wl" uniqKey="Deng W">WL Deng</name></author><author><name sortKey="Jan, Fj" uniqKey="Jan F">FJ Jan</name></author><author><name sortKey="Chang, Cj" uniqKey="Chang C">CJ Chang</name></author><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id><journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id><journal-title-group><journal-title>BMC Genomics</journal-title></journal-title-group><issn pub-type="epub">1471-2164</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">30909861</article-id><article-id pub-id-type="pmc">6434890</article-id><article-id pub-id-type="publisher-id">5565</article-id><article-id pub-id-type="doi">10.1186/s12864-019-5565-9</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Identification of genetic relationships and subspecies signatures in <italic>Xylella fastidiosa</italic></article-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-0173-3970</contrib-id><name><surname>Denancé</surname><given-names>Nicolas</given-names></name><address><email>nicolas.denance@orange.fr</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Briand</surname><given-names>Martial</given-names></name><address><email>martial.briand@inra.fr</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Gaborieau</surname><given-names>Romain</given-names></name><address><email>romain.gaborieau@hotmail.fr</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Gaillard</surname><given-names>Sylvain</given-names></name><address><email>sylvain.gaillard@inra.fr</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-1442-917X</contrib-id><name><surname>Jacques</surname><given-names>Marie-Agnès</given-names></name><address><phone>+33 241 225 707</phone><email>marie-agnes.jacques@inra.fr</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><aff id="Aff1">IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé cedex, France</aff></contrib-group><pub-date pub-type="epub"><day>25</day><month>3</month><year>2019</year></pub-date><pub-date pub-type="pmc-release"><day>25</day><month>3</month><year>2019</year></pub-date><pub-date pub-type="collection"><year>2019</year></pub-date><volume>20</volume><elocation-id>239</elocation-id><history><date date-type="received"><day>22</day><month>8</month><year>2018</year></date><date date-type="accepted"><day>25</day><month>2</month><year>2019</year></date></history><permissions><copyright-statement>© The Author(s). 2019</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold>This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p id="Par1">The phytopathogenic bacterium <italic>Xylella fastidiosa</italic> was thought to be restricted to the Americas where it infects and kills numerous hosts. Its detection worldwide has been blooming since 2013 in Europe and Asia. Genetically diverse, this species is divided into six subspecies but genetic traits governing this classification are poorly understood.</p></sec><sec><title>Results</title><p id="Par2">SkIf (Specific k-mers Identification) was designed and exploited for comparative genomics on a dataset of 46 <italic>X. fastidiosa</italic> genomes, including seven newly sequenced individuals. It was helpful to quickly check the synonymy between strains from different collections. SkIf identified specific SNPs within 16S rRNA sequences that can be employed for predicting the distribution of <italic>Xylella</italic> through data mining. Applied to inter- and intra-subspecies analyses, it identified specific k-mers in genes affiliated to differential gene ontologies. Chemotaxis-related genes more prevalently possess specific k-mers in genomes from subspecies <italic>fastidiosa, morus</italic> and <italic>sandyi</italic> taken as a whole group. In the subspecies <italic>pauca</italic> increased abundance of specific k-mers was found in genes associated with the bacterial cell wall/envelope/plasma membrane. Most often, the k-mer specificity occurred in core genes with non-synonymous SNPs in their sequences in genomes of the other subspecies, suggesting putative impact in the protein functions. The presence of two integrative and conjugative elements (ICEs) was identified, one chromosomic and an entire plasmid in a single strain of <italic>X. fastidiosa</italic> subsp. <italic>pauca</italic>. Finally, a revised taxonomy of <italic>X. fastidiosa</italic> into three major clades defined by the subspecies <italic>pauca</italic> (clade I), <italic>multiplex</italic> (clade II) and the combination of <italic>fastidiosa, morus</italic> and <italic>sandyi</italic> (clade III) was strongly supported by k-mers specifically associated with these subspecies.</p></sec><sec><title>Conclusions</title><p id="Par3">SkIf is a robust and rapid software, freely available, that can be dedicated to the comparison of sequence datasets and is applicable to any field of research. Applied to <italic>X. fastidiosa</italic>, an emerging pathogen in Europe<italic>,</italic> it provided an important resource to mine for identifying genetic markers of subspecies to optimize the strategies attempted to limit the pathogen dissemination in novel areas.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12864-019-5565-9) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>16S rRNA gene</kwd><kwd>Horizontal gene transfer</kwd><kwd>Phylogeny</kwd><kwd>K-mer</kwd><kwd>SkIf</kwd><kwd>Taxonomy</kwd></kwd-group><funding-group><award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100007601</institution-id><institution>RFI Objectif Végétal</institution></institution-wrap></funding-source><award-id>635646</award-id><principal-award-recipient><name><surname>Denancé</surname><given-names>Nicolas</given-names></name></principal-award-recipient></award-group></funding-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2019</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="Sec1"><title>Background</title><p id="Par13"><italic>Xylella fastidiosa</italic> is a species of plant pathogenic bacteria endemic in the Americas, but listed as quarantine pests elsewhere (<ext-link ext-link-type="uri" xlink:href="https://gd.eppo.int/taxon/XYLEFA/categorization">https://gd.eppo.int/taxon/XYLEFA/categorization</ext-link>). However, since 2013, various cases of emergences have been reported in Europe (Italy, France, Germany and Spain) on large ranges of host plants including olive trees, grapevine, and ornamentals [<xref ref-type="bibr" rid="CR1">1</xref>–<xref ref-type="bibr" rid="CR5">5</xref>]. In Italy, assuming that <italic>X. fastidiosa</italic> started spreading in 2010, a recent model approach suggested that it will progress through olive orchards to infect the northernmost recorded orchards within 43.5 years [<xref ref-type="bibr" rid="CR6">6</xref>]. In France, bacterial introduction was estimated between 1985 and 2001, depending on the modeled scenarios [<xref ref-type="bibr" rid="CR7">7</xref>, <xref ref-type="bibr" rid="CR8">8</xref>]. Several records of <italic>X. fastidiosa</italic> in imported materials (i.e. mostly coffee plants) were also reported over the same period in Europe [<xref ref-type="bibr" rid="CR9">9</xref>–<xref ref-type="bibr" rid="CR12">12</xref>].</p><p id="Par14"><italic>X. fastidiosa</italic> is a genetically diverse species that is currently divided into six subspecies (subsp. <italic>fastidiosa, pauca, multiplex, sandyi, morus, tashke</italic>), the four-first being the most damaging and now being found in numerous countries worldwide. But the genetic diversity of the genus <italic>Xylella</italic> is undoubtedly underestimated. Yet another species, <italic>X. taiwanensis</italic>, was recently proposed for the strains causing leaf scorch on nashi pear tree, a disease that was reported more than 25 years ago in Taiwan and initially thought to be caused by a <italic>X. fastidiosa</italic> strain [<xref ref-type="bibr" rid="CR13">13</xref>]. Recombination is known to drive <italic>X. fastidiosa</italic> evolution and adaptation to novel hosts [<xref ref-type="bibr" rid="CR11">11</xref>, <xref ref-type="bibr" rid="CR14">14</xref>–<xref ref-type="bibr" rid="CR16">16</xref>]. For example, the subspecies <italic>morus</italic> has been proposed for grouping strains issued from large events of intersubspecific recombination that were associated with a host shift [<xref ref-type="bibr" rid="CR16">16</xref>]. The recent outbreaks and interception of imported, contaminated materials in Europe as well as investigations in South America also revealed the existence of previously unknown Sequence Types of several <italic>X. fastidiosa</italic> subspecies [<xref ref-type="bibr" rid="CR2">2</xref>, <xref ref-type="bibr" rid="CR9">9</xref>, <xref ref-type="bibr" rid="CR11">11</xref>, <xref ref-type="bibr" rid="CR17">17</xref>, <xref ref-type="bibr" rid="CR18">18</xref>].</p><p id="Par15">Because management and regulations of <italic>X. fastidiosa</italic> outbreaks in France depends on the subspecies of <italic>X. fastidiosa</italic>, it is of major importance to precisely define these subspecies, understand the robustness of these groupings and their meaning in terms of specific or shared genetic material. One way to resolve such a series of interrogations is the achievement of comparative genomics to identify similarities and specificities between groups of individuals. Yet, exploring big datasets is not trivial and requires dedicated bioinformatic tools to be cost- and time-effective. Various applications use k-mers mostly to analyze sequence reads to improve the quality of genome, transcriptome and metagenome assembly [<xref ref-type="bibr" rid="CR19">19</xref>–<xref ref-type="bibr" rid="CR26">26</xref>]. K-mer are all the possible substrings of length k that are contained in a nucleotide character string. K-mer-based methods can also be employed on whole genome sequences to taxonomically assign organisms [<xref ref-type="bibr" rid="CR27">27</xref>, <xref ref-type="bibr" rid="CR28">28</xref>]. Moreover, several tools were developed to calculate pairwise relationships, like the average nucleotide identities using blast (ANIb) or MUMmer (ANIm) algorithms, and the tetranucleotide frequency correlation coefficients (TETRA), which can be accessed online through JSpecies [<xref ref-type="bibr" rid="CR29">29</xref>] or with workstation installation of python3 pyani module [<xref ref-type="bibr" rid="CR30">30</xref>].</p><p id="Par16">Here, we developed SkIf (Specific k-mers Identification) and applied it to gain a better understanding of <italic>X. fastidiosa</italic> clustering in subspecies through the detection of genomic regions specifically associated with <italic>X. fastidiosa</italic> subspecies. We also used this tool to identify specific k-mers within 16S rRNA gene and assess the occurrences of <italic>X. fastidiosa</italic> in the SILVA database as a first attempt to mine large databases to evaluate the worldwide dispersion of <italic>X. fastidiosa</italic> subspecies.</p></sec><sec id="Sec2"><title>Results</title><sec id="Sec3"><title>The genome sequence dataset</title><p id="Par17">The dataset used in this study gathered 47 <italic>Xylella</italic> genomes sequences, including 46 <italic>X. fastidiosa</italic> and one <italic>X. taiwanensis</italic> specimen (Table <xref rid="Tab1" ref-type="table">1</xref>). The <italic>X. fastidiosa</italic> subspecies <italic>tashke</italic> could not be included as no strain or genome sequence are available. In some analyses, the three strains belonging to <italic>X. fastidiosa</italic> subsp. <italic>sandyi</italic> were separated into two groups, containing either the original strain Ann-1 (<italic>sandyi</italic>) or the more recently discovered relatives CO33 and CFBP 8356 (<italic>sandyi</italic>-like) both belonging to the unusual <italic>sandyi</italic> ST72 [<xref ref-type="bibr" rid="CR17">17</xref>]<italic>.</italic> The CFBP 8073 strain, described as an atypical <italic>X. fastidiosa</italic> subsp. <italic>fastidiosa</italic> strain [<xref ref-type="bibr" rid="CR11">11</xref>] was either included or not for analyses of this subspecies. The <italic>X. fastidiosa</italic> genome sequences involve 39 publicly available ones and seven newly individuals. The strains sequenced in this work were selected based on their country of isolation, genetic diversity and host range, inferred from their belonging to the subspecies <italic>fastidiosa</italic> (CFBP 7969, CFBP 7970, CFBP 8071, CFBP 8082, and CFBP 8351), <italic>sandyi</italic> (CFBP 8356) and <italic>multiplex</italic> (CFBP 8078). Genome sequence characteristics are described in Table <xref rid="Tab2" ref-type="table">2</xref>.<table-wrap id="Tab1"><label>Table 1</label><caption><p>List of the 47 <italic>Xylella</italic> genome sequences used in this study</p></caption><table frame="hsides" rules="groups"><thead><tr><th>Genotype</th><th>Strain</th><th>ST<sup>a</sup></th><th>Host plant</th><th>Country (year)<sup>b</sup></th><th>Accession number</th><th>Reference</th></tr></thead><tbody><tr><td><italic>X. fastidiosa</italic></td><td>ATCC 35879</td><td>2</td><td><italic>Vitis vinifera</italic></td><td>FL, USA (1987)</td><td>NZ_JQAP00000000</td><td>Unpublished</td></tr><tr><td>subsp.</td><td>DSM 10026</td><td>2</td><td><italic>Vitis vinifera</italic></td><td>FL, USA (1987)</td><td>NZ_FQWN01000006</td><td>Unpublished</td></tr><tr><td><italic>fastidiosa</italic></td><td>CFBP 7969</td><td>2</td><td><italic>Vitis rotundifolia</italic></td><td>NC, USA (1985)</td><td>PHFQ00000000</td><td>This study</td></tr><tr><td></td><td>CFBP 7970</td><td>2</td><td><italic>Vitis vinifera</italic></td><td>FL, USA (1987)</td><td>PHFR00000000</td><td>This study</td></tr><tr><td></td><td>CFBP 8071</td><td>1</td><td><italic>Prunus dulcis</italic></td><td>CA, USA (1987)</td><td>PHFP00000000</td><td>This study</td></tr><tr><td></td><td>CFBP 8073</td><td>75</td><td><italic>Coffea canephora</italic></td><td>Mexico (2012)</td><td>LKES00000000</td><td>[<xref ref-type="bibr" rid="CR11">11</xref>]</td></tr><tr><td></td><td>CFBP 8082</td><td>2</td><td><italic>Ambrosia artemifolia</italic></td><td>FL, USA (1983)</td><td>PHFT00000000</td><td>This study</td></tr><tr><td></td><td>CFBP 8351</td><td>1</td><td><italic>Vitis</italic> sp.</td><td>CA, USA (1993)</td><td>PHFU00000000</td><td>This study</td></tr><tr><td></td><td>EB92–1</td><td>1</td><td><italic>Sambucus nigra</italic></td><td>FL, USA (1992)</td><td>AFDJ00000000</td><td>[<xref ref-type="bibr" rid="CR67">67</xref>]</td></tr><tr><td></td><td>GB514</td><td>1</td><td><italic>Vitis vinifera</italic></td><td>TX, USA (2007)</td><td>NC_017562</td><td>[<xref ref-type="bibr" rid="CR68">68</xref>]</td></tr><tr><td></td><td>M23</td><td>1</td><td><italic>Prunus dulcis</italic></td><td>CA, USA (2003)</td><td>NC_010577</td><td>[<xref ref-type="bibr" rid="CR69">69</xref>]</td></tr><tr><td></td><td>Stag’s Leap</td><td>1</td><td><italic>Vitis vinifera</italic></td><td>CA, USA (1994)</td><td>LSMJ010000</td><td>[<xref ref-type="bibr" rid="CR70">70</xref>]</td></tr><tr><td></td><td>Temecula1</td><td>1</td><td><italic>Vitis vinifera</italic></td><td>CA, USA 1998)</td><td>NC_004556</td><td>[<xref ref-type="bibr" rid="CR58">58</xref>]</td></tr><tr><td><italic>X. f.</italic> subsp.</td><td>ATCC 35871</td><td>41</td><td><italic>Prunus salicina</italic></td><td>CA, USA (1983)</td><td>NZ_AUAJ00000000</td><td>Unpublished</td></tr><tr><td><italic>multiplex</italic></td><td>BB01</td><td>42</td><td><italic>Vaccinium corymbosum</italic></td><td>GA, USA (2016)</td><td>NZ_MPAZ01000000</td><td>[<xref ref-type="bibr" rid="CR71">71</xref>]</td></tr><tr><td></td><td>CFBP 8078</td><td>51</td><td><italic>Vinca</italic> sp.</td><td>FL, USA (1983)</td><td>PHFS00000000</td><td>This study</td></tr><tr><td></td><td>CFBP 8416</td><td>7</td><td><italic>Polygala myrtifolia</italic></td><td>COR, FR (2015)</td><td>LUYC00000000</td><td>[<xref ref-type="bibr" rid="CR2">2</xref>]</td></tr><tr><td></td><td>CFBP 8417</td><td>6</td><td><italic>Spartium junceum</italic></td><td>COR, FR (2015)</td><td>LUYB00000000</td><td>[<xref ref-type="bibr" rid="CR2">2</xref>]</td></tr><tr><td></td><td>CFBP 8418</td><td>6</td><td><italic>Spartium junceum</italic></td><td>COR, FR (2015)</td><td>LUYA00000000</td><td>[<xref ref-type="bibr" rid="CR2">2</xref>]</td></tr><tr><td></td><td>Dixon</td><td>6</td><td><italic>Prunus dulcis</italic></td><td>CA, USA (1994)</td><td>AAAL00000000</td><td>[<xref ref-type="bibr" rid="CR72">72</xref>]</td></tr><tr><td></td><td>Griffin-1</td><td>7</td><td><italic>Quercus rubra</italic></td><td>GA, USA (2006)</td><td>AVGA00000000</td><td>[<xref ref-type="bibr" rid="CR73">73</xref>]</td></tr><tr><td></td><td>M12</td><td>7</td><td><italic>Prunus dulcis</italic></td><td>CA, USA (2003)</td><td>NC_010513</td><td>[<xref ref-type="bibr" rid="CR69">69</xref>]</td></tr><tr><td></td><td>Sy-VA</td><td>8</td><td><italic>Platanus occidentalis</italic></td><td>VA, USA (2002)</td><td>JMHP00000000</td><td>[<xref ref-type="bibr" rid="CR74">74</xref>]</td></tr><tr><td><italic>X. f.</italic> subsp.</td><td>Ann-1</td><td>5</td><td><italic>Nerium oleander</italic></td><td>CA, USA (1995)</td><td>CP006696</td><td>[<xref ref-type="bibr" rid="CR75">75</xref>]</td></tr><tr><td><italic>sandyi</italic></td><td>CFBP 8356</td><td>72</td><td><italic>Coffea arabica</italic></td><td>Costa Rica (2015)</td><td>PHFV00000000</td><td>This study</td></tr><tr><td></td><td>Co33</td><td>72</td><td><italic>Coffea arabica</italic></td><td>Costa Rica (2014)</td><td>LJZW00000000</td><td>[<xref ref-type="bibr" rid="CR76">76</xref>]</td></tr><tr><td><italic>X. f.</italic> subsp.</td><td>Mul0034</td><td>30</td><td><italic>Morus alba</italic></td><td>USA (2003)</td><td>CP006740</td><td>[<xref ref-type="bibr" rid="CR77">77</xref>]</td></tr><tr><td><italic>morus</italic></td><td>Mul-MD</td><td>29</td><td><italic>Morus alba</italic></td><td>MD, USA (2011)</td><td>AXDP00000000</td><td>[<xref ref-type="bibr" rid="CR77">77</xref>]</td></tr><tr><td><italic>X. f.</italic> subsp.</td><td>32</td><td>16</td><td><italic>Coffea arabica</italic></td><td>Brazil (1997)</td><td>AWYH00000000</td><td>[<xref ref-type="bibr" rid="CR78">78</xref>]</td></tr><tr><td><italic>pauca</italic></td><td>3124</td><td>16</td><td><italic>Coffea</italic> sp.</td><td>Brazil (2009)</td><td>CP009829</td><td>Unpublished</td></tr><tr><td></td><td>11,399</td><td>12</td><td><italic>Citrus cinensis</italic></td><td>Brazil (1996)</td><td>NZ_JNBT01000030</td><td>[<xref ref-type="bibr" rid="CR79">79</xref>]</td></tr><tr><td></td><td>6c</td><td>14</td><td><italic>Coffea arabica</italic></td><td>Brazil (1997)</td><td>AXBS00000000</td><td>[<xref ref-type="bibr" rid="CR78">78</xref>]</td></tr><tr><td></td><td>9a5c</td><td>13</td><td><italic>Citrus cinensis</italic></td><td>Brazil (1992)</td><td>NC_002488</td><td>[<xref ref-type="bibr" rid="CR57">57</xref>]</td></tr><tr><td></td><td>CFBP 8072</td><td>74</td><td><italic>Coffea Arabica</italic></td><td>Ecuador (2012)</td><td>LKDK00000000</td><td>[<xref ref-type="bibr" rid="CR11">11</xref>]</td></tr><tr><td></td><td>CoDiRO</td><td>53</td><td><italic>Catharanthus roseus</italic><sup><italic>c</italic></sup></td><td>Italy (2013)</td><td>JUJW00000000</td><td>[<xref ref-type="bibr" rid="CR33">33</xref>]</td></tr><tr><td></td><td>COF0324</td><td>14</td><td><italic>Coffea</italic> sp.</td><td>Costa Rica (2006)</td><td>LRVG01000000</td><td>Unpublished</td></tr><tr><td></td><td>COF0407</td><td>53</td><td><italic>Coffea</italic> sp.</td><td>Costa Rica (2009)</td><td>LRVJ00000000</td><td>Unpublished</td></tr><tr><td></td><td>CVC0251</td><td>12</td><td><italic>Citrus cinensis</italic></td><td>Brazil (1999)</td><td>LRVE01000000</td><td>Unpublished</td></tr><tr><td></td><td>CVC0256</td><td>12</td><td><italic>Citrus cinensis</italic></td><td>Brazil (1999)</td><td>LRVF01000000</td><td>Unpublished</td></tr><tr><td></td><td>Fb7</td><td>69</td><td><italic>Citrus sinensis</italic></td><td>Argentina (1998)</td><td>CP010051</td><td>Unpublished</td></tr><tr><td></td><td>Hib4</td><td>70</td><td><italic>Hibiscus fragilis</italic></td><td>Brazil (2000)</td><td>CP009885</td><td>Unpublished</td></tr><tr><td></td><td>J1a12</td><td>12</td><td><italic>Citrus</italic> sp.</td><td>Brazil (2001)</td><td>CP009823</td><td>Unpublished</td></tr><tr><td></td><td>OLS0478</td><td>53</td><td><italic>Nerium oleander</italic></td><td>Costa Rica (2010)</td><td>LRVI00000000</td><td>Unpublished</td></tr><tr><td></td><td>OLS0479</td><td>53</td><td><italic>Nerium oleander</italic></td><td>Costa Rica (2010)</td><td>LRVH00000000</td><td>Unpublished</td></tr><tr><td></td><td>Pr8x</td><td>14</td><td><italic>Prunus (Plum)</italic></td><td>Brazil (2009)</td><td>CP009826</td><td>Unpublished</td></tr><tr><td></td><td>U24D</td><td>13</td><td><italic>Citrus sinensis</italic></td><td>Brazil (2000)</td><td>CP009790</td><td>Unpublished</td></tr><tr><td><italic>X. taiwanensis</italic></td><td>PLS 229</td><td>–</td><td><italic>Pyrus pyrifolia</italic></td><td>Taiwan (−)</td><td>JDSQ00000000</td><td>[<xref ref-type="bibr" rid="CR80">80</xref>]</td></tr></tbody></table><table-wrap-foot><p><sup>a</sup>Sequence Type determined following the MSLT scheme dedicated to <italic>X. fastidiosa</italic> [<xref ref-type="bibr" rid="CR52">52</xref>]</p><p><sup>b</sup>Exact year of isolation or oldest year of literature citing the stain</p><p><sup>c</sup>DNA was recovered from infected periwinkle. This genome is the one of the CoDiRO strain, the agent responsible for the Olive Quick Decline Syndrome in Italy (46)</p></table-wrap-foot></table-wrap><table-wrap id="Tab2"><label>Table 2</label><caption><p>List of <italic>Xylella fastidiosa</italic> strains sequenced for this study and genome properties</p></caption><table frame="hsides" rules="groups"><thead><tr><th>Strain</th><th>Accession</th><th>Nb of reads<sup>a</sup></th><th>Cover.<sup>b</sup></th><th>Assemby size (bp)</th><th>Nb contigs<sup>c</sup></th><th>N50</th><th>Mean size (bp)</th><th>Largest (bp)</th><th>GC %</th></tr></thead><tbody><tr><td>CFBP 7969</td><td>PHFQ00000000</td><td>7,952,452</td><td>957x</td><td>2,436,752</td><td>89</td><td>116,341</td><td>27,379</td><td>445,308</td><td>51.48</td></tr><tr><td>CFBP 7970</td><td>PHFR00000000</td><td>8,041,300</td><td>968x</td><td>2,493,794</td><td>93</td><td>104,928</td><td>26,815</td><td>258,911</td><td>51.45</td></tr><tr><td>CFBP 8071</td><td>PHFP00000000</td><td>7,606,748</td><td>916x</td><td>2,489,737</td><td>101</td><td>104,990</td><td>24,651</td><td>297,538</td><td>51.48</td></tr><tr><td>CFBP 8082</td><td>PHFT00000000</td><td>7,610,344</td><td>916x</td><td>2,532,132</td><td>118</td><td>104,927</td><td>21,459</td><td>301,313</td><td>51.51</td></tr><tr><td>CFBP 8351</td><td>PHFU00000000</td><td>8,741,758</td><td>1053x</td><td>2,479,202</td><td>93</td><td>104,608</td><td>26,658</td><td>266,361</td><td>51.45</td></tr><tr><td>CFBP 8078</td><td>PHFS00000000</td><td>8,807,962</td><td>1060x</td><td>2,602,010</td><td>191</td><td>87,559</td><td>13,623</td><td>204,167</td><td>51.67</td></tr><tr><td>CFBP 8356</td><td>PHFV00000000</td><td>8,088,406</td><td>974x</td><td>2,541,621</td><td>197</td><td>93,086</td><td>12,902</td><td>190,454</td><td>51.58</td></tr></tbody></table><table-wrap-foot><p><sup>a</sup>pair-end (301 bp)</p><p><sup>b</sup>Coverage calculated for a mean genome of 2.5 Mb</p><p><sup>c</sup>Larger than 500 bp</p></table-wrap-foot></table-wrap></p></sec><sec id="Sec4"><title>Evaluation of strain synonymy using k-mers</title><p id="Par18">CFBP 7970, the <italic>X. fastidiosa</italic> and <italic>X. fastidiosa</italic> subsp. <italic>fastidiosa</italic> type strain [<xref ref-type="bibr" rid="CR31">31</xref>], has various synonymous names (ATCC 35879, DSM 10026, LMG17159, <ext-link ext-link-type="uri" xlink:href="http://www.straininfo.net/strains/901514">http://www.straininfo.net/strains/901514</ext-link> or <ext-link ext-link-type="uri" xlink:href="http://www.bacterio.net/xylella.html">http://www.bacterio.net/xylella.html</ext-link>) in other collections, as a result of strain exchanges between the American (ATCC), German (DSMZ), Belgian (LMG), and French (CIRM-CFBP) collections [<xref ref-type="bibr" rid="CR32">32</xref>]. As no genome sequences were available at the beginning of this study for any of these strains, CFBP 7970 was included in our dataset and its genome was sequenced. Later on, the genome sequences of the strains ATCC 35879 and DSM 10026 were released. Although the genome sequences of the three strains were very similar (99.83–99.97% ANIb), they were not strictly identical (Additional file <xref rid="MOESM1" ref-type="media">1</xref>). The use of SkIf identified DNA fragments that were specific to two genome sequences, but absent in the third one, yielding in 95, 192, and 594 k-mers specifically present in the pairs ATCC 35879/DSM 10026, CFBP 7970/DSM 10026, ATCC 35879/CFBP 7970, respectively (Additional file <xref rid="MOESM2" ref-type="media">2</xref>). The absence of some mers in genome sequence could be due to sequencing artefacts (e.g. sequencing technology employed, average coverage and assembly methods) that resulted in specific SNPs (Table <xref rid="Tab3" ref-type="table">3</xref>). However, 16 mers (ranging from 29 to 9,178 nt and totalizing 36,845 bp in size) were detected in a single contig (41,458 bp) in CFBP 7970 and into several DSM 10026 contigs but were absent from ATCC 35879 genome sequence (Additional file <xref rid="MOESM2" ref-type="media">2</xref>). These sequences shared high identity levels with a plasmid found in multiple <italic>Xylella</italic> subspecies, known as pXF-De Donno (subsp. <italic>pauca</italic> De Donno strain), pXF-RIV5 (subsp. <italic>multiplex</italic> RIV5 strain), pXF-FAS01 (subsp. <italic>fastidiosa</italic> M23 strain) or present but unnamed elsewhere (like in subsp. <italic>pauca</italic> CoDiRO strain and subsp. <italic>multiplex</italic> Dixon strain) [<xref ref-type="bibr" rid="CR2">2</xref>, <xref ref-type="bibr" rid="CR33">33</xref>–<xref ref-type="bibr" rid="CR35">35</xref>]. But the blast analysis suggested its possible presence, as partial matches (3.8 -6 kb in total) with high but not perfect identity levels (95–99%) were found when searched against the genome sequence of ATCC 35879 (Additional file <xref rid="MOESM2" ref-type="media">2</xref>; Additional file <xref rid="MOESM3" ref-type="media">3</xref>).<table-wrap id="Tab3"><label>Table 3</label><caption><p>Properties of genome sequences of strains CFBP 7970, DSM 10026 and ATCC 35879</p></caption><table frame="hsides" rules="groups"><thead><tr><th></th><th>CFBP 7970<sup>a</sup></th><th>DSM 10026<sup>b</sup></th><th>ATCC 35879<sup>c</sup></th></tr></thead><tbody><tr><td>Sequencing technology</td><td>Ilumina MiSeq</td><td>Shot gun</td><td>Illumina MiSeq</td></tr><tr><td>Assembling method</td><td>Velvet<break></break>SOAPdenovo SOAPGapCloser</td><td>Not available</td><td>CLC Genomic Workbench</td></tr><tr><td>Genome size</td><td>2,493,794 bp</td><td>2,426,538 bp</td><td>2,522,328 bp</td></tr><tr><td>Number of contigs</td><td>93</td><td>72</td><td>16</td></tr><tr><td>Minimal size of contigs</td><td>500 bp</td><td>1 kb</td><td>1.2 kb</td></tr><tr><td>Coverage</td><td>968x</td><td>416x</td><td>1380x</td></tr></tbody></table><table-wrap-foot><p><sup>a</sup> Data from the present study</p><p><sup>b</sup> More details at: <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/genome/173?genome_assembly_id=295121">https://www.ncbi.nlm.nih.gov/genome/173?genome_assembly_id=295121</ext-link></p><p><sup>c</sup> More details at: <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/genome/173?genome_assembly_id=212014">https://www.ncbi.nlm.nih.gov/genome/173?genome_assembly_id=212014</ext-link></p></table-wrap-foot></table-wrap></p></sec><sec id="Sec5"><title>Data mining of the 16S rRNA SILVA database to assign occurrences of <italic>Xylella</italic> sp.</title><p id="Par19">The availability of the 47 <italic>Xylella</italic> genome sequences renders possible the analysis of the allelic diversity of the 16S rRNA marker gene. This housekeeping marker is widely used in bacterial phylogeny and taxonomy studies for various reasons including its vertical inheritance and ubiquity in prokaryotes. It is also commonly used to survey microbial communities and as such is a marker to survey largely the environment. A total of 74 16S rRNA gene sequences was retrieved from our dataset, these either being present in one (<italic>n</italic> = 20) or two copies (<italic>n</italic> = 27) in <italic>X. fastidiosa</italic> and <italic>X. taiwanensis</italic> (Table <xref rid="Tab4" ref-type="table">4</xref>). We detected 19 SNPs (over 1547 nucleotides, 1.22%) specific to <italic>X. taiwanensis</italic> PLS 229 16S rRNA (Additional file <xref rid="MOESM4" ref-type="media">4</xref>).<table-wrap id="Tab4"><label>Table 4</label><caption><p>Repertoire of 16S rRNA gene sequences in 47 genomes of <italic>Xylella</italic> sp</p></caption><table frame="hsides" rules="groups"><thead><tr><th><italic>Xylella</italic> genomes (total; with 1 copy; with 2 copies)</th><th>Codes of strains having one copy of 16S rRNA</th><th>Codes of strains having two copies of 16S rRNA</th></tr></thead><tbody><tr><td>X. <italic>fastidiosa</italic> subsp. <italic>fastidiosa</italic> (<italic>n</italic> = 13;3;10)</td><td>EB92–1, CFBP 8073, CFBP 8351</td><td>ATCC 35879, CFBP 7969, CFBP 7970, CFBP 8071, CFBP 8082, DSM10026, GB514, M23, Stag’s Leap, Temecula1</td></tr><tr><td>X. <italic>fastidiosa</italic> subsp. <italic>multiplex</italic> (<italic>n</italic> = 10;8;2)</td><td>ATCC 35871, BB01, CFBP 8078, CFBP 8417, CFBP 8418, Dixon, Griffin-1, Sy-VA</td><td>CFBP 8416, M12</td></tr><tr><td>X. <italic>fastidiosa</italic> subsp. <italic>morus</italic>(<italic>n</italic> = 2;1;1)</td><td>Mul-MD</td><td>Mul0034</td></tr><tr><td>X. <italic>fastidiosa</italic> subsp. <italic>sandyi</italic> (<italic>n</italic> = 3;1;2)</td><td>CFBP 8356</td><td>Ann-1, CO33</td></tr><tr><td>X. <italic>fastidiosa</italic> subsp. <italic>pauca</italic> (<italic>n</italic> = 18;6;12)</td><td>CFBP 8072, COF0324, COF0407, OLS0479, Xf6c, Xf32</td><td>11,399, 3124, 9a5c, CoDiRO, CVC0251, CVC0256, Fb7, Hib4, J1a12, OLS0478, Pr8x, U24D</td></tr><tr><td>X. <italic>taiwanensis</italic> (<italic>n</italic> = 1;1;0)</td><td>PLS 229</td><td>–</td></tr></tbody></table></table-wrap></p><p id="Par20">Specific mers were searched for within the <italic>Xylella</italic> genus (i.e., the in-group included the 74 <italic>Xylella</italic> 16S rRNA copies; the out-group included all the SSU sequences from the Silva database other than Xylella-tagged) and the <italic>X. fastidiosa</italic> species (i.e., the genome sequence of <italic>X. taiwanensis</italic> PLS 229 strain was included in the out-group). Five long-mers (referred to as LongXyl#1 to #5) specific to <italic>Xylella</italic> genus and four long-mers (referred to as LongXylefa#1 to #4) specific to the <italic>X. fastidiosa</italic> species were identified. LongXyl (23-43 nt) and LongXylefa (23-31 nt) mers located between positions 212 and 866, and positions 202 and 1013, respectively, which include the V3-V4 hypervariable regions widely used in community profiling approaches (Additional file <xref rid="MOESM5" ref-type="media">5</xref>). Specific signatures obtained from eight nucleotide positions in the 16S rRNA alignment discriminated alleles from <italic>X. fastidiosa</italic> subsp. <italic>fastidiosa</italic>, <italic>multiplex</italic>, <italic>morus, sandyi</italic> and <italic>pauca</italic> (Table <xref rid="Tab5" ref-type="table">5</xref>).<table-wrap id="Tab5"><label>Table 5</label><caption><p>Specific signatures in 16S rRNA nucleotide sequences to discriminate <italic>X. fastidiosa</italic> subspecies</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="2"><italic>X. fastidiosa</italic> subsp. (nb of genome sequences)</th><th colspan="8">SNPs at the designed positions<sup>a</sup></th></tr><tr><th>75<sup>a</sup></th><th>76</th><th>151</th><th>455</th><th>474</th><th>1127</th><th>1264</th><th>1340</th></tr></thead><tbody><tr><td><italic>fastidiosa</italic> (<italic>n</italic> = 13)</td><td>C</td><td>A</td><td>C</td><td>G</td><td>–</td><td>G</td><td>A</td><td>C</td></tr><tr><td><italic>morus</italic> (<italic>n</italic> = 2)</td><td>C</td><td>A</td><td>C</td><td>G</td><td>–</td><td>T</td><td>A</td><td>C</td></tr><tr><td><italic>multiplex</italic> (<italic>n</italic> = 10)</td><td>C</td><td>A</td><td>T</td><td>A</td><td>–</td><td>G</td><td>G</td><td>C</td></tr><tr><td><italic>sandyi</italic> (<italic>n</italic> = 1)<sup>b</sup></td><td>C</td><td>A</td><td>T</td><td>A</td><td>T</td><td>G</td><td>A</td><td>C</td></tr><tr><td><italic>sandyi</italic>-like (<italic>n</italic> = 2)<sup>c</sup></td><td>T</td><td>A</td><td>C</td><td>A</td><td>–</td><td>G</td><td>G</td><td>C</td></tr><tr><td><italic>pauca</italic> (<italic>n</italic> = 18)</td><td>C</td><td>G</td><td>T</td><td>A</td><td>–</td><td>G</td><td>A</td><td>T</td></tr></tbody></table><table-wrap-foot><p><sup>a</sup>refers to SNP positions within the alignment of the copies of 16S rRNA (Additional file <xref rid="MOESM4" ref-type="media">4</xref>)</p><p><sup>b</sup>refers to Ann-1strain only</p><p><sup>c</sup>refers to strains CFBP 8356 and CO33 strains</p></table-wrap-foot></table-wrap></p><p id="Par21">The occurrence of these specific mers in 16S rRNA nucleotide sequences was investigated within the SILVA rRNA database (Additional file <xref rid="MOESM4" ref-type="media">4</xref>). A large proportion of the sequences retrieved from the SILVA database (<italic>n</italic> = 118/195) covered less than half of the total gene length, and only a minority (<italic>n</italic> = 70/195) covered at least three fourth of the length. After nucleotide alignment, 53 of these sequences including the LongXyl and LongXylefa specific signatures were retained (Additional file <xref rid="MOESM4" ref-type="media">4</xref>). Based on their genetic signatures, 51 sequences were assigned to subsp. <italic>multiplex</italic> (<italic>n</italic> = 32), <italic>fastidiosa</italic> (n = 11), <italic>pauca</italic> (<italic>n</italic> = 5), <italic>sandyi</italic> (<italic>n</italic> = 2) and <italic>morus</italic> (n = 1), while two sequences (EU560720.1 and EU560722.1) could not be assigned because they did not cover most of the eight discriminant nucleotide positions (Additional file <xref rid="MOESM5" ref-type="media">5</xref>). The validity of this presumptive taxonomic affiliation was consolidated by the description of the sample, which were in adequacy with the current host range of these subspecies. Indeed, samples from subsp. <italic>fastidiosa</italic> mainly come from alfalfa or grapevine, while those from subsp. <italic>multiplex</italic> were collected on various oak species, those from subsp. <italic>sandyi</italic> were isolated from oleander, those from subsp. <italic>pauca</italic> from periwinkle, coffee or olive trees, and the one from subsp. <italic>morus</italic> came from mulberry.</p></sec><sec id="Sec6"><title>Identification of allelic variants specific to each <italic>X. fastidiosa</italic> subspecies</title><p id="Par22">Beyond focusing on a single gene (16S rRNA), we applied SkIf to a whole genome-based analysis. Seven groups of strains were defined: <italic>fastidiosa</italic> (two groups), <italic>pauca</italic>, <italic>multiplex</italic>, <italic>morus</italic> and <italic>sandyi</italic> (two groups). The two <italic>fastidiosa</italic> groups differed by the presence/absence of the strain CFBP 8073, while one <italic>sandyi</italic> group included only the original member Ann-1, and the <italic>sandyi</italic>-like group included only CFBP 8356 and CO33 strains. Specific mers were searched for in each group against all the others.</p><p id="Par23">Overall, long-mers were identified all along the genomes (Fig. <xref rid="Fig1" ref-type="fig">1</xref>), mainly matching coding sequences (71–80% depending on the subspecies), with one to several long-mers in the identified CDS (Table <xref rid="Tab6" ref-type="table">6</xref>A; Additional file <xref rid="MOESM6" ref-type="media">6</xref>). Gene set enrichment analysis was performed by comparing the predicted functions associated with these specific CDSs to the overall predicted proteomes. Fischer’s exact test revealed multiple GO terms over- (mostly) or under- (rarely) represented for the seven groups. Overall, only one GO term (catalytic activity) was always found enriched, except for the subspecies <italic>morus</italic>, while 10 other GO terms were found enriched in all groups except in subspecies <italic>morus</italic> and <italic>sandyi</italic> (Table <xref rid="Tab7" ref-type="table">7</xref>; Additional file <xref rid="MOESM7" ref-type="media">7</xref>; Fig. <xref rid="Fig2" ref-type="fig">2</xref>). Several GO terms were only identified in a single subspecies (Table <xref rid="Tab8" ref-type="table">8</xref>), suggesting that associated mechanisms might be key markers of <italic>X. fastidiosa</italic> subspecies evolution. As for subspecies <italic>pauca</italic> it concerned 175 GO terms, including 20 terms associated with the bacterial cell wall/envelope/plasma membrane and 16 related to nucleotide metabolic/biosynthetic process, especially for purine, as well as 4 terms under-represented dealing with viral or symbiont processes. As for subspecies <italic>fastidiosa</italic> (without CFBP 8073) it concerned six GO terms related to DNA modification and vitamin process. The subspecies <italic>multiplex</italic> specific GO terms deal with metabolic process, catalytic activity and conformation of DNA and organelle organization. The subspecies <italic>morus</italic> had only one ontology enriched, associated with DNA replication.<fig id="Fig1"><label>Fig. 1</label><caption><p>Distribution of k-mers along the <italic>X. fastidiosa</italic> genome sequences. Frequency of core (black) and specific (colored) k-mers mapped onto the genome of reference (mentioned into brackets) of each subspecies. <bold>a</bold> subsp. <italic>fastidiosa</italic> with or without CFBP 8073 strain. <bold>b</bold> subsp. <italic>sandyi</italic>. <bold>c</bold> subsp. <italic>morus.</italic><bold>d</bold> subsp. <italic>multiplex.</italic><bold>e</bold> subsp. <italic>pauca</italic></p></caption><graphic xlink:href="12864_2019_5565_Fig1_HTML" id="MO1"></graphic></fig><table-wrap id="Tab6"><label>Table 6</label><caption><p>Main features related to the specific mers identified in <italic>X. fastidiosa</italic> subspecies</p></caption><table frame="hsides" rules="groups"><tbody><tr><td>A. <italic>X. fastidiosa</italic> subspecies</td><td>FAS<sup>1</sup></td><td>FAS2<sup>1</sup></td><td>SAN<sup>1</sup></td><td>SAN2<sup>1</sup></td><td>MOR<sup>1</sup></td><td>MUL<sup>1</sup></td><td>PAU<sup>1</sup></td><td></td></tr><tr><td>number of mers</td><td>2905</td><td>1978</td><td>9808</td><td>5765</td><td>3094</td><td>4906</td><td>11,365</td><td></td></tr><tr><td>number of unique mers</td><td>2836</td><td>1957</td><td>9431</td><td>5636</td><td>2995</td><td>4813</td><td>11,162</td><td></td></tr><tr><td>total mer size (bp)</td><td>133,179</td><td>85,038</td><td>518,683</td><td>292,740</td><td>142,614</td><td>258,228</td><td>627,685</td><td></td></tr><tr><td>number of mers in CDS</td><td>2172</td><td>1411</td><td>7783</td><td>4161</td><td>2341</td><td>3603</td><td>9088</td><td></td></tr><tr><td>number of unique CDS</td><td>1142</td><td>811</td><td>2406</td><td>1646</td><td>1115</td><td>1119</td><td>1711</td><td></td></tr><tr><td>total mer size in CDS (bp)</td><td>100,015</td><td>60,092</td><td>414,736</td><td>215,901</td><td>108,336</td><td>189,973</td><td>504,054</td><td></td></tr><tr><td>number of mers in intergenic regions</td><td>733</td><td>567</td><td>2025</td><td>1604</td><td>753</td><td>1303</td><td>2277</td><td></td></tr><tr><td>total mer size in intergenic regions (bp)</td><td>33,164</td><td>24,946</td><td>103,947</td><td>76,839</td><td>34,278</td><td>68,255</td><td>123,631</td><td></td></tr><tr><td>B. Combination <italic>morus</italic> + other subspecies</td><td>MOR-FAS<sup>1</sup></td><td>MOR-FAS2<sup>1</sup></td><td>MOR-SAN<sup>1</sup></td><td>MOR-SAN2<sup>1</sup></td><td>MOR-SAN-SAN2<sup>1</sup></td><td>MOR-SAN-SAN2-FAS2<sup>1</sup></td><td>MOR-MUL<sup>1</sup></td><td>MOR-PAU<sup>1</sup></td></tr><tr><td>number of mers</td><td>495</td><td>1236</td><td>352</td><td>371</td><td>237</td><td>3389</td><td>2131</td><td>71</td></tr><tr><td>number of unique mers</td><td>491</td><td>1222</td><td>347</td><td>358</td><td>235</td><td>3369</td><td>2072</td><td>71</td></tr><tr><td>total mer size (bp)</td><td>20,058</td><td>53,052</td><td>13,123</td><td>14,066</td><td>8019</td><td>136,470</td><td>98,450</td><td>2377</td></tr><tr><td>number of mers in CDS</td><td>331</td><td>825</td><td>258</td><td>243</td><td>116</td><td>2367</td><td>1638</td><td>58</td></tr><tr><td>number of unique CDS</td><td>216</td><td>430</td><td>192</td><td>178</td><td>103</td><td>806</td><td>572</td><td>41</td></tr><tr><td>total mer size in CDS (bp)</td><td>13,428</td><td>36,147</td><td>9816</td><td>9275</td><td>4249</td><td>96,946</td><td>76,167</td><td>2018</td></tr><tr><td>number of mers in intergenic regions</td><td>164</td><td>411</td><td>94</td><td>128</td><td>121</td><td>1022</td><td>493</td><td>13</td></tr><tr><td>total mer size in intergenic regions (bp)</td><td>6630</td><td>16,905</td><td>3307</td><td>4791</td><td>3770</td><td>39,524</td><td>22,283</td><td>359</td></tr><tr><td>C. Within subspecies <italic>pauca</italic></td><td><italic>pauca</italic> I.1<sup>1</sup></td><td><italic>pauca</italic> I.2<sup>1</sup></td><td><italic>pauca</italic> I.3<sup>1</sup></td><td>CFBP 8072<sup>1</sup></td><td>Hib4<sup>1</sup></td><td colspan="3"></td></tr><tr><td>number of mers</td><td>1266</td><td>2360</td><td>3885</td><td>4775</td><td>4694</td><td colspan="3"></td></tr><tr><td>number of unique mers</td><td>1238</td><td>2323</td><td>3644</td><td>4663</td><td>4596</td><td colspan="3"></td></tr><tr><td>total mer size (bp)</td><td>59,733</td><td>121,367</td><td>207,098</td><td>283,540</td><td>341,563</td><td colspan="3"></td></tr><tr><td>number of mers in CDS</td><td>1003</td><td>1776</td><td>3194</td><td>3150</td><td>3338</td><td colspan="3"></td></tr><tr><td>number of unique CDS</td><td>486</td><td>716</td><td>1147</td><td>1205</td><td>1324</td><td colspan="3"></td></tr><tr><td>total mer size in CDS (bp)</td><td>47,655</td><td>92,528</td><td>173,936</td><td>194,240</td><td>269,888</td><td colspan="3"></td></tr><tr><td>number of mers in intergenic regions</td><td>263</td><td>584</td><td>690</td><td>1625</td><td>1356</td><td colspan="3"></td></tr><tr><td>total mer size in intergenic regions (bp)</td><td>12,078</td><td>28,839</td><td>33,162</td><td>89,300</td><td>71,675</td><td colspan="3"></td></tr></tbody></table><table-wrap-foot><p><sup>1</sup>Composition of the groups:</p><p><bold>MOR</bold> (subsp. <italic>morus</italic>): Mul-MD and Mul0034 (Reference: 2,666,577 bp). <bold>FAS</bold> (subsp. <italic>fastidiosa</italic>): ATCC 35879, DSM 10026, CFBP 7969, CFBP 7970, CFBP 8071, CFBP 8082, CFBP 8351, EB92–1, GB514, M23, Stag’s Leap and Temecula1 (Reference: 2,521,148 bp). <bold>FAS2</bold> (subsp. <italic>fastidiosa</italic>): All the members of the group FAS (with Temecula1 as reference), plus CFBP 8073. <bold>MUL</bold> (subsp. <italic>multiplex</italic>): ATCC 35871, BB01, CFBP 8078, CFBP 8416, CFBP 8417, CFBP 8418, Dixon, Griffin-1, Sy-VA and M12 (Reference: 2,475,130 bp). <bold>SAN</bold> (subsp. <italic>sandyi</italic>): Ann-1 (Reference: 2,780,908 bp). <bold>SAN2</bold> (subsp. <italic>sandyi</italic>-like): CFBP 8356 and CO33 (Reference: 2,416,985 bp). <bold>PAU</bold> (subsp. <italic>pauca</italic>): 32, 3124, 11,399, 6c, CFBP 8072, CoDiRO, COF0324, COF0407, CVC0251, CVC0256, Fb7, Hib4, J1a12, OLS0478, OLS0479, Pr8x, U24D and 9a5c (Reference: 2,731,750 bp). <bold><italic>pauca</italic></bold><bold>I.1</bold> (subsp. <italic>pauca</italic>): U24D, Fb7, CVC0251, CVC0256, J1a12, 11,399, 3124, 32 and 9a5c (Reference: 2,731,750 bp). <bold><italic>pauca</italic></bold><bold>I.2</bold> (subsp. <italic>pauca</italic>): 6c, COF0324 and Pr8x (Reference: 2,666,242 bp). <bold><italic>pauca</italic></bold><bold>I.3</bold> (subsp. <italic>pauca</italic>): COF0407, OLS0478, OLS0479 and CoDiRO (Reference: 2,542,932 bp). <bold>CFBP 8072</bold> (subsp. <italic>pauca</italic>; 2,496,662 bp). <bold>Hib4</bold> (subsp. <italic>pauca;</italic> 2,877,548 bp)</p></table-wrap-foot></table-wrap><table-wrap id="Tab7"><label>Table 7</label><caption><p>Main Gene Ontologies (GO) identified as enriched in almost all the subspecies for the CDS harboring specific mers</p></caption><table frame="hsides" rules="groups"><thead><tr><th>GO term<sup>1</sup></th><th>Description</th><th>FAS<sup>2,3</sup></th><th>FAS2<sup>2,3</sup></th><th>MUL<sup>2,3</sup></th><th>PAU<sup>2,3</sup></th><th>SAN<sup>2,3</sup></th><th>SAN2<sup>2,3</sup></th></tr></thead><tbody><tr><td>GO:0003824</td><td>catalytic activity</td><td>473/368<break></break>669/912<break></break>1.64e-7/7.48e-11</td><td>343/498<break></break>468/1113<break></break>4.79e-5/4.20e-8</td><td>358/308<break></break>761/935<break></break>0.0082/1.18e-4</td><td>672/143<break></break>1039/796<break></break>4.35e-37/3.55e-40</td><td>779/86<break></break>1627/311<break></break>0.0108/1.34e-5</td><td>630/229<break></break>1016/670<break></break>1.05e-7/4.37e-11</td></tr><tr><td>GO:0000166</td><td>nucleotide binding</td><td>138/96<break></break>1004/1184<break></break>0.0246/1.46e-4</td><td>106/128<break></break>705/1483<break></break>0.0115/7.90e-5</td><td>143/90<break></break>976/1153<break></break>9.99e-4/8.70e-6</td><td>240/32<break></break>1471/907<break></break>2.40e-18/2.18e-20</td><td>–</td><td>228/54<break></break>1418/845<break></break>2.30e-7/3.81e-10</td></tr><tr><td>GO:0017076</td><td>purine nucleotide binding</td><td>109/73<break></break>1033/1207<break></break>0.0469/3.69e-4</td><td>87/95<break></break>724/1516<break></break>0.0077/3.91e-5</td><td>118/70<break></break>1001/1173<break></break>0.0012/1.25e-5</td><td>197/20<break></break>1514/919<break></break>4.04e-18/4.45e-20</td><td>–</td><td>181/44<break></break>1465/855<break></break>2.08e-5/7.77e-8</td></tr><tr><td>GO:0032553</td><td>ribonucleotide binding</td><td>114/74<break></break>1028/1206<break></break>0.0246/1.33e-4</td><td>89/99<break></break>722/1512<break></break>0.0086/5.12e-5</td><td>121/72<break></break>998/1171<break></break>0.0011/1.12e-5</td><td>203/23<break></break>1508/916<break></break>2.25e-17/2.67e-19</td><td>–</td><td>186/48<break></break>1460/851<break></break>5.83e-5/2.89e-7</td></tr><tr><td>GO:0032555</td><td>purine ribonucleotide binding</td><td>108/73<break></break>1034/1207<break></break>0.0469/4.80e-4</td><td>87/94<break></break>724/1517<break></break>0.0060/2.64e-5</td><td>117/70<break></break>1002/1173<break></break>0.0015/1.70e-5</td><td>197/19<break></break>1514/920<break></break>1.07e-18/8.34e-21</td><td>–</td><td>181/44<break></break>1465/855<break></break>2.08e-5/7.77e-8</td></tr><tr><td>GO:1901265</td><td>nucleoside phosphate binding</td><td>138/96<break></break>1004/1184<break></break>0.0246/1.46e-4</td><td>106/128<break></break>705/1483<break></break>0.0115/7.90e-5</td><td>143/90<break></break>976/1153<break></break>9.99e-4/8.70e-6</td><td>240/32<break></break>1471/907<break></break>2.40e-18/2.18e-20</td><td>–</td><td>228/54<break></break>1418/845<break></break>2.30e-7/3.81e-10</td></tr><tr><td>GO:0036094</td><td>small molecule binding</td><td>153/103<break></break>989/1177<break></break>0.0077/2.11e-5</td><td>114/142<break></break>697/1469<break></break>0.0142/1.10e-4</td><td>155/100<break></break>964/1143<break></break>8.42e-4/5.87e-6</td><td>266/33<break></break>1445/906<break></break>1.49e-21/6.68e-24</td><td>–</td><td>251/62<break></break>1395/837<break></break>2.30e-7/2.82e-10</td></tr><tr><td>GO:0043168</td><td>anion binding</td><td>140/87<break></break>1002/1193<break></break>0.0030/4.98e-6</td><td>102/125<break></break>709/1486<break></break>0.0206/2.07e-4</td><td>140/88<break></break>979/1155<break></break>0.0010/9.88e-6</td><td>242/27<break></break>1469/912<break></break>4.32e-21/2.11e-23</td><td>–</td><td>226/59<break></break>1420/840<break></break>7.16e-6/1.77e-8</td></tr><tr><td>GO:0097367</td><td>carbohydrate derivative binding</td><td>117/81<break></break>1025/1199<break></break>0.0469/4.68e-4</td><td>94/104<break></break>717/1507<break></break>0.0060/2.74e-5</td><td>126/73<break></break>993/1170<break></break>5.43e-4/2.60e-6</td><td>209/23<break></break>1502/916<break></break>2.40e-18/2.31e-20</td><td>–</td><td>190/50<break></break>1456/849<break></break>7.27e-5/3.90e-7</td></tr><tr><td>GO:0005488</td><td>binding</td><td>323/277<break></break>819/1003<break></break>0.0253/1.61e-4</td><td>247/353<break></break>564/1258<break></break>0.0020/5.52e-6</td><td>296/245<break></break>823/998<break></break>0.0078/1.06e-4</td><td>547/140<break></break>1164/799<break></break>1.14e-20/6.54e-23</td><td>–</td><td>502/187<break></break>1144/712<break></break>3.03e-5/1.25e-7</td></tr><tr><td>GO:0008152</td><td>metabolic process</td><td>465/411<break></break>677/869<break></break>0.0055/1.26e-5</td><td>355/521<break></break>456/1090<break></break>4.79e-5/4.37e-8</td><td>397/331<break></break>722/912<break></break>5.94e-4/3.44e-6</td><td>723/168<break></break>988/771<break></break>4.40e-36/5.38e-39</td><td>–</td><td>644/264<break></break>1002/635<break></break>1.36e-4/7.91e-7</td></tr></tbody></table><table-wrap-foot><p><sup>1</sup>Complete datasets are provided in Additional file <xref rid="MOESM7" ref-type="media">7</xref></p><p><sup>2</sup>Top line: number of GO-associated CDSs in the list of CDSs harboring specific mers (query) / number of GO-associated CDSs in the CDSs of reference genome that do not harbor specific mers. Middle line: number of non-annotated (no GOs) CDSs in the list of CDSs harboring specific mers (query) / number of non-annotated (no GOs) CDSs in the CDSs of reference genome that do not harbor specific mers. The addition of the four values in each column correspond to the total number of CDS of the reference genome. The addition of the numerator values corresponds to the number of CDS in the query list. The addition of the denominator values corresponds to the number of CDSs of the reference genome that are not in the list of CDSs harboring specific mers. Bottom line: FDR/ <italic>P</italic>-value</p><p><sup>3</sup>Composition of the groups: FAS (subsp. <italic>fastidiosa</italic>, 12): ATCC 35879, DSM 10026, CFBP 7969, CFBP 7970, CFBP 8071, CFBP 8082, CFBP 8351, EB92–1, GB514, M23, Stag’s Leap, Temecula1. FAS2 (subsp. <italic>fastidiosa</italic>, 13): All the members of the group FAS, plus CFBP 8073. MUL (subsp. <italic>multiplex</italic>, 10): ATCC 35871, BB01, CFBP 8078, CFBP 8416, CFBP 8417, CFBP 8418, Dixon, Griffin-1, M12, Sy-VA. SAN (subsp. <italic>sandyi</italic>, 1): Ann-1. SAN2 (subsp. <italic>sandyi</italic>-like, 2): CO33 and CFBP 8356. PAU (subsp. <italic>pauca</italic>, 18): 32, 3124, 11,399, 6c, 9a5c, CFBP 8072, CoDiRO, COF0324, COF0407, CVC0251, CVC0256, Fb7, Hib4, J1a12, OLS0478, OLS0479, Pr8x, U24D</p></table-wrap-foot></table-wrap><fig id="Fig2"><label>Fig. 2</label><caption><p>Overlap between gene ontologies differentially represented (over or under) in genes harboring specific k-mers. <bold>a</bold> Relationships between six groups: FAS and FAS2, subsp. <italic>fastidiosa</italic> without or with CFBP 8073, respectively; MUL, subsp. <italic>multiplex</italic>; SAN and SAN2, subsp. <italic>sandyi</italic> and <italic>sandyi</italic>-like, respectively; PAU, subsp. <italic>pauca</italic>. Note: the subsp. <italic>morus</italic> is not indicated on the Venn diagram as it was identified only one GO term, specific to it. <bold>b</bold> Relationships between three groups (<italic>pauca</italic>, <italic>multiplex</italic> and the third one resulting from the grouping of subsp. <italic>fastidiosa</italic>, <italic>sandyi</italic> and <italic>morus</italic>)</p></caption><graphic xlink:href="12864_2019_5565_Fig2_HTML" id="MO2"></graphic></fig><table-wrap id="Tab8"><label>Table 8</label><caption><p>Selected differentially represented Gene Ontologies of CDS with specific mers in <italic>X</italic>. <italic>fastidiosa</italic> subspecies or subclades</p></caption><table frame="hsides" rules="groups"><thead><tr><th>GO term<sup>1</sup></th><th>Description</th><th>FDR/<italic>p</italic>-value</th><th>Annot. test/ref<sup>2</sup></th><th>Non annot. Test/ref<sup>3</sup></th><th>Enrichment</th></tr></thead><tbody><tr><td colspan="6">Specific to subsp. <italic>pauca</italic>: associated with the bacterial cell wall/envelope/plasma membrane; nucleotide metabolic/biosynthetic process, especially for purine</td></tr><tr><td> GO:0000270</td><td>peptidoglycan metabolic process</td><td>4.40e-36/5.38e-39</td><td>723/168</td><td>988/771</td><td>over</td></tr><tr><td> GO:0000902</td><td>cell morphogenesis</td><td>4.21e-4/2.27e-5</td><td>25/0</td><td>1686/939</td><td>over</td></tr><tr><td> GO:0005886</td><td>plasma membrane</td><td>0.0017/1.15e-4</td><td>96/23</td><td>1615/916</td><td>over</td></tr><tr><td> GO:0009252</td><td>peptidoglycan biosynthetic process</td><td>0.0029/2.08e-4</td><td>20/0</td><td>1691/939</td><td>over</td></tr><tr><td> GO:0009273</td><td>peptidoglycan-based cell wall biogenesis</td><td>0.0029/2.08e-4</td><td>20/0</td><td>1691/939</td><td>over</td></tr><tr><td> GO:0009279</td><td>cell outer membrane</td><td>0.0346/0.0035</td><td>19/1</td><td>1692/938</td><td>over</td></tr><tr><td> GO:0009653</td><td>anatomical structure morphogenesis</td><td>4.21e-4/2.272e-5</td><td>25/0</td><td>1686/939</td><td>over</td></tr><tr><td> GO:0016021</td><td>integral component of membrane</td><td>0.0060/4.49e-4</td><td>292/112</td><td>1419/827</td><td>over</td></tr><tr><td> GO:0019867</td><td>outer membrane</td><td>0.0458/0.0047</td><td>25/3</td><td>1686/936</td><td>over</td></tr><tr><td> GO:0030312</td><td>external encapsulating structure</td><td>0.0088/7.40e-4</td><td>22/1</td><td>1689/938</td><td>over</td></tr><tr><td> GO:0031224</td><td>intrinsic component of membrane</td><td>0.0049/3.68e-4</td><td>293/112</td><td>1418/827</td><td>over</td></tr><tr><td> GO:0042546</td><td>cell wall biogenesis</td><td>0.0029/2.08e-4</td><td>20/0</td><td>1691/939</td><td>over</td></tr><tr><td> GO:0044036</td><td>cell wall macromolecule metabolic process</td><td>0.0012/7.19e-5</td><td>23/0</td><td>1688/939</td><td>over</td></tr><tr><td> GO:0044038</td><td>cell wall macromolecule biosynthetic process</td><td>0.0029/2.08e-4</td><td>20/0</td><td>1691/939</td><td>over</td></tr><tr><td> GO:0044425</td><td>membrane part</td><td>0.0014/8.82eE-5</td><td>302/112</td><td>1409/827</td><td>over</td></tr><tr><td> GO:0044462</td><td>external encapsulating structure part</td><td>0.0346/0.0035</td><td>19/1</td><td>1692/938</td><td>over</td></tr><tr><td> GO:0045229</td><td>external encapsulating structure organization</td><td>0.0023/1.55e-4</td><td>26/1</td><td>1685/938</td><td>over</td></tr><tr><td> GO:0048856</td><td>anatomical structure development</td><td>4.21e-4/2.27e-5</td><td>25/0</td><td>1686/939</td><td>over</td></tr><tr><td> GO:0071554</td><td>cell wall organization or biogenesis</td><td>0.0094/7.93e-4</td><td>23/1</td><td>1688/938</td><td>over</td></tr><tr><td> GO:0071555</td><td>cell wall organization</td><td>0.0346/0.0035</td><td>19/1</td><td>1692/938</td><td>over</td></tr><tr><td> GO:0006164</td><td>purine nucleotide biosynthetic process</td><td>0.0079/6.34e-4</td><td>27/2</td><td>1684/937</td><td>over</td></tr><tr><td> GO:0009127</td><td>purine nucleoside monophosphate biosynthetic process</td><td>0.0088/7.40e-4</td><td>22/1</td><td>1689/938</td><td>over</td></tr><tr><td> GO:0009144</td><td>purine nucleoside triphosphate metabolic process</td><td>0.0035/2.62e-4</td><td>28/1</td><td>1686/938</td><td>over</td></tr><tr><td> GO:0009152</td><td>purine ribonucleotide biosynthetic process</td><td>0.0122/0.0010</td><td>26/2</td><td>1685/937</td><td>over</td></tr><tr><td> GO:0009168</td><td>purine ribonucleoside monophosphate biosynthetic process</td><td>0.0088/7.4042e-4</td><td>22/1</td><td>1689/938</td><td>over</td></tr><tr><td> GO:0009205</td><td>purine ribonucleoside triphosphate metabolic process</td><td>0.0035/2.6218e-4</td><td>25/1</td><td>1686/938</td><td>over</td></tr><tr><td> GO:0072522</td><td>purine-containing compound biosynthetic process</td><td>0.0346/0.0034</td><td>18/1</td><td>1693/938</td><td>over</td></tr><tr><td> GO:0072528</td><td>pyrimidine-containing compound biosynthetic process</td><td>0.0034/2.457e-4</td><td>29/2</td><td>1682/937</td><td>over</td></tr><tr><td> GO:0009117</td><td>nucleotide metabolic process</td><td>0.0012/7.00e-5</td><td>64/11</td><td>1647/928</td><td>over</td></tr><tr><td> GO:0009123</td><td>nucleoside monophosphate metabolic process</td><td>1.59e-5/5.71e-7</td><td>49/3</td><td>1662/936</td><td>over</td></tr><tr><td> GO:0009124</td><td>nucleoside monophosphate biosynthetic process</td><td>0.0014/8.89e-5</td><td>32/2</td><td>1679/937</td><td>over</td></tr><tr><td> GO:0009141</td><td>nucleoside triphosphate metabolic process</td><td>0.0034/2.45e-4</td><td>29/2</td><td>1682/937</td><td>over</td></tr><tr><td> GO:0009156</td><td>ribonucleoside monophosphate biosynthetic process</td><td>6.00e-4/3.25e-5</td><td>30/1</td><td>1681/938</td><td>over</td></tr><tr><td> GO:0009165</td><td>nucleotide biosynthetic process</td><td>0.0106/8.96e-4</td><td>43/7</td><td>1668/932</td><td>over</td></tr><tr><td> GO:0009199</td><td>ribonucleoside triphosphate metabolic process</td><td>0.0023/1.55e-4</td><td>26/1</td><td>1685/938</td><td>over</td></tr><tr><td> GO:0009260</td><td>ribonucleotide biosynthetic process</td><td>6.15e-4/3.36e-5</td><td>35/2</td><td>1676/937</td><td>over</td></tr><tr><td> GO:0016032</td><td>viral process</td><td>0.0213/0.0019</td><td>0/6</td><td>1711/933</td><td>under</td></tr><tr><td> GO:0019058</td><td>viral life cycle</td><td>0.0213/0.0019</td><td>0/6</td><td>1711/933</td><td>under</td></tr><tr><td> GO:0019068</td><td>virion assembly</td><td>0.0213/0.0019</td><td>0/6</td><td>1711/933</td><td>under</td></tr><tr><td> GO:0044403</td><td>Symbiont process</td><td>0.0213/0.0019</td><td>0/6</td><td>1711/933</td><td>under</td></tr><tr><td colspan="6">Specific to subsp. <italic>fastidiosa</italic> (without CFBP 8073; group FAS): associated with DNA modification; vitamin process</td></tr><tr><td> GO:0006304</td><td>DNA modification</td><td>0.0030/5.64e-6</td><td>16/0</td><td>1126/1280</td><td>over</td></tr><tr><td> GO:0006305</td><td>DNA alkylation</td><td>0.0469/5.31e-4</td><td>10/0</td><td>1132/1280</td><td>over</td></tr><tr><td> GO:0006306</td><td>DNA methylation</td><td>0.0469/5.31e-4</td><td>10/0</td><td>1132/1280</td><td>over</td></tr><tr><td> GO:0044728</td><td>DNA methylation or demethylation</td><td>0.0469/5.31e-4</td><td>10/0</td><td>1132/1280</td><td>over</td></tr><tr><td> GO:0009110</td><td>vitamin biosynthetic process</td><td>0.0469/5.56e-4</td><td>18/3</td><td>1124/1277</td><td>over</td></tr><tr><td> GO:0042364</td><td>water-soluble vitamin biosynthetic process</td><td>0.0469/5.56e-4</td><td>18/3</td><td>1124/1277</td><td>over</td></tr><tr><td colspan="6">Specific to subsp. <italic>multiplex</italic>: associated with metabolic process, catalytic activity and conformation of DNA; organelle organization</td></tr><tr><td> GO:0006259</td><td>DNA metabolic process</td><td>0.0021/2.52e-5</td><td>53/21</td><td>1066/1222</td><td>over</td></tr><tr><td> GO:0071103</td><td>DNA conformation change</td><td>0.0324/5.80eE-4</td><td>13/1</td><td>1106/1242</td><td>over</td></tr><tr><td> GO:0140097</td><td>catalytic activity, acting on DNA</td><td>0.0018/2.11eE-5</td><td>33/8</td><td>1086/1235</td><td>over</td></tr><tr><td> GO:0006996</td><td>organelle organization</td><td>0.0256/4.47e-4</td><td>162</td><td>1103/1241</td><td>over</td></tr><tr><td colspan="6">Specific to subsp. <italic>morus</italic>: associated with DNA replication</td></tr><tr><td> GO:0006260</td><td>DNA replication</td><td>0.0485/1.99e-5</td><td>31/10</td><td>1084/1491</td><td>over</td></tr><tr><td colspan="6">Specific to the combination of subsp. <italic>morus</italic> and <italic>multiplex</italic>: associated with amino acid biosynthetic processes; ion binding</td></tr><tr><td> GO:1901607</td><td>alpha-amino acid biosynthetic process</td><td>0.0390/2.30e-4</td><td>26/35</td><td>546/2009</td><td>over</td></tr><tr><td colspan="6">Specific to the combination of subsp. <italic>morus</italic>, <italic>fastidiosa</italic> (including CFBP 8073), <italic>sandyi</italic>, <italic>sandyi</italic>-like (=clade III): associated with cellular component or protein complex disassembly; signaling; metabolic process; ATP generation; carbohydrates / polysaccharides; nucleoside/nucleotides; peptidyl-proline; response to chemical; tRNA binding; chemotaxis</td></tr><tr><td> GO:0022411</td><td>cellular component disassembly</td><td>0.0168/8.44e-4</td><td>6/0</td><td>800/1810</td><td>over</td></tr><tr><td> GO:0032984</td><td>macromolecular complex disassembly</td><td>0.0168/8.44e-4</td><td>6/0</td><td>800/1810</td><td>over</td></tr><tr><td> GO:0043241</td><td>protein complex disassembly</td><td>0.0168/8.44e-4</td><td>6/0</td><td>800/1810</td><td>over</td></tr><tr><td> GO:0023052</td><td>signaling</td><td>0.0496/0.0031</td><td>18/14</td><td>788/1796</td><td>over</td></tr><tr><td> GO:0007165</td><td>signal transduction</td><td>0.0496/0.0031</td><td>18/14</td><td>788/1796</td><td>over</td></tr><tr><td> GO:0006090</td><td>pyruvate metabolic process</td><td>0.0086/3.44e-4</td><td>13/5</td><td>793/1805</td><td>over</td></tr><tr><td> GO:0006096</td><td>glycolytic process</td><td>0.0149/5.74e-4</td><td>17/10</td><td>789/1800</td><td>over</td></tr><tr><td> GO:0006733</td><td>oxidoreduction coenzyme metabolic process</td><td>0.0343/0.0018</td><td>8/2</td><td>798/1808</td><td>over</td></tr><tr><td> GO:0044264</td><td>cellular polysaccharide metabolic process</td><td>0.0149/7.01e-4</td><td>9/2</td><td>797/1808</td><td>over</td></tr><tr><td> GO:0006757</td><td>ATP generation from ADP</td><td>0.0078/3.08e-4</td><td>11/3</td><td>795/1807</td><td>over</td></tr><tr><td> GO:0016052</td><td>carbohydrate catabolic process</td><td>0.0359/0.0020</td><td>10/4</td><td>796/1806</td><td>over</td></tr><tr><td> GO:0005976</td><td>polysaccharide metabolic process</td><td>0.0359/0.0020</td><td>9/3</td><td>797/1807</td><td>over</td></tr><tr><td> GO:0006165</td><td>nucleoside diphosphate phosphorylation</td><td>0.0168/8.36e-4</td><td>11/4</td><td>795/1806</td><td>over</td></tr><tr><td> GO:0009132</td><td>nucleoside diphosphate metabolic process</td><td>0.0066/2.55e-4</td><td>10/2</td><td>796/1808</td><td>over</td></tr><tr><td> GO:0009135</td><td>purine nucleoside diphosphate metabolic process</td><td>0.0066/2.55e-4</td><td>10/2</td><td>796/1808</td><td>over</td></tr><tr><td> GO:0009179</td><td>purine ribonucleoside diphosphate metabolic process</td><td>0.0066/2.55e-4</td><td>10/2</td><td>796/1808</td><td>over</td></tr><tr><td> GO:0009185</td><td>ribonucleoside diphosphate metabolic process</td><td>0.0383/0.0022</td><td>13/7</td><td>793/1803</td><td>over</td></tr><tr><td> GO:0019362</td><td>pyridine nucleotide metabolic process</td><td>0.0383/0.0022</td><td>13/7</td><td>793/1803</td><td>over</td></tr><tr><td> GO:0046496</td><td>nicotinamide nucleotide metabolic process</td><td>0.0066/2.58e-4</td><td>7/0</td><td>799/1810</td><td>over</td></tr><tr><td> GO:0003755</td><td>peptidyl-prolyl cis-trans isomerase activity</td><td>0.0066/2.58e-4</td><td>7/0</td><td>799/1810</td><td>over</td></tr><tr><td> GO:0000413</td><td>protein peptidyl-prolyl isomerization</td><td>0.0066/2.58e-4</td><td>7/0</td><td>799/1810</td><td>over</td></tr><tr><td> GO:0016859</td><td>cis-trans isomerase activity</td><td>0.0383/0.0022</td><td>13/7</td><td>793/1803</td><td>over</td></tr><tr><td> GO:0018208</td><td>peptidyl-proline modification</td><td>0.0168/8.36e-4</td><td>11/4</td><td>795/1806</td><td>over</td></tr><tr><td> GO:0042221</td><td>response to chemical</td><td>0.0454/0.00275</td><td>5/0</td><td>801/1810</td><td>over</td></tr><tr><td> GO:0000049</td><td>tRNA binding</td><td>0.0454/0.00275</td><td>5/0</td><td>801/1810</td><td>over</td></tr><tr><td> GO:0006935</td><td>chemotaxis</td><td>0.0454/0.00275</td><td>5/0</td><td>801/1810</td><td>over</td></tr><tr><td> GO:0040011</td><td>locomotion</td><td>0.0168/8.44e-4</td><td>6/0</td><td>800/1810</td><td>over</td></tr><tr><td> GO:0042330</td><td>taxis</td><td>0.0168/8.44e-4</td><td>6/0</td><td>800/1810</td><td>over</td></tr><tr><td colspan="6">Specific to the subclade I.3 from subsp. <italic>pauca</italic>: transport, recombination, organelle part</td></tr><tr><td> GO:0006310</td><td>DNA recombination</td><td>0.0093/5.91e-4</td><td>0/12</td><td>1147/1281</td><td>under</td></tr><tr><td> GO:0006812</td><td>cation transport</td><td>0.0368/0.0029</td><td>2/15</td><td>1145/1278</td><td>under</td></tr><tr><td> GO:0015672</td><td>monovalent inorganic cation transport</td><td>0.0282/0.0022</td><td>1/13</td><td>1146/1280</td><td>under</td></tr><tr><td> GO:0034220</td><td>ion transmembrane transport</td><td>0.0089/5.56e-4</td><td>2/19</td><td>1145/1274</td><td>under</td></tr><tr><td> GO:0098655</td><td>cation transmembrane transport</td><td>0.0167/0.0012</td><td>1/14</td><td>1146/1279</td><td>under</td></tr><tr><td> GO:0098660</td><td>inorganic ion transmembrane transport</td><td>0.0103/6.72e-4</td><td>1/15</td><td>1146/1278</td><td>under</td></tr><tr><td> GO:0098662</td><td>inorganic cation transmembrane transport</td><td>0.0488/0.0040</td><td>1/12</td><td>1146/1281</td><td>under</td></tr><tr><td> GO:0008324</td><td>cation transmembrane transporter activity</td><td>0.0282/0.0022</td><td>1/13</td><td>1146/1280</td><td>under</td></tr><tr><td> GO:0044422</td><td>organelle part</td><td>0.0167/0.0012</td><td>1/14</td><td>1146/1279</td><td>under</td></tr><tr><td> GO:0044446</td><td>intracellular organelle part</td><td>0.0167/0.0012</td><td>1/14</td><td>1146/1279</td><td>under</td></tr><tr><td colspan="6">Specific to the CFBP 8072 genome from subsp. <italic>pauca</italic>: nucleoside and carboxylic acid biosynthetic processes</td></tr><tr><td> GO:0009142</td><td>nucleoside triphosphate biosynthetic process</td><td>0.0303/0.0020</td><td>0/8</td><td>1205/1024</td><td>under</td></tr><tr><td> GO:0072330</td><td>monocarboxylic acid biosynthetic process</td><td>0.0158/9.28e-4</td><td>0/9</td><td>1205/1023</td><td>under</td></tr><tr><td colspan="6">Specific to the Hib4 genome from subsp. <italic>pauca</italic>: response to stress, transfer/transport activity, iron-sulfur binding, component assembly/organization</td></tr><tr><td> GO:0006950</td><td>response to stress</td><td>1.39e-4/1.05e-5</td><td>1/17</td><td>1323/1047</td><td>under</td></tr><tr><td> GO:0006979</td><td>response to oxidative stress</td><td>0.0279/0.0034</td><td>0/7</td><td>1324/1057</td><td>under</td></tr><tr><td> GO:0033554</td><td>cellular response to stress</td><td>0.0153/0.0017</td><td>1/11</td><td>1323/1053</td><td>under</td></tr><tr><td> GO:0008565</td><td>protein transporter activity</td><td>0.0279/0.0034</td><td>1/10</td><td>1323/1054</td><td>under</td></tr><tr><td> GO:0009055</td><td>electron transfer activity</td><td>0.0279/0.0034</td><td>0/7</td><td>1324/1057</td><td>under</td></tr><tr><td> GO:0015197</td><td>peptide transporter activity</td><td>0.0153/0.0017</td><td>1/11</td><td>1323/1053</td><td>under</td></tr><tr><td> GO:0016667</td><td>oxidoreductase activity, acting on a sulfur group of donors</td><td>0.0135/0.0015</td><td>0/8</td><td>1324/1056</td><td>under</td></tr><tr><td> GO:0051540</td><td>metal cluster binding</td><td>0.0055/5.56e-4</td><td>2/14</td><td>1322/1050</td><td>under</td></tr><tr><td> GO:0051536</td><td>iron-sulfur cluster binding</td><td>0.0055/5.56e-4</td><td>2/14</td><td>1322/1050</td><td>under</td></tr><tr><td> GO:0051539</td><td>4 iron, 4 sulfur cluster binding</td><td>0.0279/0.0034</td><td>1/10</td><td>1323/1054</td><td>under</td></tr><tr><td> GO:0022607</td><td>cellular component assembly</td><td>0.0023/2.15e-4</td><td>1/13</td><td>1323/1051</td><td>under</td></tr><tr><td> GO:0043933</td><td>macromolecular complex subunit organization</td><td>0.0066/6.79e-4</td><td>0/9</td><td>1324/1055</td><td>under</td></tr></tbody></table><table-wrap-foot><p><sup>1</sup>Complete datasets are provided in Additional file <xref rid="MOESM7" ref-type="media">7</xref></p><p><sup>2</sup>Annot test/ref.: number of GO-associated CDS in the list of CDS harboring specific mers (query) / number of GO-associated CDS in the reference genome</p><p><sup>3</sup>Non-annot test/ref.: number of non-annotated (no GOs) CDS in the list of CDS harboring specific mers (query) / number of non-annotated (no GOs) CDS in the reference genome</p></table-wrap-foot></table-wrap></p></sec><sec id="Sec7"><title>Reconstruction of the parental origin of the subspecies <italic>morus</italic></title><p id="Par24">The subspecies <italic>morus</italic> was proposed to group strains pathogenic on <italic>Morus</italic> that derived from largescale intersubspecific homologous recombination events between ancestors from at least subspecies <italic>fastidiosa</italic> and <italic>multiplex</italic>. This assumption is based on the analysis of seven housekeeping genes [<xref ref-type="bibr" rid="CR16">16</xref>]. We challenged it with whole-genome sequence datasets to further understand the contribution of the subspecies <italic>fastidiosa</italic>, <italic>multiplex</italic> and others in the parenthood of the subspecies <italic>morus</italic>. We used SkIf to identify mers specific of the <italic>morus</italic> group (i.e. two strains, Mul-MD and Mul0034) plus one of each of the other groups (Table <xref rid="Tab6" ref-type="table">6</xref>B; Additional file <xref rid="MOESM6" ref-type="media">6</xref>). The highest level of specific mers was found for the combination <italic>morus</italic> x <italic>fastidiosa</italic> x <italic>sandyi</italic>: the highest mer cumulated size represented 5% of the Mul0034 genome in size (which does not mean that all the 5% are unique to Mul0034). The <italic>morus</italic> x <italic>multiplex</italic> (3.6%) and <italic>morus</italic> x <italic>pauca</italic> (< 0.1%) relationships were lower. To illustrate these findings, the specific mers were mapped onto the Mul0034 genome and were found to be distributed all along the sequence (Fig. <xref rid="Fig3" ref-type="fig">3</xref>). These results on closest relationships between genomes of subspecies <italic>fastidiosa, sandyi,</italic> and <italic>morus</italic> are coherent with the ANIb values (Additional file <xref rid="MOESM1" ref-type="media">1</xref>). Enrichment tests identified shared GO terms for the various combinations indicated (Table <xref rid="Tab6" ref-type="table">6</xref>B). For the combination <italic>morus</italic> x <italic>multiplex,</italic> one GO term linked to the amino acid biosynthetic process was specifically recorded. At the level of <italic>fastidiosa</italic> x <italic>sandyi</italic> x <italic>sandyi</italic>-like x <italic>morus</italic>, 28 GO terms were specifically identified, associated with various processes like cellular component or protein complex disassembly, peptidyl-proline activity and chemotaxis.<fig id="Fig3"><label>Fig. 3</label><caption><p>Distribution of k-mers specific to the <italic>X. fastidiosa</italic> subspecies <italic>morus</italic> and others. <bold>a</bold> core k-merome of <italic>X. fastidiosa</italic> species. <bold>b</bold> specific subsp. <italic>morus</italic>. <bold>c, d, e</bold> specific subsp. <italic>morus</italic> + <italic>sandyi</italic> and/or <italic>sandyi</italic>-like. <bold>f</bold> specific subsp. <italic>morus</italic> + <italic>multiplex.</italic><bold>g, h</bold> specific subsp. <italic>morus</italic> + <italic>fastidiosa</italic> (with/without CFBP 8073 strain). <bold>i</bold> specific subsp. <italic>morus</italic> + <italic>fastidiosa</italic> (with CFBP 8073) + subsp. <italic>sandyi</italic> + subsp. <italic>sandyi</italic>-like<italic>.</italic><bold>j</bold> specific subsp. <italic>morus</italic> + <italic>pauca</italic>. Frequency of k-mers are mapped onto the genome of reference for subsp. <italic>morus</italic> (Mul0034)</p></caption><graphic xlink:href="12864_2019_5565_Fig3_HTML" id="MO3"></graphic></fig></p><p id="Par25">A focus on these 28 categories was performed. Due to the redundancy within the GO hierarchical nomenclature, the 28 GOs were reduced to six. All the CDS harboring specific long-mers in Mul0034 genome were retrieved, as well as their closest homologs in the in- (subsp. <italic>fastidiosa, sandyi, sandyi</italic>-like<italic>, morus</italic>) and the out- (subsp. <italic>multiplex</italic> or <italic>pauca</italic>) groups. This corresponded to 26 CDS found each in a single copy in all the 46 <italic>Xf</italic> genomes, indicating that they belong to the <italic>Xf</italic> core genome. For each gene, the sequences were aligned together with the specific long-mers (80 long-mers in total), against the sequence in Mul0034 used as a reference. First, perfect identity in long-mer sequence was conserved among all the genomes of subsp. <italic>fastidiosa, sandyi, sandyi</italic>-like<italic>,</italic> and <italic>morus</italic>. In contrast, SNPs were always found in the alignment of <italic>multiplex</italic> and <italic>pauca</italic> sequences. In comparison with <italic>multiplex</italic>, 46/80 long-mers had only synonymous SNPs and 34 had non-synonymous SNPs in the gene sequences. Considering the 26 CDS, 18 harbored non-synonymous SNPs. In comparison with <italic>pauca</italic>, half long-mers had only synonymous SNPs and half had non-synonymous SNPs in the gene sequences. Considering the 26 CDS, 21 harbored non-synonymous SNPs (Additional file <xref rid="MOESM8" ref-type="media">8</xref>).</p></sec><sec id="Sec8"><title>Genetic diversity within the subspecies <italic>pauca</italic></title><p id="Par26">ANIb values clearly showed genetic heterogeneity among strains of the subspecies <italic>pauca</italic>. Three lineages were differentiated: subclade I.1 included seven citrus strains (9a5c, U24D, Fb7, CVC0251, CVC0256, J1a12 and 11,399) and two coffee strains (3124 and 32); subclade I.2 included two coffee (6c and COF0324) and one Prunus (Pr8x) strains, and subclade I.3 included the ST53 strains CoDiRO, COF0407, OLS0478 and OLS0479. Two strains, CFBP 8072 and Hib4 were isolated, as they appeared outside (Additional file <xref rid="MOESM1" ref-type="media">1</xref>).</p><p id="Par27">A search for specific mers within these three subclades (Table <xref rid="Tab6" ref-type="table">6</xref>C, Additional file <xref rid="MOESM6" ref-type="media">6</xref>) and the identification of associated GO terms (Table <xref rid="Tab8" ref-type="table">8</xref>; Additional file <xref rid="MOESM7" ref-type="media">7</xref>) were performed. At the level of subspecies <italic>pauca</italic> it concerned 175 GO terms, including 16 terms related to nucleotide metabolic/biosynthetic process, especially for purine and 20 terms associated with the bacterial cell wall/envelope/plasma membrane. A focus on these 20 categories was performed. Due to redundancy within the GO hierarchical nomenclature, the 20 GOs were reduced to eight. All the CDS harboring specific long-mers in 9a5c genome were retrieved, as well as their closest homologs in the in- (subsp.<italic>pauca</italic>) and the out- (subsp. <italic>multiplex</italic> or <italic>fastidiosa, sandyi, sandyi</italic>-like<italic>,</italic> and <italic>morus</italic>) groups. This correspond to 105 CDS found each in a single copy in almost all the 46 <italic>Xf</italic> genomes. For each gene, the sequences were aligned together with the specific long-mers (746 k-mers in total), against the sequence in 9a5c used as a reference. First, perfect identity in long-mer sequence was conserved among all the genomes of subsp. <italic>pauca</italic>, except for 6 long-mers with small variants in a few <italic>pauca</italic> strains. In contrast, SNPs were always found in the alignment with <italic>multiplex</italic> and <italic>fastidiosa, sandyi, sandyi</italic>-like<italic>, morus</italic> sequences. In comparison with <italic>multiplex</italic>, 390/746 long-mers had only synonymous SNPs, 354 had non-synonymous SNPs and 2 long-mers were not found. Considering the 105 CDS, 93 harbored non-synonymous SNPs. In comparison with <italic>fastidiosa, sandyi, sandyi</italic>-like<italic>,</italic> and <italic>morus</italic>, 368 long-mers had only synonymous SNPs and 378 had non-synonymous SNPs in the gene sequences. Considering the 105 CDS, 92 harbored non-synonymous SNPs (Additional file <xref rid="MOESM8" ref-type="media">8</xref>). The search for enriched GO was also performed at the subclade level. For the subclade I.1, only one term was found (catalytic activity, GO:0003824). In all other studied cases (subclades or individual strains within subsp. <italic>pauca</italic>), all the GO terms identified were under-represented. This might be explained by a recent evolution in these strains/subclades, rendering the corresponding SNPs in these functional gene ontologies less frequent. Two regions harboring specific mers in 13 <italic>pauca</italic> strains (subclades I.2 and I.3, plus Hib4) and absent in the others (subclade I.3 plus CFBP 8072) were identified (Fig. <xref rid="Fig4" ref-type="fig">4</xref>). These include genes encoding various enzymes (endonuclease, hydrogenase, hydrolase, integrase/recombinase, methyltransferase, peptidase, polyketide synthase, reductase, terminase, topoisomerase) and genes associated with bacteriophages (Additional file <xref rid="MOESM6" ref-type="media">6</xref>). For subclade I.3, 10 GO terms were specific, dealing with transport, recombination, and organelle part. CFBP 8072 has two specific GO terms nucleoside triphosphate biosynthetic process and monocarboxylic acid biosynthetic process. As for the Hib4 genome, 12 terms were found as unique, associated with iron-sulfur complex, or transport activity.<fig id="Fig4"><label>Fig. 4</label><caption><p>Distribution of k-mers specific to the <italic>X. fastidiosa</italic> subspecies <italic>pauca</italic> and its subclades. <bold>a</bold> core k-merome of <italic>X. fastidiosa</italic> species. <bold>b</bold> specific subsp. <italic>pauca</italic>. <bold>c</bold> specific of subclade I.2, I.3 and strain Hib4 from subsp. <italic>pauca</italic>. Frequency of k-mers are mapped onto the genome of reference for subsp. <italic>morus</italic> (Mul0034)</p></caption><graphic xlink:href="12864_2019_5565_Fig4_HTML" id="MO4"></graphic></fig></p></sec><sec id="Sec9"><title>Identification of chromosome and plasmid specific islands unique in <italic>X. fastidiosa</italic> Hib4</title><p id="Par28">The k-mer approach identified three large genomic regions that were specific to the strain Hib4. A fragment of 34,148 bp (long-mer2422 in Additional file <xref rid="MOESM6" ref-type="media">6</xref>) appeared to be chromosomic. It contained 34 genes coding for 12 hypothetical/conserved proteins, 8 conjugal transfer proteins (including TraG), 3 membrane proteins, 2 methyltransferases, and one acriflavine resistance protein B, DEAD/DEAH box helicase, DSBA oxidoreductase, hemolysin secretion protein D, integrating conjugative element protein pill (pfgi-1), lytic transglycosylase, multidrug transporter, RAQPRD family plasmid, and superoxide dismutase (Additional file <xref rid="MOESM6" ref-type="media">6</xref>). The screen (blastn) of the Nucleotide collection (nr/nt) database revealed that it shared high identities (> 90%) with sequences of <italic>Cupriavidus</italic> sp., <italic>Comamonas testosterone</italic>, <italic>Pseudomonas aeruginosa</italic>, <italic>Klebsiella pneumoniae</italic> and <italic>Bordetella petrii</italic>, but the largest fragments cover no more than 60% of the <italic>X. fastidiosa</italic> long-mer (Additional file <xref rid="MOESM9" ref-type="media">9</xref>).</p><p id="Par29">Two large regions of 32,804 bp (long-mer4538 in Additional file <xref rid="MOESM6" ref-type="media">6</xref>) and 16,015 bp (long-mer4596) localized onto the plasmid pXF64-HB. Together with smaller specific long-mers (long-mer4536 to 4596), they accounted for 60,224 bp over the 64,251 bp total size of this plasmid <ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP009886.1">https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP009886.1</ext-link>). It contained 39 genes, including genes coding hypothetical proteins (23), conjugal transfer proteins (7; TraH, I, J, K, N, Q, U, W), and one DNA topoisomerase, endonuclease, helicase, lytic transglycosylase, membrane protein, mobilization protein, protein mobD, relaxase, and TrbA (Additional file <xref rid="MOESM6" ref-type="media">6</xref>). The plasmid could have been acquired from a strain of <italic>Paraburkholderia hospita</italic> (93% identity over 86% length of the plasmid), <italic>P. aromaticivorans</italic> (86% identity over 83% length) or even <italic>Burkholderia vietnamiensis</italic> (81% identity over 76% length) or <italic>Xanthomonas euvesicatoria</italic> (80% identity over 72% length) (Additional file <xref rid="MOESM9" ref-type="media">9</xref>).</p></sec><sec id="Sec10"><title>Robust whole genome-based <italic>X. fastidiosa</italic> clustering with shared k-mers</title><p id="Par30">After looking at specific k-mers in whole genome sequences using SkIf, we employed a complementary approach to draw a robust image of the genetic relationships among individuals, based on shared k-mers. Simka [<xref ref-type="bibr" rid="CR23">23</xref>] provided a distance matrix that was transformed in a similarity matrix corresponding to the percent of shared k-mers to assess strain relationships (Additional file <xref rid="MOESM10" ref-type="media">10</xref>). The k-mer-based dendrogram showed a general distribution into three major clades, represented by the subspecies <italic>pauca</italic> (clade I), <italic>multiplex</italic> (clade II), and the union of subspecies <italic>fastidiosa¸ sandyi</italic> and <italic>morus</italic> (clade III; Fig. <xref rid="Fig5" ref-type="fig">5</xref>). It is congruent with the one obtained with ANIb illustrated by with a strong linear regression (r<sup>2</sup> = 0.9945; Fig. <xref rid="Fig6" ref-type="fig">6</xref>). The current clustering of <italic>X. fastidiosa</italic> in five subspecies should be restricted to three subspecies, a proposal that is supported by ANIb and shared k-mers values (99.00% and 0.86, respectively) for clade III (Fig. <xref rid="Fig6" ref-type="fig">6</xref>, Additional files <xref rid="MOESM1" ref-type="media">1</xref> and <xref rid="MOESM10" ref-type="media">10</xref>). This mostly differ from the view obtained with a MLSA scheme (7 genes) by the repositioning of the subspecies <italic>morus</italic> (Fig. <xref rid="Fig5" ref-type="fig">5</xref>). We finally mapped the key points resulting from SkIf (specific k-mers) analysis on the dendrogram (shared k-mers) to illustrate how <italic>X. fastidiosa</italic> genetic diversity can be associated with particular traits (Fig. <xref rid="Fig5" ref-type="fig">5</xref>).<fig id="Fig5"><label>Fig. 5</label><caption><p>Phylogenetic representation of <italic>X. fastidiosa</italic> using k-mers, ANIb and MLSA schemes. All the representations were constructed using the 46 <italic>X. fastidiosa</italic>, with addition of the <italic>X. taiwanensis</italic> genome sequence. <bold>a</bold> Whole genome-based dendrogram built with distance matrixes obtained after running simka (shared k-mers of 22 nucleotides) or ANIb (1020 nt) algorithms. Some specificities and similarities in enriched gene ontologies or identification of plasmid and chromosomic sequences specific to <italic>X. fastidiosa</italic> are highlighted at nodes or subclades. <bold>b</bold> Maximum-Likelihood (ML) tree constructed with 1000 replicates for bootstrap values using the concatenated sequences (4161 bp) of seven housekeeping genes from a MultiLocus Sequence Analysis (MLSA) scheme. Key features related to <italic>X. fastidiosa</italic> subspecies obtained through the combination of specific k-mer identified and gene ontologies enrichment tests are indicated at nodes</p></caption><graphic xlink:href="12864_2019_5565_Fig5_HTML" id="MO5"></graphic></fig><fig id="Fig6"><label>Fig. 6</label><caption><p>Inter- and intrasubspecies comparisons of ANIb and shared k-mers values. <bold>a</bold> Boxplot of the ANIb values calculated from our genome dataset. <bold>b</bold> Boxplot of the shared k-mer values. <bold>c</bold> Dot plot of the ANIb and shared k-mer mean values. Linear regression and its corresponding r<sup>2</sup> is indicated. For intrasubpecies comparisons, the number of plotted values corresponds to [(number of genome) <sup>2</sup> - number of genome]. For intersubspecies comparisons, it corresponds to [(2 * number of genome subspecies A * number of genome subspecies B)]. Number of genomes: <italic>fastidiosa</italic> (13)<italic>, morus</italic> (2)<italic>, sandyi</italic> (3)<italic>, multiplex</italic> (10)<italic>, pauca</italic> (18)</p></caption><graphic xlink:href="12864_2019_5565_Fig6_HTML" id="MO6"></graphic></fig></p></sec></sec><sec id="Sec11"><title>Discussion</title><p id="Par31">While tools based on k-mers are mainly used to improve genome assembly [<xref ref-type="bibr" rid="CR36">36</xref>, <xref ref-type="bibr" rid="CR37">37</xref>], SkIf (<ext-link ext-link-type="uri" xlink:href="https://sourcesup.renater.fr/wiki/skif/">https://sourcesup.renater.fr/wiki/skif/</ext-link>) was developed to quickly extract information from genomic datasets from already assembled genomes. It allows to decipher genomic fragments associated with traits shared by a group of sequences of interest. This strategy is applicable to any scientific questions requesting the comparison of user-defined groups of sequences.</p><p id="Par32">Because management of <italic>X. fastidiosa</italic> outbreaks in France depends on the subspecies of <italic>X fastidiosa</italic>, it is of major importance to precisely define these subspecies, understand the robustness of these groupings and their meaning in terms of shared and specific genetic material. In order to detect genomic regions specifically associated with a group of organisms (i.e. a subspecies) we applied SkIf to gain a better understanding of <italic>X. fastidiosa</italic> clusterings in subspecies. This tool was also used to mine large databases as a first step to evaluate worldwide dispersion of <italic>X. fastidiosa</italic> in natural settings.</p><p id="Par33">The phylogeny provided by shared k-mers was highly similar to the one based on ANIb, a reference method for analyzing phylogeny of bacteria [<xref ref-type="bibr" rid="CR38">38</xref>, <xref ref-type="bibr" rid="CR39">39</xref>]. However, phylogenies were much more quickly constructed using shared k-mers than were ANI calculations in JSpecies. Here, k-mers of 22 nt were used while ANIb and TETRA are calculated from k-mers of 1020 and 4 nt, respectively, and ANIm values result from the maximal unique match decomposition of two genomes [<xref ref-type="bibr" rid="CR40">40</xref>–<xref ref-type="bibr" rid="CR42">42</xref>].</p><p id="Par34">The current grouping of <italic>X. fastidiosa</italic> in five subspecies is inappropriate and is not supported by genomic data. This is obvious regarding the phylogenies reconstructed using shared-k-mers and ANIb (Fig. <xref rid="Fig5" ref-type="fig">5</xref>) and it is coherent with a previous proposal [<xref ref-type="bibr" rid="CR43">43</xref>]. Three-well demarcated genomic clusters were retrieved in phylogenetic trees reconstructed from 46 genome sequences. <italic>X. fastidiosa</italic> subsp. <italic>fastidiosa</italic> embraced, in addition to the classical subsp<italic>. fastidiosa</italic> strains, the more recently proposed <italic>sandyi</italic> and <italic>morus</italic> subspecies. Mean ANIb values of 99% are found within the former subspecies, while ANIb value with the two later are below 98% (Fig. <xref rid="Fig6" ref-type="fig">6</xref>). The two-other subspecies, <italic>multiplex</italic> and <italic>pauca,</italic> were well supported, even if subsp. <italic>pauca</italic> showed a clear divergence between the lineage of strains isolated from citrus and coffee in Brazil vs. the lineage of other strains isolated from coffee from Central America and olive. Indeed, mean ANIb value of 99.44% was calculated within the multiplex subspecies, while ANIb values below than 97% were found with the other two subspecies. Concerning <italic>pauc</italic>a, mean ANIb value of 98.48% was calculated for the 18 genome sequences included in this subspecies while ANIb values of less than 97% were obtained with the two-other species. This mean ANIb value of only 98.66% within <italic>pauca</italic> clearly illustrate the largest diversity found in this subspecies in comparison to the <italic>fastidiosa</italic> and <italic>multiplex</italic> ones. This grouping in a subsp. <italic>fastidiosa</italic> sensu <italic>largo</italic> also matches with an enrichment in 28 GO terms associated with various processes like cellular component or protein complex disassembly, peptidyl-proline activity and chemotaxis. Interestingly, GO-enriched associated CDSs, which harbor k-mers specific to this clade, have homologs in all other <italic>X. fastidiosa</italic> genomes, but most often these homologs present non-synonymous SNPs, avoiding perfect matches with the k-mers. More importantly, this suggests diversity in protein sequences with putative impact on their functions. Referring to the definition of the species and a threshold value of ANI at 95% [<xref ref-type="bibr" rid="CR39">39</xref>] values calculated here on 46 genomes sequences indicate that <italic>X. fastidiosa</italic> with its diversity forms a unique species.</p><p id="Par35">Grouping the subspecies <italic>morus</italic> within a subspecies <italic>fastidiosa</italic> sensu <italic>largo</italic> is coherent with the results of the analysis made to uncover the origin of the subsp. <italic>morus</italic>. This subspecies was proposed to group strains pathogenic on mulberry trees that derived from recombination events between ancestors of the subspecies <italic>fastidiosa</italic> and <italic>multiplex</italic> [<xref ref-type="bibr" rid="CR16">16</xref>]. The use of SkIf showed that the cumulated size of the mers uniquely shared within genomes of the clade III (subsp. <italic>morus, fastidiosa, sandyi</italic> and relatives) represents 5% of the Mul0034 genome, while those uniquely shared between subsp. <italic>morus</italic> and <italic>multiplex</italic> count for 3.7%. That showed a closest proximity of <italic>morus</italic> with <italic>fastidiosa</italic> and <italic>sandyi</italic> strains than with <italic>multiplex</italic>. But because some mers are uniquely associated with the two <italic>morus</italic> genomes (Additional file <xref rid="MOESM6" ref-type="media">6</xref>), some genetic material of an unknown origin has been introduced in <italic>morus</italic> subspecies genome during evolutionary history.</p><p id="Par36">The evolutionary history of <italic>X. fastidiosa</italic> is also driven by the acquisition of genetic material from heterologous origin. Recently the genome sequence of Hib4 strain was released. This strain presents three large genomic fragments that are unique within <italic>X. fastidiosa</italic>. One of these regions is chromosomic, the two others locate on a large plasmid (~64kbp) that is not found in any other <italic>X. fastidiosa</italic> genome sequence but share strong homology with plasmids from <italic>Burkholderia hospita</italic> DSM17164 [<xref ref-type="bibr" rid="CR44">44</xref>], <italic>P. aromaticivorans</italic> BN5 [<xref ref-type="bibr" rid="CR45">45</xref>], <italic>Burkholderia vietnamensis</italic> G4 [<xref ref-type="bibr" rid="CR46">46</xref>], or <italic>Xanthomonas euvesicatoria</italic> LMG930 [<xref ref-type="bibr" rid="CR47">47</xref>] strains (Additional file <xref rid="MOESM9" ref-type="media">9</xref>). It should be mentioned that so far it is the only case of a plasmid that is not distributed in various strains within <italic>X. fastidiosa</italic> and that originates from a non-<italic>Xylella</italic> strain. Thus, it is tempting to hypothesize on how the acquisition could have occurred, while not easy as these species were isolated from various natural environments including water, soil and plants. Interestingly, <italic>X. euvesicatoria</italic> LMG932 was isolated from <italic>Capsicum frutescensi</italic> in Brazil [<xref ref-type="bibr" rid="CR48">48</xref>], the country of origin of <italic>X. fastidiosa</italic> Hib4 strain isolated from <italic>Hibiscus fragilis</italic>. Several strains of <italic>Burkholderia vietnamensis</italic> were isolated from Coffee plants in Mexico [<xref ref-type="bibr" rid="CR49">49</xref>], while other were isolated from a Brazilian cystic fibrosis patient [<xref ref-type="bibr" rid="CR50">50</xref>]. These findings illustrate the presence of putative plasmid donor either in the country (Brazil) were Hib4 was isolated and on a host (coffee) in a country (Mexico) were <italic>X. fastidiosa</italic> is known to occur. Another particularity of Hib4 is that its harbors two specific regions, only shared with strains of the subsp. pauca subclades I.1 and I.2 (Fig. <xref rid="Fig4" ref-type="fig">4</xref>). These genomic regions presumably result from a bacteriophage origin. They could have been acquired specifically by a common ancestor of subclades I.1, I.2 and Hib4 or they could have been lost during evolution, accentuating the degree of divergence with other <italic>pauca</italic> strains.</p><p id="Par37">Microbial collections exchange strains, but mistakes during collection curation cannot be totally excluded, engendering distribution of mislabeled strains, as already shown for <italic>X. fastidiosa</italic> [<xref ref-type="bibr" rid="CR51">51</xref>]. SkIf proved useful to survey microbial collections for synonyms. Here, following the release of the genome sequence of the <italic>X. fastidiosa</italic> type strain from three origins (CFBP 7970 in the present study, ATCC 35879, DSM 10026), SkIf was used to check the relevance of their synonymy. While not strictly identical due to sequencing and assembly biases, the most striking feature was the putative absence of a large fragment in ATCC 35879, corresponding to a plasmid carrying a complete type IV secretion system [<xref ref-type="bibr" rid="CR34">34</xref>]. Yet, based on our analysis, it is possible that the plasmid could be present in ATCC 35879, but could have been partially lost during the read filtering and assembly process, or even during strain cultivation. The synonymy between the three strains would therefore be valid. An alternative scenario might be that the plasmid-like sequences have been integrated into the chromosome of ATCC 35879 whilst the plasmid was lost, and in this case, only CFBP 7970 and ATCC 35879 are indeed synonymous. The definite answer will come from an analysis of the raw reads of ATCC 35879 to check for the presence/absence of the plasmid (raw reads are currently not available in SRA) or from a plasmid extraction from the specimen stored at ATCC.</p><p id="Par38">Occurrences of <italic>X. fastidiosa</italic> found in Silva rRNA database were assigned to subspecies that are coherent with sample designation. Specific mers of the genus <italic>Xylella</italic> and of the various subspecies of <italic>X. fastidiosa</italic> were retrieved in the V3-V4 region of the 16S rRNA encoding genes. One use of these tools is to taxonomically assign at the subspecies level the occurrences of <italic>X. fastidiosa</italic> from large database. The sample description and especially the name of the plant species of isolation allow to validate the assignation provided by specific mers. It should however be noticed, that some plant species like almond, olive tree, oleander, coffee tree, or citrus may be host of several <italic>X. fastidiosa</italic> subspecies (<ext-link ext-link-type="uri" xlink:href="http://www.pubmlst.org/xfastidiosa">www.pubmlst.org/xfastidiosa</ext-link>) [<xref ref-type="bibr" rid="CR52">52</xref>] and in consequence this a posteriori validation will not always be possible. Long read sequencing will generate more full length 16 s rRNA gene sequences which will facilitate subspecies discrimination. Another tempting use of these tools could be to survey large metagenome database for occurrences of these markers. This is however currently not feasible due to an astonishingly too long time required to download data or incapacity to browse those databases using our markers. Another use will be to design primers and if required probes for PCR detection-identification of <italic>X. fastidiosa</italic> in plant material.</p></sec><sec id="Sec12"><title>Conclusions</title><p id="Par39">Skif is a freely available, bioinformatic tool dedicated to the identification of specific mers. Although the results presented here were applied in the context of the emerging plant pathogen <italic>Xylella fastidiosa</italic> in Europe, this software is useful to answer many other questions beyond this scope. It is adapted to mine various group of sequences (gene, protein, genome, metagenome databases) defined by the user to identify specific or shared features. In the context of <italic>X. fastidiosa</italic> it allowed to i) refine the current grouping in subspecies that are not supported by genomic data; ii) trace the origin of the subspecies <italic>morus</italic>, a plasmid from Hib4 strain and the extent of synonymy among specimen representing the same initial strain in microbial collections; and iii) design markers that are specific to each subspecies of <italic>X. fastidiosa</italic>.</p></sec><sec id="Sec13"><title>Methods</title><sec id="Sec14"><title>Bacterial strains and growth conditions</title><p id="Par40">The seven strains of <italic>X. fastidiosa</italic> (Table <xref rid="Tab2" ref-type="table">2</xref>) used in this study were provided by the French Collection of Plant-Associated Bacteria (CIRM-CFBP; <ext-link ext-link-type="uri" xlink:href="http://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria">http://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria</ext-link>). Strains were grown on B-CYE [<xref ref-type="bibr" rid="CR53">53</xref>] medium up to 8 weeks at 28 °C. Experiments with <italic>X. fastidiosa</italic> living cells were carried out under quarantine at IRHS, Centre INRA, Beaucouzé, France under the agreement no. 2013119–0002 from the Prefecture de la Région Pays de la Loire, France.</p></sec><sec id="Sec15"><title>Genomic DNA extraction</title><p id="Par41">For genome sequencing, bacterial material was harvested on agar plates and suspended in 4.5 ml of sterile, ultrapure water. Genomic DNA was extracted with the NucleoSpin Tissue kit (Macherey-Nagel), following the manufacturer’s recommendations. DNA was recovered in 100 μl of elution buffer (5 mM Tris/HCl, pH 8.5) with final concentration ranging from 3 to 12 μg. Quality and quantity of extracted genomic DNA were checked by depositing an aliquot on agarose gel combined to the use of a nanodrop (Thermo Scientific).</p></sec><sec id="Sec16"><title>Library preparation</title><p id="Par42">Genomic DNA solutions were homogenized at 20 ng/μl in 55 μl of resuspension buffer to prepare libraries of sonicated, purified, blunted, and adenylated DNA fragments of 350 bp, following the instructions of the Illumina TruSeq DNA PCR-Free Sample Preparation Guide – Low Sample (LS) Protocol (Catalog #FC-121-9006DOC, Part #150361887 Rev. B, November 2013). Adapters were ligated using the Illumina TruSeq DNA Free PCR LT kit. Libraries were individually quantified and then mixed in a single, equimolar pool (40 nM) also quantified by qPCR following the recommendations of the Library Quantification kit (Kapa Biosystems).</p></sec><sec id="Sec17"><title>Genome sequencing, assembling, and annotation</title><p id="Par43">For sequencing, diluted libraries (4 nM) were denatured as described (Illumina Preparing DNA libraries for Sequencing on the MiSeq protocol), resulting in 20pM denatured DNA. The final DNA concentration used for sequencing was 12pM in a 600 μl volume containing 1% of PhiX control. The sample was deposited in a V3 cartridge. The seven <italic>X. fastidiosa</italic> genomes were sequenced with the Illumina MiSeq v3 600 cycles technology at the ANAN plateform, SFR QuaSav, Angers, Fr. Genome assembly was performed using a combination of Velvet [<xref ref-type="bibr" rid="CR54">54</xref>], SOAPdenovo and SOAPGapCloser [<xref ref-type="bibr" rid="CR55">55</xref>] assemblers. Structural and functional annotations were conducted with Eugene-PP algorithm [<xref ref-type="bibr" rid="CR56">56</xref>], using a concatenation of the Swissprot database and the publicly available <italic>X. fastidiosa</italic> 9a5c [<xref ref-type="bibr" rid="CR57">57</xref>] and Temecula1 [<xref ref-type="bibr" rid="CR58">58</xref>] genomes.</p></sec><sec id="Sec18"><title>Definition of the acronyms</title><p id="Par44">In this study, we used the following definitions for these five key terms: i) mer: a sequence within a nucleotide character string; ii) k-mers: all the possible substrings of length k that are contained in a nucleotide character string; iii) long-mer: a result of the concatenation of overlapping and/or consecutive mers; iv) specific mers: sequences that are exclusively found for members of the group of interest (in-group) while small variants (i.e. with a few indels or SNPs) can be found in some members of the out-groups without being strictly identical; and (v) shared mers: sequences that are found in all the members of different groups of interests or that are common to two individuals in the case of pairwise comparisons.</p></sec><sec id="Sec19"><title>Identification of shared or specific k-mers</title><p id="Par45">The percent of shared k-mers between two genome sequences were calculated from the distance matrix built using Simka [<xref ref-type="bibr" rid="CR23">23</xref>]. Parameters were selected as follow: “-kmer-size 22”, “-abundance-min 1”. SkIf (v1.2) was developed in C ++ and sequence reading was done using Bio++ bpp-seq library [<xref ref-type="bibr" rid="CR59">59</xref>]. To identify genomic regions that are specific to a group of sequences of interest, SkIf construct an abundance matrix of all mers of sequences. This matrix is used to identify the mers present in all the sequences of the group of interest (in-group) and absent in all the other sequences. Parameters were selected as follow: “-k 22”, “-a dna”, “-g = in-group list”. Then, it maps the specific mers of the in-group to the reference genome sequence of the group and provides their precise locations. By comparing mer length and the positions of the various occurrences, SkIf concatenates the overlapping mers into long-mer using the script “getLongestKmersNC.pl” (option: -k 22; available with Skif). A list of located mers or long-mers specific to the group of interest was hence obtained. Finally, we developed a wrapper for accessing this process in a user-friendly Galaxy tool (<ext-link ext-link-type="uri" xlink:href="https://iris.angers.inra.fr/galaxypub-cfbp">https://iris.angers.inra.fr/galaxypub-cfbp</ext-link>). Hence, SkIf allows to extract all specific mers of a dataset. The optimal size of the mer was fixed to 22 nt to optimize the ratio of in-group to out-group specific sequences, after a comparison of a range from 18 to 26 nt was done (data not shown).</p></sec><sec id="Sec20"><title>Analyses of genome and nucleotide sequences and phylogeny</title><p id="Par46">For the analyses of the seven housekeeping genes used in MLSA-MLST scheme designed for <italic>X. fastidiosa</italic> (<ext-link ext-link-type="uri" xlink:href="https://pubmlst.org/xfastidiosa/info/primers.shtml">https://pubmlst.org/xfastidiosa/info/primers.shtml</ext-link>) and the 16S rRNA gene and the synonymy of SNPs, nucleotide sequences were aligned using the Geneious suite, with the default parameters of the ‘MUSCLE Alignment’ and the ‘Map to Reference’ options [<xref ref-type="bibr" rid="CR60">60</xref>]. Maximum-Likelihood (ML) tree was constructed with 1000 replicates for bootstrap values using the concatenated sequences (4161 bp) of seven housekeeping genes from the MLSA scheme. ANIb values were calculated using Pyani [<xref ref-type="bibr" rid="CR30">30</xref>]. Similarity matrix (based on ANIb or shared k-mers) were transformed into distance matrix (1-ANIbs*100 or 1-shared k-mers*100) in the dist format of R using as.dist and clustered using Ward’s method [<xref ref-type="bibr" rid="CR61">61</xref>] for hierarchical clustering. Conversion of the distance matrix into dendrograms relied on as.phylo function from R ape package [<xref ref-type="bibr" rid="CR62">62</xref>]. Blastn (v2.8.0+) analyses were run against the nucleotide collection (nt; 46,977,437 sequences) [<xref ref-type="bibr" rid="CR63">63</xref>].</p></sec><sec id="Sec21"><title>Enrichment tests and Venn diagram representations</title><p id="Par47">Enrichment analyses with a Fisher’s Exact Test were performed with Blast2GO v4.1 [<xref ref-type="bibr" rid="CR64">64</xref>], using the Gene Ontology functional annotations to compare gene lists carrying specific k-mers against all the gene of the reference genomes to identify statistically significant enrichment in biological processes or molecular functions. Venn diagrams were built using jvenn (<ext-link ext-link-type="uri" xlink:href="http://jvenn.toulouse.inra.fr/app/index.html">http://jvenn.toulouse.inra.fr/app/index.html</ext-link> [<xref ref-type="bibr" rid="CR65">65</xref>].</p></sec><sec id="Sec22"><title>Development of a galaxy-based website and user guidelines</title><p id="Par48">The SkIf pipeline is free for use online (<ext-link ext-link-type="uri" xlink:href="https://iris.angers.inra.fr/galaxypub-cfbp">https://iris.angers.inra.fr/galaxypub-cfbp</ext-link>). Required input files are a zip file with all the fasta files for the in-group genome sequences; a zip file with all the fasta files for the outgroup genome sequences; the length of the k, and the identifier of the reference genome sequence from the in-group. Output files are text files with the list of the k-mers and long-mers specific to the in-group if existing. A wiki page describing SkIf is accessible at <ext-link ext-link-type="uri" xlink:href="https://sourcesup.renater.fr/wiki/skif">https://sourcesup.renater.fr/wiki/skif</ext-link>.</p></sec><sec id="Sec23"><title>Mining of 16S rRNA database</title><p id="Par49">For the genus analysis, the in-group included the 74 <italic>Xylella</italic> 16S rRNA copies and the out-group included all the small subunit rRNA gene (SSU) sequences from the Silva database (<ext-link ext-link-type="uri" xlink:href="https://www.arb-silva.de/">https://www.arb-silva.de/</ext-link>; release 128) [<xref ref-type="bibr" rid="CR66">66</xref>] other than <italic>Xylella</italic>-tagged. For the species analysis, <italic>X. taiwanensis</italic> PLS 229 strain was included in the out-group. All sequences affiliated to <italic>X. fastidiosa</italic> were included in the in-group, while all the other, non-<italic>X. fastidiosa</italic>, were included in the out-group. Ambiguous sequences (e.g. double assignation to <italic>Xylella</italic> and <italic>Xanthomonas</italic>) were excluded. SkIf software was used as described above to identify specific k-mers (−k 22) in the in-group and to concatenate consecutive ones in long-mers.</p></sec></sec><sec sec-type="supplementary-material"><title>Additional files</title><sec id="Sec24"><p><supplementary-material content-type="local-data" id="MOESM1"><media xlink:href="12864_2019_5565_MOESM1_ESM.docx"><label>Additional file 1:</label><caption><p>Pairwise comparison of 47 <italic>Xylella</italic> sp. genomes using average nucleotide identity based on blast (ANIb). (DOCX 63 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM2"><media xlink:href="12864_2019_5565_MOESM2_ESM.zip"><label>Additional file 2:</label><caption><p>K-mers resulted from the comparison of synonymous strains CFBP 7970, DSM 10026 and ATCC 35879. (ZIP 45 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM3"><media xlink:href="12864_2019_5565_MOESM3_ESM.docx"><label>Additional file 3:</label><caption><p>Blast analysis of the known <italic>X. fastidiosa</italic> plasmid sequences against the genome sequence of ATCC 35879. (DOCX 30 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM4"><media xlink:href="12864_2019_5565_MOESM4_ESM.zip"><label>Additional file 4:</label><caption><p>Raw data of analyses of the 16S rRNA gene repertoire in <italic>Xylella. (ZIP 12 kb)</italic></p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM5"><media xlink:href="12864_2019_5565_MOESM5_ESM.docx"><label>Additional file 5:</label><caption><p><italic>X. fastidiosa</italic> 16S rRNA sequences from Silva database carrying the five long-mers and taxonomically assigned to a subspecies with the SNP-based code. (DOCX 21 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM6"><media xlink:href="12864_2019_5565_MOESM6_ESM.zip"><label>Additional file 6:</label><caption><p>Raw data of the k-mers identified to be specific of the different <italic>X. fastidiosa</italic> subspecies or combinations of several subspecies. (ZIP 3012 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM7"><media xlink:href="12864_2019_5565_MOESM7_ESM.zip"><label>Additional file 7:</label><caption><p>Raw data of the gene ontologies enrichments tests with Blast2GO. (ZIP 22422 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM8"><media xlink:href="12864_2019_5565_MOESM8_ESM.zip"><label>Additional file 8:</label><caption><p>Analysis of (non-)synonymous SNPs in homologs to CDS harboring specific k-mers for selected enriched GOs. (ZIP 549 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM9"><media xlink:href="12864_2019_5565_MOESM9_ESM.docx"><label>Additional file 9:</label><caption><p>Blast analysis of the three large fragments specific to <italic>X. fastidiosa</italic> subsp. <italic>pauca</italic> Hib4 strain. (DOCX 34 kb)</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="MOESM10"><media xlink:href="12864_2019_5565_MOESM10_ESM.docx"><label>Additional file 10:</label><caption><p>Pairwise comparison of 47 <italic>Xylella</italic> sp. genomes using the occurrence of shared k-mers of length 22 bp. (DOCX 68 kb)</p></caption></media></supplementary-material></p></sec></sec></body><back><glossary><title>Abbreviations</title><def-list><def-item><term>ANIb</term><def><p id="Par4">Average nucleotide identities using blast</p></def></def-item><def-item><term>ANIm</term><def><p id="Par5">Average nucleotide identities using MUMmer</p></def></def-item><def-item><term>CDS</term><def><p id="Par6">Coding sequence</p></def></def-item><def-item><term>GO</term><def><p id="Par7">Gene ontology</p></def></def-item><def-item><term>ICE</term><def><p id="Par8">Integrative and conjugative elements</p></def></def-item><def-item><term>rRNA</term><def><p id="Par9">Ribosomal RNA</p></def></def-item><def-item><term>SkIf</term><def><p id="Par10">Specific k-mers Identification</p></def></def-item><def-item><term>SNP</term><def><p id="Par11">Single nucleotide polymorphism</p></def></def-item><def-item><term>TETRA</term><def><p id="Par12">Tetranucleotide frequency correlation coefficients</p></def></def-item></def-list></glossary><ack><title>Acknowledgements</title><p>We thank Muriel Bahut (ANAN technical facility, SFR QUASAV, Angers, FR) for genome sequencing, CIRM-CFBP (Beaucouzé, INRA, France; <ext-link ext-link-type="uri" xlink:href="http://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria">http://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria</ext-link>) for strain preservation and supply, and the CATI BBRIC for the galaxy tools allowing assembling the reads and annotating the sequences, and using Blast2GO. We acknowledge Charles Manceau (Anses, Angers, FR) for his contribution while applying for funding. We thank Matthieu Barret for fruitful discussions and critical reading of the manuscript.</p><sec id="FPar1"><title>Funding</title><p id="Par50">ND salary was funded by the regional program “Objectif Végétal, Research, Education and Innovation in Pays de la Loire”, project SapAlien 2015–2017, supported by the French Region Pays de la Loire, Angers Loire Métropole and the European Regional Development Fund. This work received support from the European Union’s Horizon 2020 research and innovation program under grant agreement 635646 POnTE (Pest Organisms Threatening Europe). The present work reflects only the authors’ view and the EU funding agency is not responsible for any use that may be made of the information it contains.</p></sec><sec id="FPar2" sec-type="data-availability"><title>Availability of data and materials</title><p id="Par51">Strains of <italic>Xylella fastidiosa</italic> deposited at the CIRM-CFBP (Angers, FR) are available upon request (<ext-link ext-link-type="uri" xlink:href="https://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria">https://www6.inra.fr/cirm_eng/CFBP-Plant-Associated-Bacteria</ext-link>). The SkIf pipeline is free to use online (<ext-link ext-link-type="uri" xlink:href="https://iris.angers.inra.fr/galaxypub-cfbp">https://iris.angers.inra.fr/galaxypub-cfbp</ext-link>). All the sequence files related to the k-mer analyses (raw data, alignments, blast, GO enrichment tests) are submitted together with the manuscript as Additional files. Genome sequences were deposited at NCBI under the following accessions numbers: PHFQ00000000 (CFBP 7969), PHFR00000000 (CFBP 7970), PHFP00000000 (CFBP8071), PHFS00000000 (CFBP 8078), PHFT00000000 (CFBP 8082), PHFU00000000 (CFBP 8351), and PHFV00000000 (CFBP 8356). Related data and reannotation of the public genomes (fasta, genbank and gff3 formats) are available upon request.</p></sec></ack><notes notes-type="author-contribution"><title>Authors’ contributions</title><p>ND designed the in silico analyses. MB, RG, and SG designed the bioinformatics tools. ND and MB performed the in silico analyses and interpreted the data. MAJ conceived the study, applied for funding, and interpreted the data. ND and MAJ wrote the manuscript. All authors read and approved the final manuscript.</p></notes><notes notes-type="COI-statement"><sec id="FPar3"><title>Ethics approval and consent to participate</title><p>Not applicable.</p></sec><sec id="FPar4"><title>Consent for publication</title><p>All the authors read and approved the manuscript.</p></sec><sec id="FPar5"><title>Competing interests</title><p>The authors declare that they have no competing interests.</p></sec><sec id="FPar6"><title>Publisher’s Note</title><p>Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.</p></sec></notes><ref-list id="Bib1"><title>References</title><ref id="CR1"><label>1.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Saponari</surname><given-names>M</given-names></name><name><surname>Boscia</surname><given-names>D</given-names></name><name><surname>Nigro</surname><given-names>F</given-names></name><name><surname>Martelli</surname><given-names>GP</given-names></name></person-group><article-title>Identification of DNA sequences related to <italic>Xylella fastidiosa</italic> in oleander, almond and olive trees exhibiting leaf scorch symptoms in Apulia (southern Italy)</article-title><source>J Plant Pathol</source><year>2013</year><volume>95</volume><issue>3</issue><fpage>668</fpage></element-citation></ref><ref id="CR2"><label>2.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Denancé</surname><given-names>N</given-names></name><name><surname>Legendre</surname><given-names>B</given-names></name><name><surname>Briand</surname><given-names>M</given-names></name><name><surname>Olivier</surname><given-names>V</given-names></name><name><surname>de Boisséson</surname><given-names>C</given-names></name><name><surname>Poliakoff</surname><given-names>F</given-names></name><etal></etal></person-group><article-title>Several subspecies and sequence types are associated to the emergence of <italic>Xylella fastidiosa</italic> in natural settings in France</article-title><source>Plant Pathol</source><year>2017</year><volume>66</volume><fpage>1054</fpage><lpage>1064</lpage></element-citation></ref><ref id="CR3"><label>3.</label><element-citation publication-type="journal"><person-group person-group-type="author"><collab>European and Mediterranean Plant Protection Organization (EPPO)</collab></person-group><article-title>First report of <italic>Xylella fastidiosa</italic> subsp. <italic>fastidiosa</italic> on <italic>Nerium oleander</italic> in Germany</article-title><source>EPPO Reporting Service</source><year>2016</year><volume>7</volume><fpage>133</fpage></element-citation></ref><ref id="CR4"><label>4.</label><element-citation publication-type="journal"><person-group person-group-type="author"><collab>European and Mediterranean Plant Protection Organization (EPPO)</collab></person-group><article-title>First report of <italic>Xylella fastidiosa</italic> in Spain</article-title><source>EPPO Reporting Service</source><year>2016</year><volume>11</volume><fpage>213</fpage></element-citation></ref><ref id="CR5"><label>5.</label><element-citation publication-type="journal"><person-group person-group-type="author"><collab>European and Mediterranean Plant Protection Organization (EPPO)</collab></person-group><article-title><italic>Xylella fastidiosa</italic> detected in mainland Spain and update for Baleares</article-title><source>EPPO Reporting Service</source><year>2017</year><volume>7</volume><fpage>133</fpage></element-citation></ref><ref id="CR6"><label>6.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Strona</surname><given-names>G</given-names></name><name><surname>Carstens</surname><given-names>CJ</given-names></name><name><surname>Beck</surname><given-names>PSA</given-names></name></person-group><article-title>Network analysis reveals why <italic>Xylella fastidiosa</italic> will persist in Europe</article-title><source>Sci Rep</source><year>2017</year><volume>7</volume><issue>71</issue><fpage>1</fpage><lpage>8</lpage><pub-id pub-id-type="pmid">28127051</pub-id></element-citation></ref><ref id="CR7"><label>7.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Soubeyrand</surname><given-names>S</given-names></name><name><surname>de Jerphanion</surname><given-names>P</given-names></name><name><surname>Martin</surname><given-names>O</given-names></name><name><surname>Saussac</surname><given-names>M</given-names></name><name><surname>Manceau</surname><given-names>C</given-names></name><name><surname>Hendrikx</surname><given-names>P</given-names></name><etal></etal></person-group><article-title>Inferring pathogen dynamics from temporal count data: the emergence of <italic>Xylella fastidiosa</italic> in France is probably not recent</article-title><source>New Phytol</source><year>2018</year><volume>219</volume><fpage>824</fpage><lpage>836</lpage><pub-id pub-id-type="pmid">29689134</pub-id></element-citation></ref><ref id="CR8"><label>8.</label><mixed-citation publication-type="other">Denancé N, Cesbron S, Briand M, Rieux A, Jacques M-A. 2017. Is Xylella fastidiosa really emerging in France ? In: Costa J, Koebnik R, eds. 1st Annual Conference of the EuroXanth – COST Action Integrating Science on <italic>Xanthomonadaceae</italic> for integrated plant disease management in Europe. Dec. 13–15, Coimbra, Portugal: EuroXanth, 7.</mixed-citation></ref><ref id="CR9"><label>9.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bergsma-Vlami</surname><given-names>M</given-names></name><name><surname>van de Bilt</surname><given-names>JLJ</given-names></name><name><surname>Tjou-Tam-Sin</surname><given-names>NNA</given-names></name><name><surname>Helderman</surname><given-names>CM</given-names></name><name><surname>Gorkink-Smits</surname><given-names>PPMA</given-names></name><name><surname>Landman</surname><given-names>NM</given-names></name><etal></etal></person-group><article-title>Assessment of the genetic diversity of <italic>Xylella fastidiosa</italic> in imported ornamental <italic>Coffea arabica</italic> plants</article-title><source>Plant Pathol</source><year>2017</year><volume>66</volume><fpage>1065</fpage><lpage>1074</lpage></element-citation></ref><ref id="CR10"><label>10.</label><element-citation publication-type="journal"><person-group person-group-type="author"><collab>European and Mediterranean Plant Protection Organization (EPPO)</collab></person-group><article-title><italic>Xylella fastidiosa</italic> detected in <italic>Coffea</italic> spp. plants imported into Switzerland</article-title><source>EPPO Reporting Service</source><year>2015</year><volume>10</volume><fpage>181</fpage></element-citation></ref><ref id="CR11"><label>11.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jacques</surname><given-names>MA</given-names></name><name><surname>Denancé</surname><given-names>N</given-names></name><name><surname>Legendre</surname><given-names>B</given-names></name><name><surname>Morel</surname><given-names>E</given-names></name><name><surname>Briand</surname><given-names>M</given-names></name><name><surname>Mississipi</surname><given-names>S</given-names></name><etal></etal></person-group><article-title>New coffee-infecting <italic>Xylella fastidiosa</italic> variants derived via homologous recombination</article-title><source>Appl Environ Microbiol</source><year>2016</year><volume>82</volume><issue>5</issue><fpage>1556</fpage><lpage>1568</lpage></element-citation></ref><ref id="CR12"><label>12.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bergsma-Vlami</surname><given-names>M</given-names></name><name><surname>van de Bilt</surname><given-names>JLJ</given-names></name><name><surname>Tjou-Tam-Sin</surname><given-names>NNA</given-names></name><name><surname>van de Vossenberg</surname><given-names>BTLH</given-names></name><name><surname>Westenberg</surname><given-names>M</given-names></name></person-group><article-title><italic>Xylella fastidiosa</italic> in <italic>Coffea arabica</italic> ornamental plants imported from Costa Rica and Honduras in the Netherlands</article-title><source>J Plant Pathol</source><year>2015</year><volume>97</volume><fpage>395</fpage></element-citation></ref><ref id="CR13"><label>13.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Su</surname><given-names>CC</given-names></name><name><surname>Deng</surname><given-names>WL</given-names></name><name><surname>Jan</surname><given-names>FJ</given-names></name><name><surname>Chang</surname><given-names>CJ</given-names></name><name><surname>Huang</surname><given-names>H</given-names></name><name><surname>Shih</surname><given-names>HT</given-names></name><etal></etal></person-group><article-title>Xylella taiwanensis sp. nov., causing pear leaf scorch disease</article-title><source>Int J Syst Evol Microbiol</source><year>2016</year><volume>66</volume><issue>11</issue><fpage>4766</fpage><lpage>4771</lpage><pub-id pub-id-type="pmid">27530392</pub-id></element-citation></ref><ref id="CR14"><label>14.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nunney</surname><given-names>L</given-names></name><name><surname>Yuan</surname><given-names>X</given-names></name><name><surname>Bromley</surname><given-names>RE</given-names></name><name><surname>Stouthamer</surname><given-names>R</given-names></name></person-group><article-title>Detecting genetic introgression: high levels of intersubspecific recombination found in <italic>Xylella fastidiosa</italic> in Brazil</article-title><source>Appl Environ Microbiol</source><year>2012</year><volume>78</volume><issue>13</issue><fpage>4702</fpage><lpage>4714</lpage><pub-id pub-id-type="pmid">22544234</pub-id></element-citation></ref><ref id="CR15"><label>15.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nunney</surname><given-names>L</given-names></name><name><surname>Ortiz</surname><given-names>B</given-names></name><name><surname>Russell</surname><given-names>SA</given-names></name><name><surname>Ruiz-Sanchez</surname><given-names>R</given-names></name><name><surname>Stouthamer</surname><given-names>R</given-names></name></person-group><article-title>The complex biogeography of the plant pathogen <italic>Xylella fastidiosa</italic>: genetic evidence of introductions and subspecific introgression in Central America</article-title><source>PLoS One</source><year>2014</year><volume>9</volume><fpage>e112463</fpage><pub-id pub-id-type="pmid">25379725</pub-id></element-citation></ref><ref id="CR16"><label>16.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nunney</surname><given-names>L</given-names></name><name><surname>Schuenzel</surname><given-names>EL</given-names></name><name><surname>Scally</surname><given-names>M</given-names></name><name><surname>Bromley</surname><given-names>RE</given-names></name><name><surname>Stouthamer</surname><given-names>R</given-names></name></person-group><article-title>Large-scale intersubspecific recombination in the plant-pathogenic bacterium <italic>Xylella fastidiosa</italic> is associated with the host shift to mulberry</article-title><source>Appl Environ Microbiol</source><year>2014</year><volume>80</volume><issue>10</issue><fpage>3025</fpage><lpage>3033</lpage><pub-id pub-id-type="pmid">24610840</pub-id></element-citation></ref><ref id="CR17"><label>17.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Loconsole</surname><given-names>G</given-names></name><name><surname>Saponari</surname><given-names>M</given-names></name><name><surname>Boscia</surname><given-names>D</given-names></name><name><surname>D’Attoma</surname><given-names>G</given-names></name><name><surname>Morelli</surname><given-names>M</given-names></name><name><surname>Martelli</surname><given-names>GP</given-names></name><etal></etal></person-group><article-title>Intercepted isolates of <italic>Xylella fastidiosa</italic> in Europe reveal novel genetic diversity</article-title><source>Eur J Plant Pathol</source><year>2016</year><volume>146</volume><issue>1</issue><fpage>85</fpage><lpage>94</lpage></element-citation></ref><ref id="CR18"><label>18.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Coletta-Filho</surname><given-names>HD</given-names></name><name><surname>Francisco</surname><given-names>CS</given-names></name><name><surname>Lopes</surname><given-names>JRS</given-names></name><name><surname>Muller</surname><given-names>C</given-names></name><name><surname>Almeida</surname><given-names>RPP</given-names></name></person-group><article-title>Homologous recombination and <italic>Xylella fastidiosa</italic> host–pathogen associations in South America</article-title><source>Phytopathol</source><year>2017</year><volume>107</volume><fpage>305</fpage><lpage>312</lpage></element-citation></ref><ref id="CR19"><label>19.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rizk</surname><given-names>G</given-names></name><name><surname>Lavenier</surname><given-names>D</given-names></name><name><surname>Chikhi</surname><given-names>R</given-names></name></person-group><article-title>DSK: k-mer counting with very low memory usage</article-title><source>Bioinformatics</source><year>2013</year><volume>29</volume><issue>5</issue><fpage>652</fpage><lpage>653</lpage><pub-id pub-id-type="pmid">23325618</pub-id></element-citation></ref><ref id="CR20"><label>20.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ghandi</surname><given-names>M</given-names></name><name><surname>Lee</surname><given-names>D</given-names></name><name><surname>Mohammad-Noori</surname><given-names>M</given-names></name><name><surname>Beer</surname><given-names>MA</given-names></name></person-group><article-title>Enhanced regulatory sequence prediction using gapped k-mer features</article-title><source>PLoS Comput Biol</source><year>2014</year><volume>10</volume><issue>7</issue><fpage>e1003711</fpage><pub-id pub-id-type="pmid">25033408</pub-id></element-citation></ref><ref id="CR21"><label>21.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Melsted</surname><given-names>P</given-names></name><name><surname>Halldórsson</surname><given-names>BV</given-names></name></person-group><article-title>KmerStream: streaming algorithms for k -mer abundance estimation</article-title><source>Bioinformatics</source><year>2014</year><volume>30</volume><issue>24</issue><fpage>3541</fpage><lpage>3547</lpage><pub-id pub-id-type="pmid">25355787</pub-id></element-citation></ref><ref id="CR22"><label>22.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Abo</surname><given-names>RP</given-names></name><name><surname>Ducar</surname><given-names>M</given-names></name><name><surname>Garcia</surname><given-names>EP</given-names></name><name><surname>Thorner</surname><given-names>AR</given-names></name><name><surname>Rojas-Rudilla</surname><given-names>V</given-names></name><name><surname>Lin</surname><given-names>L</given-names></name><etal></etal></person-group><article-title>BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers</article-title><source>Nucl. Acids Res</source><year>2015</year><volume>43</volume><issue>3</issue><fpage>e19</fpage><pub-id pub-id-type="pmid">25428359</pub-id></element-citation></ref><ref id="CR23"><label>23.</label><mixed-citation publication-type="other">Plaza Onate F, Batto J-M, Juste C, Fadlallah J, Fougeroux C, Gouas D, et al. Quality control of microbiota metagenomics by k-mer analysis. BMC Genomics. 2015;16:183.</mixed-citation></ref><ref id="CR24"><label>24.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mapleson</surname><given-names>D</given-names></name><name><surname>Garcia Accinelli</surname><given-names>G</given-names></name><name><surname>Kettleborough</surname><given-names>G</given-names></name><name><surname>Wright</surname><given-names>J</given-names></name><name><surname>Clavijo</surname><given-names>BJ</given-names></name></person-group><article-title>KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies</article-title><source>Bioinformatics.</source><year>2017</year><volume>33</volume><issue>4</issue><fpage>574</fpage><lpage>576</lpage><pub-id pub-id-type="pmid">27797770</pub-id></element-citation></ref><ref id="CR25"><label>25.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Marinier</surname><given-names>E</given-names></name><name><surname>Zaheer</surname><given-names>R</given-names></name><name><surname>Berry</surname><given-names>C</given-names></name><name><surname>Weedmark</surname><given-names>KA</given-names></name><name><surname>Domaratzki</surname><given-names>M</given-names></name><name><surname>Mabon</surname><given-names>P</given-names></name><etal></etal></person-group><article-title>Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations</article-title><source>Nucl. Acids Res</source><year>2017</year><volume>45</volume><issue>18</issue><fpage>e159</fpage><pub-id pub-id-type="pmid">29048594</pub-id></element-citation></ref><ref id="CR26"><label>26.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pandey</surname><given-names>P</given-names></name><name><surname>Bender</surname><given-names>MA</given-names></name><name><surname>Johnson</surname><given-names>R</given-names></name><name><surname>Patro</surname><given-names>R</given-names></name></person-group><article-title>Squeakr: an exact and approximate k-mer counting system</article-title><source>Bioinformatics</source><year>2018</year><volume>34</volume><issue>4</issue><fpage>568</fpage><lpage>575</lpage><pub-id pub-id-type="pmid">29444235</pub-id></element-citation></ref><ref id="CR27"><label>27.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hasman</surname><given-names>H</given-names></name><name><surname>Saputra</surname><given-names>D</given-names></name><name><surname>Sicheritz-Ponten</surname><given-names>T</given-names></name><name><surname>Lund</surname><given-names>O</given-names></name><name><surname>Svendsen</surname><given-names>CA</given-names></name><name><surname>Frimodt-Møller</surname><given-names>N</given-names></name><etal></etal></person-group><article-title>Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples</article-title><source>J Clin Microbiol</source><year>2014</year><volume>52</volume><fpage>139</fpage><lpage>146</lpage><pub-id pub-id-type="pmid">24172157</pub-id></element-citation></ref><ref id="CR28"><label>28.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chattaway</surname><given-names>MA</given-names></name><name><surname>Schaefer</surname><given-names>U</given-names></name><name><surname>Tewolde</surname><given-names>R</given-names></name><name><surname>Dallman</surname><given-names>TJ</given-names></name><name><surname>Jenkins</surname><given-names>C</given-names></name></person-group><article-title>Identification of <italic>Escherichia coli</italic> and <italic>Shigella</italic> species from whole-genome sequences</article-title><source>J Clin Microbiol</source><year>2017</year><volume>55</volume><issue>2</issue><fpage>616</fpage><lpage>623</lpage><pub-id pub-id-type="pmid">27974538</pub-id></element-citation></ref><ref id="CR29"><label>29.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Richter</surname><given-names>M</given-names></name><name><surname>Rosselló-Móra</surname><given-names>R</given-names></name><name><surname>Glöckner</surname><given-names>FO</given-names></name><name><surname>Peplies</surname><given-names>J</given-names></name></person-group><article-title>JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison</article-title><source>Bioinformatics</source><year>2016</year><volume>32</volume><issue>6</issue><fpage>929</fpage><lpage>931</lpage><pub-id pub-id-type="pmid">26576653</pub-id></element-citation></ref><ref id="CR30"><label>30.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pritchard</surname><given-names>L</given-names></name><name><surname>Glover</surname><given-names>RH</given-names></name><name><surname>Humphris</surname><given-names>S</given-names></name><name><surname>Elphinstone</surname><given-names>JG</given-names></name><name><surname>Toth</surname><given-names>IK</given-names></name></person-group><article-title>Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens</article-title><source>Anal Methods</source><year>2016</year><volume>8</volume><fpage>12</fpage><lpage>24</lpage></element-citation></ref><ref id="CR31"><label>31.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schaad</surname><given-names>NW</given-names></name><name><surname>Postnikova</surname><given-names>E</given-names></name><name><surname>Lacy</surname><given-names>G</given-names></name><name><surname>Fatmi</surname><given-names>M</given-names></name><name><surname>Chang</surname><given-names>CJ</given-names></name></person-group><article-title><italic>Xylella fastidiosa</italic> subspecies: <italic>X. fastidiosa</italic> subsp. <italic>piercei</italic> subsp. nov., <italic>X. fastidiosa</italic> subsp. <italic>multiplex</italic> subsp. nov., and <italic>X. fastidiosa</italic> subsp. <italic>pauca</italic> subsp. nov</article-title><source>Syst Appl Microbiol</source><year>2004</year><volume>27</volume><fpage>290</fpage><lpage>300</lpage><pub-id pub-id-type="pmid">15214634</pub-id></element-citation></ref><ref id="CR32"><label>32.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Verslyppe</surname><given-names>B</given-names></name><name><surname>De Smet</surname><given-names>W</given-names></name><name><surname>De Baets</surname><given-names>B</given-names></name><name><surname>De Vos</surname><given-names>P</given-names></name><name><surname>Dawyndt</surname><given-names>D</given-names></name></person-group><article-title>StrainInfo introduces electronic passports for microorganisms</article-title><source>Syst Appl Microbiol</source><year>2014</year><volume>37</volume><fpage>42</fpage><lpage>50</lpage><pub-id pub-id-type="pmid">24321274</pub-id></element-citation></ref><ref id="CR33"><label>33.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Giampetruzzi</surname><given-names>A</given-names></name><name><surname>Chiumenti</surname><given-names>M</given-names></name><name><surname>Saponari</surname><given-names>M</given-names></name><name><surname>Donvito</surname><given-names>G</given-names></name><name><surname>Italiano</surname><given-names>A</given-names></name><name><surname>Loconsole</surname><given-names>G</given-names></name><etal></etal></person-group><article-title>Draft genome sequence of the <italic>Xylella fastidiosa</italic> CoDiRO strain</article-title><source>Genome Announc</source><year>2015</year><volume>3</volume><fpage>e01538</fpage><lpage>e01514</lpage><pub-id pub-id-type="pmid">25676759</pub-id></element-citation></ref><ref id="CR34"><label>34.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rogers</surname><given-names>EE</given-names></name><name><surname>Stenger</surname><given-names>DC</given-names></name></person-group><article-title>A conjugative 38 kb plasmid is present in multiple subspecies of <italic>Xylella fastidiosa</italic></article-title><source>PLoS One</source><year>2012</year><volume>7</volume><fpage>e52131</fpage><pub-id pub-id-type="pmid">23251694</pub-id></element-citation></ref><ref id="CR35"><label>35.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Giampetruzzi</surname><given-names>A</given-names></name><name><surname>Saponari</surname><given-names>M</given-names></name><name><surname>Almeida</surname><given-names>RPP</given-names></name><name><surname>Essakhi</surname><given-names>S</given-names></name><name><surname>Boscia</surname><given-names>D</given-names></name><name><surname>Loconsole</surname><given-names>G</given-names></name><etal></etal></person-group><article-title>Complete genome sequence of the olive-infecting strain <italic>Xylella fastidiosa</italic> subsp. <italic>pauca</italic> De Donno</article-title><source>Genome Announc</source><year>2017</year><volume>6</volume><issue>5</issue><fpage>e00569</fpage><lpage>e00517</lpage></element-citation></ref><ref id="CR36"><label>36.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Al-Okaily</surname><given-names>A</given-names></name></person-group><article-title>HGA: denovo genome assembly method for bacterial genomes using high coverage short sequencing reads</article-title><source>BMC Genomics</source><year>2016</year><volume>17</volume><fpage>193</fpage><pub-id pub-id-type="pmid">26945881</pub-id></element-citation></ref><ref id="CR37"><label>37.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Powers</surname><given-names>JG</given-names></name><name><surname>Weigman</surname><given-names>VJ</given-names></name><name><surname>Shu</surname><given-names>J</given-names></name><name><surname>Pufky</surname><given-names>JM</given-names></name><name><surname>Cox</surname><given-names>D</given-names></name><name><surname>Hurban</surname><given-names>P</given-names></name></person-group><article-title>Efficient and accurate whole genome assembly and methylome profiling of E coli</article-title><source>BMC Genomics</source><year>2013</year><volume>14</volume><fpage>675</fpage><pub-id pub-id-type="pmid">24090403</pub-id></element-citation></ref><ref id="CR38"><label>38.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Konstantinidis</surname><given-names>KT</given-names></name><name><surname>Tiedje</surname><given-names>JM</given-names></name></person-group><article-title>Genomic insights that advance the species definition for prokaryotes</article-title><source>Proc Natl Acad Sci U S A</source><year>2005</year><volume>102</volume><fpage>2567</fpage><lpage>2572</lpage><pub-id pub-id-type="pmid">15701695</pub-id></element-citation></ref><ref id="CR39"><label>39.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Richter</surname><given-names>M</given-names></name><name><surname>Rossello-Mora</surname><given-names>R</given-names></name></person-group><article-title>Shifting the genomic gold standard for the prokaryotic species definition</article-title><source>Proc Natl Acad Sci U S A</source><year>2009</year><volume>106</volume><fpage>19126</fpage><lpage>19131</lpage><pub-id pub-id-type="pmid">19855009</pub-id></element-citation></ref><ref id="CR40"><label>40.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Delcher</surname><given-names>AL</given-names></name><name><surname>Kasif</surname><given-names>S</given-names></name><name><surname>Fleischmann</surname><given-names>RD</given-names></name><name><surname>Peterson</surname><given-names>J</given-names></name><name><surname>White</surname><given-names>O</given-names></name><name><surname>Salzberg</surname><given-names>SL</given-names></name></person-group><article-title>Alignment of whole genomes</article-title><source>Nucleic Acids Res</source><year>1999</year><volume>27</volume><fpage>2369</fpage><lpage>2376</lpage><pub-id pub-id-type="pmid">10325427</pub-id></element-citation></ref><ref id="CR41"><label>41.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Teeling</surname><given-names>H</given-names></name><name><surname>Waldmann</surname><given-names>J</given-names></name><name><surname>Lombardot</surname><given-names>T</given-names></name><name><surname>Bauer</surname><given-names>M</given-names></name><name><surname>Glöckner</surname><given-names>FO</given-names></name></person-group><article-title>TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences</article-title><source>BMC Bioinformatics</source><year>2004</year><volume>26</volume><issue>5</issue><fpage>163</fpage></element-citation></ref><ref id="CR42"><label>42.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goris</surname><given-names>J</given-names></name><name><surname>Konstantinidis</surname><given-names>KT</given-names></name><name><surname>Klappenbach</surname><given-names>JA</given-names></name><name><surname>Coenye</surname><given-names>T</given-names></name><name><surname>Vandamme</surname><given-names>P</given-names></name><name><surname>Tiedje</surname><given-names>JM</given-names></name></person-group><article-title>DNA-DNA hybridization values and their relationship to whole-genome sequence similarities</article-title><source>Int J Syst Evol Microbiol</source><year>2007</year><volume>57</volume><fpage>81</fpage><lpage>91</lpage><pub-id pub-id-type="pmid">17220447</pub-id></element-citation></ref><ref id="CR43"><label>43.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Marcelletti</surname><given-names>S</given-names></name><name><surname>Scortichini</surname><given-names>M</given-names></name></person-group><article-title>Genome-wide comparison and taxonomic relatedness of multiple <italic>Xylella fastidiosa</italic> strains reveal the occurrence of three subspecies and a new <italic>Xylella</italic> species</article-title><source>Arch Microbiol</source><year>2016</year><volume>198</volume><issue>8</issue><fpage>803</fpage><lpage>812</lpage><pub-id pub-id-type="pmid">27209415</pub-id></element-citation></ref><ref id="CR44"><label>44.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Goris</surname><given-names>J</given-names></name><name><surname>Dejonghe</surname><given-names>W</given-names></name><name><surname>Falsen</surname><given-names>E</given-names></name><name><surname>De Clerck</surname><given-names>E</given-names></name><name><surname>Geeraerts</surname><given-names>B</given-names></name><name><surname>Willems</surname><given-names>A</given-names></name><etal></etal></person-group><article-title>Diversity of Transconjugants that acquired plasmid pJP4 or pEMT1 after inoculation of a donor strain in the A- and B-horizon of an agricultural soil and description of <italic>Burkholderia hospita</italic> sp. nov. and <italic>Burkholderia terricola</italic> sp. nov</article-title><source>Syst Appl Mircobiol</source><year>2002</year><volume>25</volume><issue>3</issue><fpage>340</fpage><lpage>352</lpage></element-citation></ref><ref id="CR45"><label>45.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>Y</given-names></name><name><surname>Jeon</surname><given-names>CO</given-names></name></person-group><article-title>Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil</article-title><source>Int J Syst Evol Microbiol</source><year>2018</year><volume>68</volume><issue>4</issue><fpage>1251</fpage><lpage>1257</lpage><pub-id pub-id-type="pmid">29461181</pub-id></element-citation></ref><ref id="CR46"><label>46.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nelson</surname><given-names>MJK</given-names></name><name><surname>Montgomery</surname><given-names>SO</given-names></name><name><surname>O’Neill</surname><given-names>EJ</given-names></name><name><surname>Pritchard</surname><given-names>PH</given-names></name></person-group><article-title>Aerobic metabolism of trichloroethylene by a bacterial isolate</article-title><source>Appl Environ Microbiol</source><year>1986</year><volume>52</volume><issue>2</issue><fpage>383</fpage><lpage>384</lpage><pub-id pub-id-type="pmid">16347139</pub-id></element-citation></ref><ref id="CR47"><label>47.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jones</surname><given-names>JB</given-names></name><name><surname>Lacy</surname><given-names>GH</given-names></name><name><surname>Bouzar</surname><given-names>H</given-names></name><name><surname>Stall</surname><given-names>RE</given-names></name><name><surname>Schaad</surname><given-names>NW</given-names></name></person-group><article-title>Reclassification of the Xanthomonads Associated with Bacterial Spot Disease of Tomato and Pepper</article-title><source>Syst Appl Microbiol</source><year>2004</year><volume>27</volume><fpage>755</fpage><lpage>762</lpage><pub-id pub-id-type="pmid">15612634</pub-id></element-citation></ref><ref id="CR48"><label>48.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Albuquerque</surname><given-names>P</given-names></name><name><surname>Caridade</surname><given-names>CMR</given-names></name><name><surname>Rodrigues</surname><given-names>AS</given-names></name><name><surname>Marcal</surname><given-names>ARS</given-names></name><name><surname>Cruz</surname><given-names>J</given-names></name><name><surname>Cruz</surname><given-names>L</given-names></name><etal></etal></person-group><article-title>Evolutionary and experimental assessment of novel markers for detection of <italic>Xanthomonas euvesicatoria</italic> in plant samples</article-title><source>PLoS ONE</source><year>2012</year><volume>7</volume><issue>5</issue><fpage>e37836</fpage><pub-id pub-id-type="pmid">22655073</pub-id></element-citation></ref><ref id="CR49"><label>49.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Estrada-De Los Santos</surname><given-names>P</given-names></name><name><surname>Bustillos-Cristales</surname><given-names>R</given-names></name><name><surname>Caballero-Mellado</surname><given-names>J</given-names></name></person-group><article-title><italic>Burkholderia</italic>, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution</article-title><source>Appl Environ Microbiol</source><year>2001</year><volume>67</volume><issue>6</issue><fpage>2790</fpage><lpage>2798</lpage><pub-id pub-id-type="pmid">11375196</pub-id></element-citation></ref><ref id="CR50"><label>50.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Carvalho</surname><given-names>GM</given-names></name><name><surname>Carvalho</surname><given-names>AP</given-names></name><name><surname>Folescu</surname><given-names>TW</given-names></name><name><surname>Higa</surname><given-names>L</given-names></name><name><surname>Teixeira</surname><given-names>LM</given-names></name><name><surname>Plotkowski</surname><given-names>MC</given-names></name><etal></etal></person-group><article-title>Transient isolation of <italic>Burkholderia multivorans</italic> and <italic>Burkholderia cenocepacia</italic> from a Brazilian cystic fibrosis patient chronically colonized with <italic>Burkholderia vietnamiensis</italic></article-title><source>J Cyst Fibros</source><year>2005</year><volume>4</volume><issue>4</issue><fpage>267</fpage><lpage>270</lpage><pub-id pub-id-type="pmid">16266831</pub-id></element-citation></ref><ref id="CR51"><label>51.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nunney</surname><given-names>L</given-names></name><name><surname>Elfekih</surname><given-names>S</given-names></name><name><surname>Stouthamer</surname><given-names>R</given-names></name></person-group><article-title>The importance of multilocus sequence typing: cautionary tales from the bacterium <italic>Xylella fastidiosa</italic></article-title><source>Phytopathol</source><year>2012</year><volume>102</volume><fpage>456</fpage><lpage>460</lpage></element-citation></ref><ref id="CR52"><label>52.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yuan</surname><given-names>X</given-names></name><name><surname>Morano</surname><given-names>L</given-names></name><name><surname>Bromley</surname><given-names>R</given-names></name><name><surname>Spring-Pearson</surname><given-names>S</given-names></name><name><surname>Stouthamer</surname><given-names>R</given-names></name><name><surname>Nunney</surname><given-names>L</given-names></name></person-group><article-title>Multilocus sequence typing of <italic>Xylella fastidiosa</italic> causing Pierce's disease and oleander leaf scorch in the United States</article-title><source>Phytopathol</source><year>2010</year><volume>100</volume><fpage>601</fpage><lpage>611</lpage></element-citation></ref><ref id="CR53"><label>53.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wells</surname><given-names>JM</given-names></name><name><surname>Raju</surname><given-names>BC</given-names></name><name><surname>Nyland</surname><given-names>G</given-names></name><name><surname>Lowe</surname><given-names>SK</given-names></name></person-group><article-title>Medium for isolation and growth of bacteria associated with plum leaf scald and phony peach diseases</article-title><source>Appl Environ Microbiol</source><year>1981</year><volume>42</volume><fpage>357</fpage><lpage>363</lpage><pub-id pub-id-type="pmid">16345835</pub-id></element-citation></ref><ref id="CR54"><label>54.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zerbino</surname><given-names>DR</given-names></name><name><surname>Birney</surname><given-names>E</given-names></name></person-group><article-title>Velvet: algorithms for de novo short read assembly using de Bruijn graphs</article-title><source>Genome Res</source><year>2008</year><volume>18</volume><fpage>821</fpage><lpage>829</lpage><pub-id pub-id-type="pmid">18349386</pub-id></element-citation></ref><ref id="CR55"><label>55.</label><mixed-citation publication-type="other">Luo R, Liu B, Xie P, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 20112;1:18.</mixed-citation></ref><ref id="CR56"><label>56.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sallet</surname><given-names>E</given-names></name><name><surname>Gouzy</surname><given-names>J</given-names></name><name><surname>Schiex</surname><given-names>T</given-names></name></person-group><article-title>EuGene-PP: a next generation automated annotation pipeline for prokaryotic genomes</article-title><source>Bioinformatics</source><year>2014</year><volume>30</volume><fpage>2659</fpage><lpage>2661</lpage><pub-id pub-id-type="pmid">24880686</pub-id></element-citation></ref><ref id="CR57"><label>57.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Simpson</surname><given-names>AJ</given-names></name><name><surname>Reinach</surname><given-names>FC</given-names></name><name><surname>Arruda</surname><given-names>P</given-names></name><name><surname>Abreu</surname><given-names>FA</given-names></name><name><surname>Acencio</surname><given-names>M</given-names></name><name><surname>Alvarenga</surname><given-names>R</given-names></name><etal></etal></person-group><article-title>The genome sequence of the plant pathogen <italic>Xylella fastidiosa</italic></article-title><source>Nature</source><year>2000</year><volume>406</volume><fpage>151</fpage><lpage>159</lpage><pub-id pub-id-type="pmid">10910347</pub-id></element-citation></ref><ref id="CR58"><label>58.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Van Sluys</surname><given-names>MA</given-names></name><name><surname>de Oliveira</surname><given-names>MC</given-names></name><name><surname>Monteiro-Vitorello</surname><given-names>CB</given-names></name><name><surname>Miyaki</surname><given-names>CY</given-names></name><name><surname>Furlan</surname><given-names>LR</given-names></name><name><surname>Camargo</surname><given-names>LE</given-names></name><etal></etal></person-group><article-title>Comparative analyses of the complete genomes sequences of Pierce’s disease and citrus variegated chlorosis strains of <italic>Xylella fastidiosa</italic></article-title><source>J Bact</source><year>2003</year><volume>185</volume><fpage>1018</fpage><lpage>1026</lpage><pub-id pub-id-type="pmid">12533478</pub-id></element-citation></ref><ref id="CR59"><label>59.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Guéguen</surname><given-names>L</given-names></name><name><surname>Gaillard</surname><given-names>S</given-names></name><name><surname>Boussau</surname><given-names>B</given-names></name><name><surname>Gouy</surname><given-names>M</given-names></name><name><surname>Groussin</surname><given-names>M</given-names></name><name><surname>Rochette</surname><given-names>NC</given-names></name><etal></etal></person-group><article-title>Bio++: efficient extensible libraries and tools for computational molecular evolution</article-title><source>Mol Biol Evol</source><year>2013</year><volume>30</volume><issue>8</issue><fpage>1745</fpage><lpage>1750</lpage><pub-id pub-id-type="pmid">23699471</pub-id></element-citation></ref><ref id="CR60"><label>60.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kearse</surname><given-names>M</given-names></name><name><surname>Moir</surname><given-names>R</given-names></name><name><surname>Wilson</surname><given-names>A</given-names></name><name><surname>Stones-Havas</surname><given-names>S</given-names></name><name><surname>Cheung</surname><given-names>M</given-names></name><name><surname>Sturrock</surname><given-names>S</given-names></name><etal></etal></person-group><article-title>Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data</article-title><source>Bioinformatics</source><year>2012</year><volume>28</volume><fpage>1647</fpage><lpage>1649</lpage><pub-id pub-id-type="pmid">22543367</pub-id></element-citation></ref><ref id="CR61"><label>61.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ward</surname><given-names>JH</given-names><suffix>Jr</suffix></name></person-group><article-title>Hierarchical grouping to optimize an objective function</article-title><source>J Am Stat Assoc</source><year>1963</year><volume>58</volume><fpage>236</fpage><lpage>244</lpage></element-citation></ref><ref id="CR62"><label>62.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Paradis</surname><given-names>E</given-names></name><name><surname>Claude</surname><given-names>J</given-names></name><name><surname>Strimmer</surname><given-names>K</given-names></name></person-group><article-title>APE: analyses of phylogenetics and evolution in R language</article-title><source>Bioinformatics</source><year>2004</year><volume>20</volume><issue>2</issue><fpage>289</fpage><lpage>290</lpage><pub-id pub-id-type="pmid">14734327</pub-id></element-citation></ref><ref id="CR63"><label>63.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname><given-names>Z</given-names></name><name><surname>Schwartz</surname><given-names>S</given-names></name><name><surname>Wagner</surname><given-names>L</given-names></name><name><surname>Miller</surname><given-names>W</given-names></name></person-group><article-title>A greedy algorithm for aligning DNA sequences</article-title><source>J Comput Biol</source><year>2000</year><volume>7</volume><fpage>203</fpage><lpage>214</lpage><pub-id pub-id-type="pmid">10890397</pub-id></element-citation></ref><ref id="CR64"><label>64.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Götz</surname><given-names>S</given-names></name><name><surname>García-Gómez</surname><given-names>JM</given-names></name><name><surname>Terol</surname><given-names>J</given-names></name><name><surname>Williams</surname><given-names>TD</given-names></name><name><surname>Nagaraj</surname><given-names>SH</given-names></name><name><surname>Nueda</surname><given-names>MJ</given-names></name><etal></etal></person-group><article-title>High-throughput functional annotation and data mining with the Blast2GO suite</article-title><source>Nucl Acids Res</source><year>2008</year><volume>36</volume><issue>10</issue><fpage>3420</fpage><lpage>3435</lpage><pub-id pub-id-type="pmid">18445632</pub-id></element-citation></ref><ref id="CR65"><label>65.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bardou</surname><given-names>P</given-names></name><name><surname>Mariette</surname><given-names>J</given-names></name><name><surname>Escudié</surname><given-names>F</given-names></name><name><surname>Djemiel</surname><given-names>C</given-names></name><name><surname>Klopp</surname><given-names>C</given-names></name></person-group><article-title>jvenn: an interactive Venn diagram viewer</article-title><source>BMC Bioinformatics</source><year>2014</year><volume>15</volume><fpage>293</fpage><pub-id pub-id-type="pmid">25176396</pub-id></element-citation></ref><ref id="CR66"><label>66.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Quast</surname><given-names>C</given-names></name><name><surname>Pruesse</surname><given-names>E</given-names></name><name><surname>Yilmaz</surname><given-names>P</given-names></name><name><surname>Gerken</surname><given-names>J</given-names></name><name><surname>Schweer</surname><given-names>T</given-names></name><name><surname>Yarza</surname><given-names>P</given-names></name><etal></etal></person-group><article-title>The SILVA ribosomal RNA gene database project: improved data processing and web-based tools</article-title><source>Nucl. Acids Res</source><year>2013</year><volume>41</volume><issue>D1</issue><fpage>D590</fpage><lpage>D596</lpage><pub-id pub-id-type="pmid">23193283</pub-id></element-citation></ref><ref id="CR67"><label>67.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname><given-names>S</given-names></name><name><surname>Flores-Cruz</surname><given-names>Z</given-names></name><name><surname>Kumar</surname><given-names>D</given-names></name><name><surname>Chakrabarty</surname><given-names>P</given-names></name><name><surname>Hopkins</surname><given-names>DL</given-names></name><name><surname>Gabriel</surname><given-names>DW</given-names></name></person-group><article-title>The <italic>Xylella fastidiosa</italic> biocontrol strain EB92-1 genome is very similar and syntenic to Pierce's disease strains</article-title><source>J Bacteriol</source><year>2011</year><volume>193</volume><issue>19</issue><fpage>5576</fpage><lpage>5577</lpage><pub-id pub-id-type="pmid">21914886</pub-id></element-citation></ref><ref id="CR68"><label>68.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schreiber</surname><given-names>HL</given-names></name><name><surname>Koirala</surname><given-names>M</given-names></name><name><surname>Lara</surname><given-names>A</given-names></name><name><surname>Ojeda</surname><given-names>M</given-names></name><name><surname>Dowd</surname><given-names>SE</given-names></name><name><surname>Bextine</surname><given-names>B</given-names></name><etal></etal></person-group><article-title>Unraveling the first <italic>Xylella fastidiosa</italic> subsp. <italic>fastidiosa</italic> genome from Texas. Southwest</article-title><source>Entomol</source><year>2010</year><volume>35</volume><issue>3</issue><fpage>479</fpage><lpage>483</lpage></element-citation></ref><ref id="CR69"><label>69.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>J</given-names></name><name><surname>Xie</surname><given-names>G</given-names></name><name><surname>Han</surname><given-names>S</given-names></name><name><surname>Chertkov</surname><given-names>O</given-names></name><name><surname>Sims</surname><given-names>D</given-names></name><name><surname>Civerolo</surname><given-names>EL</given-names></name></person-group><article-title>Whole-genome sequences of two <italic>Xylella fastidiosa</italic> strains (M12 and M23) causing almond leaf scorch disease in California</article-title><source>J Bacteriol</source><year>2010</year><volume>192</volume><fpage>4534</fpage><pub-id pub-id-type="pmid">20601474</pub-id></element-citation></ref><ref id="CR70"><label>70.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>J</given-names></name><name><surname>Wu</surname><given-names>F</given-names></name><name><surname>Zheng</surname><given-names>Z</given-names></name><name><surname>Deng</surname><given-names>X</given-names></name><name><surname>Burbank</surname><given-names>LP</given-names></name><name><surname>Stenger</surname><given-names>DC</given-names></name></person-group><article-title>Draft genome sequence of <italic>Xylella fastidiosa</italic> subsp. <italic>fastidiosa</italic> strain Stag's leap</article-title><source>Genome Announc</source><year>2016</year><volume>4</volume><fpage>e00240</fpage><lpage>e00216</lpage><pub-id pub-id-type="pmid">27103713</pub-id></element-citation></ref><ref id="CR71"><label>71.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Van Horn</surname><given-names>C</given-names></name><name><surname>Chang</surname><given-names>CJ</given-names></name><name><surname>Chen</surname><given-names>J</given-names></name></person-group><article-title><italic>De Novo</italic> whole-genome sequence of <italic>Xylella fastidiosa</italic> subsp. <italic>multiplex</italic> strain BB01 isolated from a blueberry in Georgia, USA</article-title><source>Genome Announc</source><year>2017</year><volume>5</volume><issue>6</issue><fpage>e01598</fpage><lpage>e01516</lpage><pub-id pub-id-type="pmid">28183766</pub-id></element-citation></ref><ref id="CR72"><label>72.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bhattacharyya</surname><given-names>A</given-names></name><name><surname>Stilwagen</surname><given-names>S</given-names></name><name><surname>Ivanova</surname><given-names>N</given-names></name><name><surname>D'Souza</surname><given-names>M</given-names></name><name><surname>Bernal</surname><given-names>A</given-names></name><name><surname>Lykidis</surname><given-names>A</given-names></name><etal></etal></person-group><article-title>Whole-genome comparative analysis of three phytopathogenic <italic>Xylella fastidiosa</italic> strains</article-title><source>Proc Natl Acad Sci U S A</source><year>2002</year><volume>99</volume><fpage>12403</fpage><lpage>12408</lpage><pub-id pub-id-type="pmid">12205291</pub-id></element-citation></ref><ref id="CR73"><label>73.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>J</given-names></name><name><surname>Huang</surname><given-names>H</given-names></name><name><surname>Chang</surname><given-names>C-J</given-names></name><name><surname>Stenger</surname><given-names>DC</given-names></name></person-group><article-title>Draft genome sequence of <italic>Xylella fastidiosa</italic> subsp. <italic>multiplex</italic> strain Griffin-1 from <italic>Quercus rubra</italic> in Georgia</article-title><source>Genome Announc</source><year>2013</year><volume>1</volume><fpage>e00756</fpage><lpage>e00713</lpage><pub-id pub-id-type="pmid">24115539</pub-id></element-citation></ref><ref id="CR74"><label>74.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Guan</surname><given-names>W</given-names></name><name><surname>Shao</surname><given-names>J</given-names></name><name><surname>Davis</surname><given-names>RE</given-names></name><name><surname>Zhao</surname><given-names>T</given-names></name><name><surname>Huang</surname><given-names>Q</given-names></name></person-group><article-title>Genome sequence of a <italic>Xylella fastidiosa</italic> strain causing sycamore leaf scorch disease in Virginia</article-title><source>Genome Announc</source><year>2014</year><volume>2</volume><fpage>e00773</fpage><lpage>e00714</lpage><pub-id pub-id-type="pmid">25146135</pub-id></element-citation></ref><ref id="CR75"><label>75.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schuenzel</surname><given-names>EL</given-names></name><name><surname>Scally</surname><given-names>M</given-names></name><name><surname>Stouthamer</surname><given-names>R</given-names></name><name><surname>Nunney</surname><given-names>L</given-names></name></person-group><article-title>A multigene phylogenetic study of clonal diversity and divergence in north American strains of the plant pathogen <italic>Xylella fastidiosa</italic></article-title><source>Appl Environ Microbiol</source><year>2005</year><volume>71</volume><fpage>3832</fpage><lpage>3839</lpage><pub-id pub-id-type="pmid">16000795</pub-id></element-citation></ref><ref id="CR76"><label>76.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Giampetruzzi</surname><given-names>A</given-names></name><name><surname>Loconsole</surname><given-names>G</given-names></name><name><surname>Boscia</surname><given-names>D</given-names></name><name><surname>Calzolari</surname><given-names>A</given-names></name><name><surname>Chiumenti</surname><given-names>M</given-names></name><name><surname>Martelli</surname><given-names>GP</given-names></name><etal></etal></person-group><article-title>Draft genome sequence of CO33, a coffee-infecting isolate of <italic>Xylella fastidiosa</italic></article-title><source>Genome Announc</source><year>2015</year><volume>3</volume><fpage>e01472</fpage><lpage>e01415</lpage><pub-id pub-id-type="pmid">26679584</pub-id></element-citation></ref><ref id="CR77"><label>77.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Guan</surname><given-names>W</given-names></name><name><surname>Shao</surname><given-names>J</given-names></name><name><surname>Zhao</surname><given-names>T</given-names></name><name><surname>Huang</surname><given-names>Q</given-names></name></person-group><article-title>Genome sequence of a <italic>Xylella fastidiosa</italic> strain causing mulberry leaf scorch disease in Maryland</article-title><source>Genome Announc</source><year>2014</year><volume>2</volume><fpage>e00916</fpage><lpage>e00913</lpage><pub-id pub-id-type="pmid">24604658</pub-id></element-citation></ref><ref id="CR78"><label>78.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Alencar</surname><given-names>VC</given-names></name><name><surname>Barbosa</surname><given-names>D</given-names></name><name><surname>Santos</surname><given-names>DS</given-names></name><name><surname>Oliveira</surname><given-names>ACF</given-names></name><name><surname>de Oliveira</surname><given-names>RC</given-names></name><name><surname>Nunes</surname><given-names>LR</given-names></name></person-group><article-title>Genomic sequencing of two coffee-infecting strains of <italic>Xylella fastidiosa</italic> isolated from Brazil</article-title><source>Genome Announc</source><year>2014</year><volume>2</volume><fpage>e01190</fpage><lpage>e01113</lpage><pub-id pub-id-type="pmid">24435874</pub-id></element-citation></ref><ref id="CR79"><label>79.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Niza</surname><given-names>B</given-names></name><name><surname>Merfa</surname><given-names>MV</given-names></name><name><surname>Alencar</surname><given-names>VC</given-names></name><name><surname>Menegidio</surname><given-names>FB</given-names></name><name><surname>Nunes</surname><given-names>LR</given-names></name><name><surname>Machado</surname><given-names>MA</given-names></name><etal></etal></person-group><article-title>Draft genome sequence of 11399, a transformable citrus-pathogenic strain of <italic>Xylella fastidiosa</italic></article-title><source>Genome Announc</source><year>2016</year><volume>13</volume><fpage>e01124</fpage><lpage>e01116</lpage></element-citation></ref><ref id="CR80"><label>80.</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Su</surname><given-names>CC</given-names></name><name><surname>Deng</surname><given-names>WL</given-names></name><name><surname>Jan</surname><given-names>FJ</given-names></name><name><surname>Chang</surname><given-names>CJ</given-names></name><name><surname>Huang</surname><given-names>H</given-names></name><name><surname>Chen</surname><given-names>J</given-names></name></person-group><article-title>Draft genome sequence of <italic>Xylella fastidiosa</italic> pear leaf scorch strain in Taiwan</article-title><source>Genome Announc</source><year>2014</year><volume>2</volume><fpage>e00166</fpage><lpage>e00114</lpage><pub-id pub-id-type="pmid">24652975</pub-id></element-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000301 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000301 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Pmc
|étape= Corpus
|type= RBID
|clé=
|texte=
}}
| This area was generated with Dilib version V0.6.33. |  |