Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.
Identifieur interne : 000099 ( Main/Curation ); précédent : 000098; suivant : 000100Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.
Auteurs : Marco A. Cristancho [Colombie] ; David Octavio Botero-Rozo [Colombie] ; William Giraldo [Colombie] ; Javier Tabima [Colombie] ; Diego Mauricio Ria O-Pach N [Colombie] ; Carolina Escobar [Colombie] ; Yomara Rozo [Colombie] ; Luis F. Rivera [Colombie] ; Andrés Durán [Colombie] ; Silvia Restrepo [Colombie] ; Tamar Eilam [Israël] ; Yehoshua Anikster [Israël] ; Alvaro L. Gaitán [Colombie]Source :
- Frontiers in plant science [ 1664-462X ] ; 2014.
Abstract
Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.
DOI: 10.3389/fpls.2014.00594
PubMed: 25400655
PubMed Central: PMC4215621
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Cristancho</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná</wicri:regionArea></affiliation></author><author><name sortKey="Botero Rozo, David Octavio" sort="Botero Rozo, David Octavio" uniqKey="Botero Rozo D" first="David Octavio" last="Botero-Rozo">David Octavio Botero-Rozo</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá</wicri:regionArea></affiliation></author><author><name sortKey="Giraldo, William" sort="Giraldo, William" uniqKey="Giraldo W" first="William" last="Giraldo">William Giraldo</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná</wicri:regionArea></affiliation></author><author><name sortKey="Tabima, Javier" sort="Tabima, Javier" uniqKey="Tabima J" first="Javier" last="Tabima">Javier Tabima</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá</wicri:regionArea></affiliation></author><author><name sortKey="Ria O Pach N, Diego Mauricio" sort="Ria O Pach N, Diego Mauricio" uniqKey="Ria O Pach N D" first="Diego Mauricio" last="Ria O-Pach N">Diego Mauricio Ria O-Pach N</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá</wicri:regionArea></affiliation></author><author><name sortKey="Escobar, Carolina" sort="Escobar, Carolina" uniqKey="Escobar C" first="Carolina" last="Escobar">Carolina Escobar</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná</wicri:regionArea></affiliation></author><author><name sortKey="Rozo, Yomara" sort="Rozo, Yomara" uniqKey="Rozo Y" first="Yomara" last="Rozo">Yomara Rozo</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná</wicri:regionArea></affiliation></author><author><name sortKey="Rivera, Luis F" sort="Rivera, Luis F" uniqKey="Rivera L" first="Luis F" last="Rivera">Luis F. Rivera</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná</wicri:regionArea></affiliation></author><author><name sortKey="Duran, Andres" sort="Duran, Andres" uniqKey="Duran A" first="Andrés" last="Durán">Andrés Durán</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná</wicri:regionArea></affiliation></author><author><name sortKey="Restrepo, Silvia" sort="Restrepo, Silvia" uniqKey="Restrepo S" first="Silvia" last="Restrepo">Silvia Restrepo</name><affiliation wicri:level="1"><nlm:affiliation>Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá</wicri:regionArea></affiliation></author><author><name sortKey="Eilam, Tamar" sort="Eilam, Tamar" uniqKey="Eilam T" first="Tamar" last="Eilam">Tamar Eilam</name><affiliation wicri:level="1"><nlm:affiliation>Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv, Israel.</nlm:affiliation><country xml:lang="fr">Israël</country><wicri:regionArea>Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv</wicri:regionArea></affiliation></author><author><name sortKey="Anikster, Yehoshua" sort="Anikster, Yehoshua" uniqKey="Anikster Y" first="Yehoshua" last="Anikster">Yehoshua Anikster</name><affiliation wicri:level="1"><nlm:affiliation>Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv, Israel.</nlm:affiliation><country xml:lang="fr">Israël</country><wicri:regionArea>Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv</wicri:regionArea></affiliation></author><author><name sortKey="Gaitan, Alvaro L" sort="Gaitan, Alvaro L" uniqKey="Gaitan A" first="Alvaro L" last="Gaitán">Alvaro L. Gaitán</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25400655</PMID><DateCompleted><Year>2014</Year><Month>11</Month><Day>17</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.</ArticleTitle><Pagination><MedlinePgn>594</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2014.00594</ELocationID><Abstract><AbstractText>Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cristancho</LastName><ForeName>Marco A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Botero-Rozo</LastName><ForeName>David Octavio</ForeName><Initials>DO</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giraldo</LastName><ForeName>William</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tabima</LastName><ForeName>Javier</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Riaño-Pachón</LastName><ForeName>Diego Mauricio</ForeName><Initials>DM</Initials><AffiliationInfo><Affiliation>Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Escobar</LastName><ForeName>Carolina</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rozo</LastName><ForeName>Yomara</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rivera</LastName><ForeName>Luis F</ForeName><Initials>LF</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Durán</LastName><ForeName>Andrés</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Restrepo</LastName><ForeName>Silvia</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eilam</LastName><ForeName>Tamar</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv, Israel.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Anikster</LastName><ForeName>Yehoshua</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv, Israel.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gaitán</LastName><ForeName>Alvaro L</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>10</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">RNA-seq</Keyword><Keyword MajorTopicYN="N">coffee</Keyword><Keyword MajorTopicYN="N">coffee rust</Keyword><Keyword MajorTopicYN="N">genetic variants</Keyword><Keyword MajorTopicYN="N">genome</Keyword><Keyword MajorTopicYN="N">plant pathogens diversity</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>05</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>10</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25400655</ArticleId><ArticleId IdType="doi">10.3389/fpls.2014.00594</ArticleId><ArticleId IdType="pmc">PMC4215621</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Cytometry A. 2003 Feb;51(2):127-8; author reply 129</Citation><ArticleIdList><ArticleId IdType="pubmed">12541287</ArticleId></ArticleIdList></Reference><Reference><Citation>Phytopathology. 2009 Dec;99(12):1355-64</Citation><ArticleIdList><ArticleId IdType="pubmed">19900001</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycologia. 2005 Mar-Apr;97(2):396-404</Citation><ArticleIdList><ArticleId IdType="pubmed">16396347</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2011 Sep;21(9):1552-60</Citation><ArticleIdList><ArticleId IdType="pubmed">21690186</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bioinform Comput Biol. 2006 Feb;4(1):1-18</Citation><ArticleIdList><ArticleId IdType="pubmed">16568539</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2010 Dec 10;330(6010):1546-8</Citation><ArticleIdList><ArticleId IdType="pubmed">21148393</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(1):e29847</Citation><ArticleIdList><ArticleId IdType="pubmed">22238666</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Microbiol. 2012 May 08;10(6):417-30</Citation><ArticleIdList><ArticleId IdType="pubmed">22565130</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20117-22</Citation><ArticleIdList><ArticleId IdType="pubmed">24277808</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Plant Sci. 2012 Aug;17(8):448-57</Citation><ArticleIdList><ArticleId IdType="pubmed">22613788</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011;6(11):e26387</Citation><ArticleIdList><ArticleId IdType="pubmed">22102860</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2004 Feb 18;32(3):e37</Citation><ArticleIdList><ArticleId IdType="pubmed">14973331</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2011 Sep 07;12(10):671-82</Citation><ArticleIdList><ArticleId IdType="pubmed">21897427</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2006 Jan;18(1):243-56</Citation><ArticleIdList><ArticleId IdType="pubmed">16326930</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2003 Sep;13(9):2178-89</Citation><ArticleIdList><ArticleId IdType="pubmed">12952885</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 May 1;25(9):1105-11</Citation><ArticleIdList><ArticleId IdType="pubmed">19289445</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2003 Feb;13(2):182-94</Citation><ArticleIdList><ArticleId IdType="pubmed">12566396</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Mar 15;27(6):764-70</Citation><ArticleIdList><ArticleId IdType="pubmed">21217122</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Aug 26;5:422</Citation><ArticleIdList><ArticleId IdType="pubmed">25206357</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycologia. 2010 Jul-Aug;102(4):887-97</Citation><ArticleIdList><ArticleId IdType="pubmed">20648755</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011 Mar 24;12:161</Citation><ArticleIdList><ArticleId IdType="pubmed">21435244</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Pathol. 2013 Jan;14(1):96-107</Citation><ArticleIdList><ArticleId IdType="pubmed">22998218</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2011 Sep 29;8(10):785-6</Citation><ArticleIdList><ArticleId IdType="pubmed">21959131</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2011 May 15;29(7):644-52</Citation><ArticleIdList><ArticleId IdType="pubmed">21572440</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Phytopathol. 2012;50:91-109</Citation><ArticleIdList><ArticleId IdType="pubmed">22559067</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Microbe Interact. 2012 Mar;25(3):279-93</Citation><ArticleIdList><ArticleId IdType="pubmed">22046958</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2013 Jan 31;493(7434):587</Citation><ArticleIdList><ArticleId IdType="pubmed">23364717</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2010 Jul 08;11:422</Citation><ArticleIdList><ArticleId IdType="pubmed">20615251</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2010 Oct 15;26(20):2620-1</Citation><ArticleIdList><ArticleId IdType="pubmed">20736339</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 1990 Oct 5;215(3):403-10</Citation><ArticleIdList><ArticleId IdType="pubmed">2231712</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013 Apr 22;14:270</Citation><ArticleIdList><ArticleId IdType="pubmed">23607900</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25</Citation><ArticleIdList><ArticleId IdType="pubmed">14534192</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Pathol. 2012 Jan;13(1):17-37</Citation><ArticleIdList><ArticleId IdType="pubmed">21726390</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2007 May 1;23(9):1061-7</Citation><ArticleIdList><ArticleId IdType="pubmed">17332020</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Comput Biol. 2011 Oct;7(10):e1002195</Citation><ArticleIdList><ArticleId IdType="pubmed">22039361</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011;6(8):e24230</Citation><ArticleIdList><ArticleId IdType="pubmed">21909385</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2011 May 31;108(22):9166-71</Citation><ArticleIdList><ArticleId IdType="pubmed">21536894</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11889-94</Citation><ArticleIdList><ArticleId IdType="pubmed">20547848</ArticleId></ArticleIdList></Reference><Reference><Citation>Funct Integr Genomics. 2011 Dec;11(4):671-7</Citation><ArticleIdList><ArticleId IdType="pubmed">21809124</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2010 Apr 15;464(7291):1033-8</Citation><ArticleIdList><ArticleId IdType="pubmed">20348908</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2014 Apr;202(2):554-64</Citation><ArticleIdList><ArticleId IdType="pubmed">24372469</ArticleId></ArticleIdList></Reference><Reference><Citation>Proteins. 2007 Sep 1;68(4):893-914</Citation><ArticleIdList><ArticleId IdType="pubmed">17557329</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011;6(11):e27217</Citation><ArticleIdList><ArticleId IdType="pubmed">22076138</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2008 Mar 6;452(7183):88-92</Citation><ArticleIdList><ArticleId IdType="pubmed">18322534</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genet. 2014 Apr 11;15:45</Citation><ArticleIdList><ArticleId IdType="pubmed">24725999</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2004 Jul;14(7):1394-403</Citation><ArticleIdList><ArticleId IdType="pubmed">15231754</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycologia. 2006 Nov-Dec;98(6):896-905</Citation><ArticleIdList><ArticleId IdType="pubmed">17486966</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Mar 24;5:98</Citation><ArticleIdList><ArticleId IdType="pubmed">24715894</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2014 Mar 14;5:88</Citation><ArticleIdList><ArticleId IdType="pubmed">24672531</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2010 Dec 10;330(6010):1543-6</Citation><ArticleIdList><ArticleId IdType="pubmed">21148392</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Commun. 2013;4:2673</Citation><ArticleIdList><ArticleId 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