A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
Identifieur interne : 000C22 ( Main/Exploration ); précédent : 000C21; suivant : 000C23A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
Auteurs : Johannes A. Hofberger [République populaire de Chine] ; Beifei Zhou [République populaire de Chine] ; Haibao Tang [États-Unis] ; Jonathan Dg Jones ; M Eric SchranzSource :
- BMC Genomics [ 1471-2164 ] ; 2014.
Abstract
Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.
To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363
By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional
The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2164-15-966
PubMed: 25380807
PubMed Central: 4289383
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants</title><author><name sortKey="Hofberger, Johannes A" sort="Hofberger, Johannes A" uniqKey="Hofberger J" first="Johannes A" last="Hofberger">Johannes A. Hofberger</name><affiliation><nlm:aff id="Aff8">Wageningen University & Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, Gelderland The Netherlands</nlm:aff><wicri:noCountry code="subfield">Gelderland The Netherlands</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff9">Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai, 200031 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Beifei" sort="Zhou, Beifei" uniqKey="Zhou B" first="Beifei" last="Zhou">Beifei Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff9">Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai, 200031 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation><affiliation><nlm:aff id="Aff10">Heidelberg Institute for Theoretical Studies-HITS, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Baden-Württemberg Germany</nlm:aff><wicri:noCountry code="subfield">Baden-Württemberg Germany</wicri:noCountry></affiliation></author><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name><affiliation><nlm:aff id="Aff11">Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian PR China</nlm:aff><wicri:noCountry code="subfield">Fujian PR China</wicri:noCountry></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff12">J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, CA 92037 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Jones, Jonathan Dg" sort="Jones, Jonathan Dg" uniqKey="Jones J" first="Jonathan Dg" last="Jones">Jonathan Dg Jones</name><affiliation><nlm:aff id="Aff13">The Sainsbury Laboratory, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UH UK</nlm:aff><wicri:noCountry code="subfield">NR4 7UH UK</wicri:noCountry></affiliation></author><author><name sortKey="Schranz, M Eric" sort="Schranz, M Eric" uniqKey="Schranz M" first="M Eric" last="Schranz">M Eric Schranz</name><affiliation><nlm:aff id="Aff8">Wageningen University & Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, Gelderland The Netherlands</nlm:aff><wicri:noCountry code="subfield">Gelderland The Netherlands</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25380807</idno><idno type="pmc">4289383</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289383</idno><idno type="RBID">PMC:4289383</idno><idno type="doi">10.1186/1471-2164-15-966</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000577</idno><idno type="wicri:Area/Pmc/Curation">000576</idno><idno type="wicri:Area/Pmc/Checkpoint">000926</idno><idno type="wicri:Area/Ncbi/Merge">001897</idno><idno type="wicri:Area/Ncbi/Curation">001897</idno><idno type="wicri:Area/Ncbi/Checkpoint">001897</idno><idno type="wicri:Area/Main/Merge">000C25</idno><idno type="wicri:Area/Main/Curation">000C22</idno><idno type="wicri:Area/Main/Exploration">000C22</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants</title><author><name sortKey="Hofberger, Johannes A" sort="Hofberger, Johannes A" uniqKey="Hofberger J" first="Johannes A" last="Hofberger">Johannes A. Hofberger</name><affiliation><nlm:aff id="Aff8">Wageningen University & Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, Gelderland The Netherlands</nlm:aff><wicri:noCountry code="subfield">Gelderland The Netherlands</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff9">Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai, 200031 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Zhou, Beifei" sort="Zhou, Beifei" uniqKey="Zhou B" first="Beifei" last="Zhou">Beifei Zhou</name><affiliation wicri:level="1"><nlm:aff id="Aff9">Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai, 200031 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Chinese Academy of Sciences/Max Planck Partner Institute for Computational Biology, 320 Yueyang Road, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation><affiliation><nlm:aff id="Aff10">Heidelberg Institute for Theoretical Studies-HITS, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Baden-Württemberg Germany</nlm:aff><wicri:noCountry code="subfield">Baden-Württemberg Germany</wicri:noCountry></affiliation></author><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name><affiliation><nlm:aff id="Aff11">Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian PR China</nlm:aff><wicri:noCountry code="subfield">Fujian PR China</wicri:noCountry></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff12">J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, CA 92037 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Jones, Jonathan Dg" sort="Jones, Jonathan Dg" uniqKey="Jones J" first="Jonathan Dg" last="Jones">Jonathan Dg Jones</name><affiliation><nlm:aff id="Aff13">The Sainsbury Laboratory, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UH UK</nlm:aff><wicri:noCountry code="subfield">NR4 7UH UK</wicri:noCountry></affiliation></author><author><name sortKey="Schranz, M Eric" sort="Schranz, M Eric" uniqKey="Schranz M" first="M Eric" last="Schranz">M Eric Schranz</name><affiliation><nlm:aff id="Aff8">Wageningen University & Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, Gelderland The Netherlands</nlm:aff><wicri:noCountry code="subfield">Gelderland The Netherlands</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.</p></sec><sec><title>Results</title><p>To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 <italic>NB-LRR</italic> genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 <italic>NB-LRR</italic> genes present in the model plant <italic>Arabidopsis</italic> and describe four distinct clusters of <italic>NB-LRR</italic> “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.</p></sec><sec><title>Conclusion</title><p>By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional <italic>NB-LRR</italic> genes from any plant species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jones, Jd" uniqKey="Jones J">JD Jones</name></author><author><name sortKey="Dangl, Jl" uniqKey="Dangl J">JL Dangl</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chinchilla, D" uniqKey="Chinchilla D">D Chinchilla</name></author><author><name sortKey="Bauer, Z" uniqKey="Bauer Z">Z Bauer</name></author><author><name sortKey="Regenass, M" uniqKey="Regenass M">M Regenass</name></author><author><name sortKey="Boller, T" uniqKey="Boller T">T Boller</name></author><author><name 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uniqKey="Li J">J Li</name></author><author><name sortKey="Zhao, X Q" uniqKey="Zhao X">X-Q Zhao</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Wong, Gk S" uniqKey="Wong G">GK-S Wong</name></author><author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krzywinski, M" uniqKey="Krzywinski M">M Krzywinski</name></author><author><name sortKey="Schein, J" uniqKey="Schein J">J Schein</name></author><author><name sortKey="Birol, I" uniqKey="Birol I">I Birol</name></author><author><name sortKey="Connors, J" uniqKey="Connors J">J Connors</name></author><author><name sortKey="Gascoyne, R" uniqKey="Gascoyne R">R Gascoyne</name></author><author><name sortKey="Horsman, D" uniqKey="Horsman D">D Horsman</name></author><author><name sortKey="Jones, Sj" uniqKey="Jones S">SJ Jones</name></author><author><name sortKey="Marra, Ma" uniqKey="Marra M">MA Marra</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><noCountry><name sortKey="Jones, Jonathan Dg" sort="Jones, Jonathan Dg" uniqKey="Jones J" first="Jonathan Dg" last="Jones">Jonathan Dg Jones</name><name sortKey="Schranz, M Eric" sort="Schranz, M Eric" uniqKey="Schranz M" first="M Eric" last="Schranz">M Eric Schranz</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Hofberger, Johannes A" sort="Hofberger, Johannes A" uniqKey="Hofberger J" first="Johannes A" last="Hofberger">Johannes A. Hofberger</name></noRegion><name sortKey="Zhou, Beifei" sort="Zhou, Beifei" uniqKey="Zhou B" first="Beifei" last="Zhou">Beifei Zhou</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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