Identification of genetic relationships and subspecies signatures in Xylella fastidiosa.
Identifieur interne : 000523 ( PubMed/Checkpoint ); précédent : 000522; suivant : 000524Identification of genetic relationships and subspecies signatures in Xylella fastidiosa.
Auteurs : Nicolas Denancé [France] ; Martial Briand [France] ; Romain Gaborieau [France] ; Sylvain Gaillard [France] ; Marie-Agnès Jacques [France]Source :
- BMC genomics [ 1471-2164 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Bacterial, DNA, Ribosomal, RNA, Ribosomal, 16S.
- classification : Xylella.
- genetics : Xylella.
- methods : Genomics, Sequence Analysis, DNA.
- Data Mining, Gene Ontology, Phylogeny, Polymorphism, Single Nucleotide.
Abstract
The phytopathogenic bacterium Xylella fastidiosa 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.
DOI: 10.1186/s12864-019-5565-9
PubMed: 30909861
Affiliations:
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pubmed:30909861Le document en format XML
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France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex</wicri:regionArea><placeName><region type="region" nuts="2">Pays de la Loire</region><settlement type="city">Beaucouzé</settlement></placeName><orgName type="university">Université d'Angers</orgName></affiliation></author><author><name sortKey="Briand, Martial" sort="Briand, Martial" uniqKey="Briand M" first="Martial" last="Briand">Martial Briand</name><affiliation wicri:level="4"><nlm:affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex</wicri:regionArea><placeName><region type="region" nuts="2">Pays de la Loire</region><settlement type="city">Beaucouzé</settlement></placeName><orgName type="university">Université d'Angers</orgName></affiliation></author><author><name sortKey="Gaborieau, Romain" sort="Gaborieau, Romain" uniqKey="Gaborieau R" first="Romain" last="Gaborieau">Romain Gaborieau</name><affiliation wicri:level="4"><nlm:affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex</wicri:regionArea><placeName><region type="region" nuts="2">Pays de la Loire</region><settlement type="city">Beaucouzé</settlement></placeName><orgName type="university">Université d'Angers</orgName></affiliation></author><author><name sortKey="Gaillard, Sylvain" sort="Gaillard, Sylvain" uniqKey="Gaillard S" first="Sylvain" last="Gaillard">Sylvain Gaillard</name><affiliation wicri:level="4"><nlm:affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex</wicri:regionArea><placeName><region type="region" nuts="2">Pays de la Loire</region><settlement type="city">Beaucouzé</settlement></placeName><orgName type="university">Université d'Angers</orgName></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 wicri:level="4"><nlm:affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France. marie-agnes.jacques@inra.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex</wicri:regionArea><placeName><region type="region" nuts="2">Pays de la Loire</region><settlement type="city">Beaucouzé</settlement></placeName><orgName type="university">Université d'Angers</orgName></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA, Bacterial (genetics)</term><term>DNA, Ribosomal (genetics)</term><term>Data Mining</term><term>Gene Ontology</term><term>Genomics (methods)</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term><term>RNA, Ribosomal, 16S (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Xylella (classification)</term><term>Xylella (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (génétique)</term><term>ADN ribosomique (génétique)</term><term>ARN ribosomique 16S (génétique)</term><term>Analyse de séquence d'ADN ()</term><term>Fouille de données</term><term>Gene Ontology</term><term>Génomique ()</term><term>Phylogénie</term><term>Polymorphisme de nucléotide simple</term><term>Xylella ()</term><term>Xylella (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term><term>DNA, Ribosomal</term><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Xylella</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Xylella</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>ADN ribosomique</term><term>ARN ribosomique 16S</term><term>Xylella</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Data Mining</term><term>Gene Ontology</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Fouille de données</term><term>Gene Ontology</term><term>Génomique</term><term>Phylogénie</term><term>Polymorphisme de nucléotide simple</term><term>Xylella</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The phytopathogenic bacterium Xylella fastidiosa 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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30909861</PMID><DateCompleted><Year>2019</Year><Month>07</Month><Day>12</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>Mar</Month><Day>25</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Identification of genetic relationships and subspecies signatures in Xylella fastidiosa.</ArticleTitle><Pagination><MedlinePgn>239</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-019-5565-9</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The phytopathogenic bacterium Xylella fastidiosa 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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">SkIf (Specific k-mers Identification) was designed and exploited for comparative genomics on a dataset of 46 X. fastidiosa 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 Xylella 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 fastidiosa, morus and sandyi taken as a whole group. In the subspecies pauca 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 X. fastidiosa subsp. pauca. Finally, a revised taxonomy of X. fastidiosa into three major clades defined by the subspecies pauca (clade I), multiplex (clade II) and the combination of fastidiosa, morus and sandyi (clade III) was strongly supported by k-mers specifically associated with these subspecies.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">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 X. fastidiosa, an emerging pathogen in Europe, 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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Denancé</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-0173-3970</Identifier><AffiliationInfo><Affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Briand</LastName><ForeName>Martial</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gaborieau</LastName><ForeName>Romain</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gaillard</LastName><ForeName>Sylvain</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jacques</LastName><ForeName>Marie-Agnès</ForeName><Initials>MA</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-1442-917X</Identifier><AffiliationInfo><Affiliation>IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France. marie-agnes.jacques@inra.fr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>635646</GrantID><Agency>RFI Objectif Végétal</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>03</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004269">DNA, Bacterial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004275">DNA, Ribosomal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004269" MajorTopicYN="N">DNA, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004275" MajorTopicYN="N">DNA, Ribosomal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D057225" MajorTopicYN="N">Data Mining</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D044167" MajorTopicYN="N">Xylella</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">16S rRNA gene</Keyword><Keyword MajorTopicYN="N">Horizontal gene transfer</Keyword><Keyword MajorTopicYN="N">K-mer</Keyword><Keyword MajorTopicYN="N">Phylogeny</Keyword><Keyword MajorTopicYN="N">SkIf</Keyword><Keyword 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first="Sylvain" last="Gaillard">Sylvain Gaillard</name><name sortKey="Jacques, Marie Agnes" sort="Jacques, Marie Agnes" uniqKey="Jacques M" first="Marie-Agnès" last="Jacques">Marie-Agnès Jacques</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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