RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants
Identifieur interne : 000068 ( Main/Exploration ); précédent : 000067; suivant : 000069RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants
Auteurs : Pingchuan Li ; Xiande Quan ; Gaofeng Jia ; Jin Xiao [République populaire de Chine] ; Sylvie Cloutier ; Frank M. YouSource :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential
An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets.
RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket:
The online version of this article (doi:10.1186/s12864-016-3197-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-3197-x
PubMed: 27806688
PubMed Central: 5093994
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants</title><author><name sortKey="Li, Pingchuan" sort="Li, Pingchuan" uniqKey="Li P" first="Pingchuan" last="Li">Pingchuan Li</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Quan, Xiande" sort="Quan, Xiande" uniqKey="Quan X" first="Xiande" last="Quan">Xiande Quan</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Jia, Gaofeng" sort="Jia, Gaofeng" uniqKey="Jia G" first="Gaofeng" last="Jia">Gaofeng Jia</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada</nlm:aff><wicri:noCountry code="subfield">SK S7N 5A8 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Xiao, Jin" sort="Xiao, Jin" uniqKey="Xiao J" first="Jin" last="Xiao">Jin Xiao</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, 210095 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Cloutier, Sylvie" sort="Cloutier, Sylvie" uniqKey="Cloutier S" first="Sylvie" last="Cloutier">Sylvie Cloutier</name><affiliation><nlm:aff id="Aff4">Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6 Canada</nlm:aff><wicri:noCountry code="subfield">ON K1A 0C6 Canada</wicri:noCountry></affiliation></author><author><name sortKey="You, Frank M" sort="You, Frank M" uniqKey="You F" first="Frank M." last="You">Frank M. You</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27806688</idno><idno type="pmc">5093994</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093994</idno><idno type="RBID">PMC:5093994</idno><idno type="doi">10.1186/s12864-016-3197-x</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000611</idno><idno type="wicri:Area/Pmc/Curation">000610</idno><idno type="wicri:Area/Pmc/Checkpoint">000052</idno><idno type="wicri:Area/Ncbi/Merge">002224</idno><idno type="wicri:Area/Ncbi/Curation">002224</idno><idno type="wicri:Area/Ncbi/Checkpoint">002224</idno><idno type="wicri:Area/Main/Merge">000068</idno><idno type="wicri:Area/Main/Curation">000068</idno><idno type="wicri:Area/Main/Exploration">000068</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants</title><author><name sortKey="Li, Pingchuan" sort="Li, Pingchuan" uniqKey="Li P" first="Pingchuan" last="Li">Pingchuan Li</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Quan, Xiande" sort="Quan, Xiande" uniqKey="Quan X" first="Xiande" last="Quan">Xiande Quan</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Jia, Gaofeng" sort="Jia, Gaofeng" uniqKey="Jia G" first="Gaofeng" last="Jia">Gaofeng Jia</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada</nlm:aff><wicri:noCountry code="subfield">SK S7N 5A8 Canada</wicri:noCountry></affiliation></author><author><name sortKey="Xiao, Jin" sort="Xiao, Jin" uniqKey="Xiao J" first="Jin" last="Xiao">Jin Xiao</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, 210095 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Cloutier, Sylvie" sort="Cloutier, Sylvie" uniqKey="Cloutier S" first="Sylvie" last="Cloutier">Sylvie Cloutier</name><affiliation><nlm:aff id="Aff4">Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6 Canada</nlm:aff><wicri:noCountry code="subfield">ON K1A 0C6 Canada</wicri:noCountry></affiliation></author><author><name sortKey="You, Frank M" sort="You, Frank M" uniqKey="You F" first="Frank M." last="You">Frank M. You</name><affiliation><nlm:aff id="Aff1">Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada</nlm:aff><wicri:noCountry code="subfield">MB R6M 1Y5 Canada</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential <italic>R</italic>-genes that contain specific conserved domains and motifs. Thus, RGAs can be predicted based on their conserved structural features using bioinformatics tools. Computer programs have been developed for the identification of individual domains and motifs from the protein sequences of RGAs but none offer a systematic assessment of the different types of RGAs. A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes.</p></sec><sec><title>Results</title><p>An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets.</p></sec><sec><title>Conclusions</title><p>RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: <ext-link ext-link-type="uri" xlink:href="https://bitbucket.org/yaanlpc/rgaugury">https://bitbucket.org/yaanlpc/rgaugury</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-3197-x) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gohre, V" uniqKey="Gohre V">V Gohre</name></author><author><name sortKey="Spallek, T" uniqKey="Spallek T">T Spallek</name></author><author><name sortKey="Haweker, H" uniqKey="Haweker H">H Haweker</name></author><author><name sortKey="Mersmann, S" uniqKey="Mersmann S">S Mersmann</name></author><author><name sortKey="Mentzel, T" uniqKey="Mentzel T">T Mentzel</name></author><author><name sortKey="Boller, T" uniqKey="Boller T">T Boller</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Q" uniqKey="Pan Q">Q Pan</name></author><author><name sortKey="Wendel, J" uniqKey="Wendel J">J Wendel</name></author><author><name sortKey="Fluhr, R" uniqKey="Fluhr R">R Fluhr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tarr, De" uniqKey="Tarr D">DE Tarr</name></author><author><name sortKey="Alexander, Hm" uniqKey="Alexander H">HM Alexander</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yue, Jx" uniqKey="Yue J">JX Yue</name></author><author><name sortKey="Meyers, Bc" uniqKey="Meyers B">BC Meyers</name></author><author><name sortKey="Chen, Jq" uniqKey="Chen J">JQ Chen</name></author><author><name sortKey="Tian, D" uniqKey="Tian D">D Tian</name></author><author><name sortKey="Yang, S" uniqKey="Yang S">S Yang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Cloutier, Sylvie" sort="Cloutier, Sylvie" uniqKey="Cloutier S" first="Sylvie" last="Cloutier">Sylvie Cloutier</name><name sortKey="Jia, Gaofeng" sort="Jia, Gaofeng" uniqKey="Jia G" first="Gaofeng" last="Jia">Gaofeng Jia</name><name sortKey="Li, Pingchuan" sort="Li, Pingchuan" uniqKey="Li P" first="Pingchuan" last="Li">Pingchuan Li</name><name sortKey="Quan, Xiande" sort="Quan, Xiande" uniqKey="Quan X" first="Xiande" last="Quan">Xiande Quan</name><name sortKey="You, Frank M" sort="You, Frank M" uniqKey="You F" first="Frank M." last="You">Frank M. You</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Xiao, Jin" sort="Xiao, Jin" uniqKey="Xiao J" first="Jin" last="Xiao">Jin Xiao</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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