An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea
Identifieur interne : 000C10 ( Main/Exploration ); précédent : 000C09; suivant : 000C11An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea
Auteurs : James T. Tambong ; Renlin Xu ; Cynthia-Anne Kaneza ; Jean-Claude NshogozabahiziSource :
- Evolutionary Bioinformatics Online [ 1176-9343 ] ; 2014.
Abstract
Partial sequences of six core genes (
Url:
DOI: 10.4137/EBO.S15738
PubMed: 25125967
PubMed Central: 4125426
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000F04
- to stream Pmc, to step Curation: 000F03
- to stream Pmc, to step Checkpoint: 000919
- to stream Ncbi, to step Merge: 001803
- to stream Ncbi, to step Curation: 001803
- to stream Ncbi, to step Checkpoint: 001803
- to stream Main, to step Merge: 000C13
- to stream Main, to step Curation: 000C10
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">An In-depth Analysis of a Multilocus Phylogeny Identifies <italic>leu</italic>S As a Reliable Phylogenetic Marker for the Genus <italic>Pantoea</italic></title><author><name sortKey="Tambong, James T" sort="Tambong, James T" uniqKey="Tambong J" first="James T" last="Tambong">James T. Tambong</name></author><author><name sortKey="Xu, Renlin" sort="Xu, Renlin" uniqKey="Xu R" first="Renlin" last="Xu">Renlin Xu</name></author><author><name sortKey="Kaneza, Cynthia Anne" sort="Kaneza, Cynthia Anne" uniqKey="Kaneza C" first="Cynthia-Anne" last="Kaneza">Cynthia-Anne Kaneza</name></author><author><name sortKey="Nshogozabahizi, Jean Claude" sort="Nshogozabahizi, Jean Claude" uniqKey="Nshogozabahizi J" first="Jean-Claude" last="Nshogozabahizi">Jean-Claude Nshogozabahizi</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25125967</idno><idno type="pmc">4125426</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125426</idno><idno type="RBID">PMC:4125426</idno><idno type="doi">10.4137/EBO.S15738</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000F04</idno><idno type="wicri:Area/Pmc/Curation">000F03</idno><idno type="wicri:Area/Pmc/Checkpoint">000919</idno><idno type="wicri:Area/Ncbi/Merge">001803</idno><idno type="wicri:Area/Ncbi/Curation">001803</idno><idno type="wicri:Area/Ncbi/Checkpoint">001803</idno><idno type="wicri:Area/Main/Merge">000C13</idno><idno type="wicri:Area/Main/Curation">000C10</idno><idno type="wicri:Area/Main/Exploration">000C10</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">An In-depth Analysis of a Multilocus Phylogeny Identifies <italic>leu</italic>S As a Reliable Phylogenetic Marker for the Genus <italic>Pantoea</italic></title><author><name sortKey="Tambong, James T" sort="Tambong, James T" uniqKey="Tambong J" first="James T" last="Tambong">James T. Tambong</name></author><author><name sortKey="Xu, Renlin" sort="Xu, Renlin" uniqKey="Xu R" first="Renlin" last="Xu">Renlin Xu</name></author><author><name sortKey="Kaneza, Cynthia Anne" sort="Kaneza, Cynthia Anne" uniqKey="Kaneza C" first="Cynthia-Anne" last="Kaneza">Cynthia-Anne Kaneza</name></author><author><name sortKey="Nshogozabahizi, Jean Claude" sort="Nshogozabahizi, Jean Claude" uniqKey="Nshogozabahizi J" first="Jean-Claude" last="Nshogozabahizi">Jean-Claude Nshogozabahizi</name></author></analytic><series><title level="j">Evolutionary Bioinformatics Online</title><idno type="eISSN">1176-9343</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Partial sequences of six core genes (<italic>fus</italic>A, <italic>gyr</italic>B, <italic>leu</italic>S, <italic>pyr</italic>G, <italic>rlp</italic>B, and <italic>rpo</italic>B) of 37 strains of <italic>Pantoea</italic> species were analyzed in order to obtain a comprehensive view regarding the phylogenetic relationships within the <italic>Pantoea</italic> genus and compare tree topologies to identify gene(s) for reliable species and subspecies differentiation. All genes used in this study were effective at species-level delineation, but the internal nodes represented conflicting common ancestors in <italic>fus</italic>A- and <italic>pyr</italic>G-based phylogenies. Concatenated gene phylogeny gave the expected DNA relatedness, underscoring the significance of a multilocus sequence analysis. Pairwise comparison of topological distances and percent similarities indicated a significant differential influence of individual genes on the concatenated tree topology. <italic>leu</italic>S- and <italic>fus</italic>A-inferred phylogenies exhibited, respectively, the lowest (4) and highest (52) topological distances to the concatenated tree. These correlated well with high (96.3%) and low (64.4%) percent similarities of <italic>leu</italic>S- and <italic>fus</italic>A-inferred tree topologies to the concatenated tree, respectively. We conclude that the concatenated tree topology is strongly influenced by the gene with the highest number of polymorphic and non-synonymous sites in the absence of significant recombination events.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Deletoile, A" uniqKey="Deletoile A">A Delétoile</name></author><author><name sortKey="Decre, D" uniqKey="Decre D">D Decré</name></author><author><name sortKey="Courant, S" uniqKey="Courant S">S Courant</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brady, Cl" uniqKey="Brady C">CL Brady</name></author><author><name sortKey="Cleenwerck, I" uniqKey="Cleenwerck I">I Cleenwerck</name></author><author><name sortKey="Venter, Sn" uniqKey="Venter S">SN Venter</name></author><author><name sortKey="Engelbeen, K" uniqKey="Engelbeen K">K Engelbeen</name></author><author><name sortKey="De Vos, P" uniqKey="De Vos P">P De Vos</name></author><author><name sortKey="Coutinho, Ta" uniqKey="Coutinho T">TA Coutinho</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Naum, M" uniqKey="Naum M">M Naum</name></author><author><name sortKey="Brown, Ew" uniqKey="Brown E">EW Brown</name></author><author><name sortKey="Mason Gamer, Rj" uniqKey="Mason Gamer R">RJ Mason-Gamer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Young, Jm" uniqKey="Young J">JM Young</name></author><author><name sortKey="Park, Dc" uniqKey="Park D">DC Park</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bishop, Cj" uniqKey="Bishop C">CJ Bishop</name></author><author><name sortKey="Aanensen, Dm" uniqKey="Aanensen D">DM Aanensen</name></author><author><name sortKey="Jordan, Ge" uniqKey="Jordan G">GE Jordan</name></author><author><name sortKey="Kilian, M" uniqKey="Kilian M">M Kilian</name></author><author><name sortKey="Hanage, Wp" uniqKey="Hanage W">WP Hanage</name></author><author><name sortKey="Spratt, Bg" uniqKey="Spratt B">BG Spratt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name></author><author><name sortKey="Dawyndt, P" uniqKey="Dawyndt P">P Dawyndt</name></author><author><name sortKey="Vandamme, P" uniqKey="Vandamme P">P Vandamme</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fraser, C" uniqKey="Fraser C">C Fraser</name></author><author><name sortKey="Hanage, Wp" uniqKey="Hanage W">WP Hanage</name></author><author><name sortKey="Spratt, Bg" uniqKey="Spratt B">BG Spratt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hanage, Wp" uniqKey="Hanage W">WP Hanage</name></author><author><name sortKey="Fraser, C" uniqKey="Fraser C">C Fraser</name></author><author><name sortKey="Spratt, Bg" uniqKey="Spratt B">BG Spratt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brady, C" uniqKey="Brady C">C Brady</name></author><author><name sortKey="Cleenwerck, I" uniqKey="Cleenwerck I">I Cleenwerck</name></author><author><name sortKey="Venter, S" uniqKey="Venter S">S Venter</name></author><author><name sortKey="Vancanneyt, M" uniqKey="Vancanneyt M">M Vancanneyt</name></author><author><name sortKey="Swings, J" uniqKey="Swings J">J Swings</name></author><author><name sortKey="Coutinho, T" uniqKey="Coutinho T">T Coutinho</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tambong, Jt" uniqKey="Tambong J">JT Tambong</name></author><author><name sortKey="De Cock, Aw" uniqKey="De Cock A">AW de Cock</name></author><author><name sortKey="Tinker, Na" uniqKey="Tinker N">NA Tinker</name></author><author><name sortKey="Levesque, Ca" uniqKey="Levesque C">CA Lévesque</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D Peterson</name></author><author><name sortKey="Peterson, N" uniqKey="Peterson N">N Peterson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wernersson, R" uniqKey="Wernersson R">R Wernersson</name></author><author><name sortKey="Pedersen, Ag" uniqKey="Pedersen A">AG Pedersen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edgar, Rc" uniqKey="Edgar R">RC Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Librado, P" uniqKey="Librado P">P Librado</name></author><author><name sortKey="Rozas, J" uniqKey="Rozas J">J Rozas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bruen, Tc" uniqKey="Bruen T">TC Bruen</name></author><author><name sortKey="Philippe, H" uniqKey="Philippe H">H Philippe</name></author><author><name sortKey="Bryant, D" uniqKey="Bryant D">D Bryant</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name></author><author><name sortKey="Bryant, D" uniqKey="Bryant D">D Bryant</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Campbell, V" uniqKey="Campbell V">V Campbell</name></author><author><name sortKey="Legendre, P" uniqKey="Legendre P">P Legendre</name></author><author><name sortKey="Lapointe, Fj" uniqKey="Lapointe F">FJ Lapointe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mulet, M" uniqKey="Mulet M">M Mulet</name></author><author><name sortKey="Lalucat, J" uniqKey="Lalucat J">J Lalucat</name></author><author><name sortKey="Garcia Valdes, E" uniqKey="Garcia Valdes E">E Garcia-Valdes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guindon, S" uniqKey="Guindon S">S Guindon</name></author><author><name sortKey="Dufayard, Jf" uniqKey="Dufayard J">JF Dufayard</name></author><author><name sortKey="Lefort, V" uniqKey="Lefort V">V Lefort</name></author><author><name sortKey="Anisimova, M" uniqKey="Anisimova M">M Anisimova</name></author><author><name sortKey="Hordijk, W" uniqKey="Hordijk W">W Hordijk</name></author><author><name sortKey="Gascuel, O" uniqKey="Gascuel O">O Gascuel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Darriba, D" uniqKey="Darriba D">D Darriba</name></author><author><name sortKey="Taboada, Gl" uniqKey="Taboada G">GL Taboada</name></author><author><name sortKey="Doallo, R" uniqKey="Doallo R">R Doallo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nye, Tm" uniqKey="Nye T">TM Nye</name></author><author><name sortKey="Lio, P" uniqKey="Lio P">P Lio</name></author><author><name sortKey="Gilks, Wr" uniqKey="Gilks W">WR Gilks</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, Z" uniqKey="Xu Z">Z Xu</name></author><author><name sortKey="Hao, B" uniqKey="Hao B">B Hao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name></author><author><name sortKey="Cohan, Fm" uniqKey="Cohan F">FM Cohan</name></author><author><name sortKey="Lawrence, Jg" uniqKey="Lawrence J">JG Lawrence</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Godoy, D" uniqKey="Godoy D">D Godoy</name></author><author><name sortKey="Randle, G" uniqKey="Randle G">G Randle</name></author><author><name sortKey="Simpson, Aj" uniqKey="Simpson A">AJ Simpson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Priest, Fg" uniqKey="Priest F">FG Priest</name></author><author><name sortKey="Barker, M" uniqKey="Barker M">M Barker</name></author><author><name sortKey="Baillie, Lw" uniqKey="Baillie L">LW Baillie</name></author><author><name sortKey="Holmes, Ec" uniqKey="Holmes E">EC Holmes</name></author><author><name sortKey="Maiden, Mc" uniqKey="Maiden M">MC Maiden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cole, Jr" uniqKey="Cole J">JR Cole</name></author><author><name sortKey="Konstandinidis, K" uniqKey="Konstandinidis K">K Konstandinidis</name></author><author><name sortKey="Farris, Rj" uniqKey="Farris R">RJ Farris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kampfer, P" uniqKey="Kampfer P">P Kampfer</name></author><author><name sortKey="Glaeser, Sp" uniqKey="Glaeser S">SP Glaeser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leclerque, A" uniqKey="Leclerque A">A Leclerque</name></author><author><name sortKey="Kleespies, Rg" uniqKey="Kleespies R">RG Kleespies</name></author><author><name sortKey="Schuster, C" uniqKey="Schuster C">C Schuster</name></author><author><name sortKey="Richards, Nk" uniqKey="Richards N">NK Richards</name></author><author><name sortKey="Marshall, Sd" uniqKey="Marshall S">SD Marshall</name></author><author><name sortKey="Jackson, Ta" uniqKey="Jackson T">TA Jackson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tang, J" uniqKey="Tang J">J Tang</name></author><author><name sortKey="Bromfield, Es" uniqKey="Bromfield E">ES Bromfield</name></author><author><name sortKey="Rodrigue, N" uniqKey="Rodrigue N">N Rodrigue</name></author><author><name sortKey="Cloutier, S" uniqKey="Cloutier S">S Cloutier</name></author><author><name sortKey="Tambong, Jt" uniqKey="Tambong J">JT Tambong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vinuesa, P" uniqKey="Vinuesa P">P Vinuesa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Didelot, X" uniqKey="Didelot X">X Didelot</name></author><author><name sortKey="Maiden, Mc" uniqKey="Maiden M">MC Maiden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thomas, Cm" uniqKey="Thomas C">CM Thomas</name></author><author><name sortKey="Nielsen, Km" uniqKey="Nielsen K">KM Nielsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vogan, Aa" uniqKey="Vogan A">AA Vogan</name></author><author><name sortKey="Higgs, Pg" uniqKey="Higgs P">PG Higgs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Penny, D" uniqKey="Penny D">D Penny</name></author><author><name sortKey="Hendy, Md" uniqKey="Hendy M">MD Hendy</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Kaneza, Cynthia Anne" sort="Kaneza, Cynthia Anne" uniqKey="Kaneza C" first="Cynthia-Anne" last="Kaneza">Cynthia-Anne Kaneza</name><name sortKey="Nshogozabahizi, Jean Claude" sort="Nshogozabahizi, Jean Claude" uniqKey="Nshogozabahizi J" first="Jean-Claude" last="Nshogozabahizi">Jean-Claude Nshogozabahizi</name><name sortKey="Tambong, James T" sort="Tambong, James T" uniqKey="Tambong J" first="James T" last="Tambong">James T. Tambong</name><name sortKey="Xu, Renlin" sort="Xu, Renlin" uniqKey="Xu R" first="Renlin" last="Xu">Renlin Xu</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000C10 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000C10 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:4125426
|texte= An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25125967" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |