Effector Repertoire of Phytophthora betacei: In Search of Possible Virulence Factors Responsible for Its Host Specificity.
Identifieur interne : 000178 ( Main/Exploration ); précédent : 000177; suivant : 000179Effector Repertoire of Phytophthora betacei: In Search of Possible Virulence Factors Responsible for Its Host Specificity.
Auteurs : Paola Rojas-Estevez ; David A. Urbina-G Mez ; David A. Ayala-Usma ; Natalia Guayazan-Palacios ; Maria Fernanda Mideros ; Adriana J. Bernal ; Martha Cardenas ; Silvia RestrepoSource :
- Frontiers in genetics [ 1664-8021 ] ; 2020.
Abstract
Phytophthora betacei is an oomycete plant pathogen closely related to Phytophthora infestans. It infects tree tomato (Solanum betaceum) in northern South America, but is, under natural conditions, unable to infect potatoes or tomatoes, the main hosts of its sister species P. infestans. We characterized, and compared the effector repertoires of P. betacei and other Phytophthora species. To this end, we used in silico approaches to predict and describe the repertoire of secreted proteins in Phytophthora species and determine unique and core effectors. P. betacei has the largest proteome and secretome of all Phytophthora species evaluated. We identified between 450 and 1933 candidate effector genes in Phytophthora ramorum, Phytophthora sojae, Phytophthora cactorum, Phytophthora parasitica, Phytophthora palmivora, P. infestans, and P. betacei genomes. The P. betacei predicted secretome contains 5653 proteins, 1126 of which are apoplastic effectors and 807cytoplasmic effectors. Genes encoding cytoplasmic effectors include 791 genes with an RxLR domain (the largest number known so far in a Phytophthora species) and 16 with a Crinkler (CRN) domain. We detected homologs of previously described avirulence gene (Avr) present in Phytophthora spp., such as Avr1, Avr3b, Avr4, and Avrblb1, suggesting a high level of effector gene conservation among Phytophthora species. Nonetheless, fewer CRN effectors were obtained in P. betacei compared to all other Phytophthora species analyzed. The comparison between P. infestans and P. betacei effector profiles shows unique features in P. betacei that might be involved in pathogenesis and host preference. Indeed, 402 unique predicted effector genes were detected in P. betacei, corresponding to 197 apoplastic effector genes, 203 RxLR cytoplasmic effector genes, and 2 effector genes with CRN domain. This is the first characterization of the effector profile of P. betacei and the broadest comparison of predicted effector repertoires in the genus Phytophthora following a standardized prediction pipeline. The resultant P. betacei putative effector repertoire provides a reasonable set of proteins whose experimental validation could lead to understand the specific virulence factors responsible for the host specificity of this species.
DOI: 10.3389/fgene.2020.00579
PubMed: 32582295
PubMed Central: PMC7295944
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Effector Repertoire of <i>Phytophthora betacei</i>: In Search of Possible Virulence Factors Responsible for Its Host Specificity.</title><author><name sortKey="Rojas Estevez, Paola" sort="Rojas Estevez, Paola" uniqKey="Rojas Estevez P" first="Paola" last="Rojas-Estevez">Paola Rojas-Estevez</name><affiliation><nlm:affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author><author><name sortKey="Urbina G Mez, David A" sort="Urbina G Mez, David A" uniqKey="Urbina G Mez D" first="David A" last="Urbina-G Mez">David A. 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Urbina-G Mez</name><affiliation><nlm:affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author><author><name sortKey="Ayala Usma, David A" sort="Ayala Usma, David A" uniqKey="Ayala Usma D" first="David A" last="Ayala-Usma">David A. Ayala-Usma</name><affiliation><nlm:affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Laboratorio de Biología Computacional y Ecología Microbiana, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author><author><name sortKey="Guayazan Palacios, Natalia" sort="Guayazan Palacios, Natalia" uniqKey="Guayazan Palacios N" first="Natalia" last="Guayazan-Palacios">Natalia Guayazan-Palacios</name><affiliation><nlm:affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author><author><name sortKey="Mideros, Maria Fernanda" sort="Mideros, Maria Fernanda" uniqKey="Mideros M" first="Maria Fernanda" last="Mideros">Maria Fernanda Mideros</name><affiliation><nlm:affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author><author><name sortKey="Bernal, Adriana J" sort="Bernal, Adriana J" uniqKey="Bernal A" first="Adriana J" last="Bernal">Adriana J. Bernal</name><affiliation><nlm:affiliation>Laboratorio de Interacciones Moleculares de Microorganismos en Agricultura, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author><author><name sortKey="Cardenas, Martha" sort="Cardenas, Martha" uniqKey="Cardenas M" first="Martha" last="Cardenas">Martha Cardenas</name><affiliation><nlm:affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author><author><name sortKey="Restrepo, Silvia" sort="Restrepo, Silvia" uniqKey="Restrepo S" first="Silvia" last="Restrepo">Silvia Restrepo</name><affiliation><nlm:affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</nlm:affiliation><wicri:noCountry code="subField">Bogota</wicri:noCountry></affiliation></author></analytic><series><title level="j">Frontiers in genetics</title><idno type="ISSN">1664-8021</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Phytophthora betacei</i> is an oomycete plant pathogen closely related to <i>Phytophthora infestans.</i> It infects tree tomato (<i>Solanum betaceum</i>) in northern South America, but is, under natural conditions, unable to infect potatoes or tomatoes, the main hosts of its sister species <i>P. infestans</i>. We characterized, and compared the effector repertoires of <i>P. betacei</i> and other <i>Phytophthora</i> species. To this end, we used <i>in silico</i> approaches to predict and describe the repertoire of secreted proteins in <i>Phytophthora</i> species and determine unique and core effectors. <i>P. betacei</i> has the largest proteome and secretome of all <i>Phytophthora</i> species evaluated. We identified between 450 and 1933 candidate effector genes in <i>Phytophthora ramorum, Phytophthora sojae, Phytophthora cactorum, Phytophthora parasitica, Phytophthora palmivora, P. infestans</i>, and <i>P. betacei</i> genomes. The <i>P. betacei</i> predicted secretome contains 5653 proteins, 1126 of which are apoplastic effectors and 807cytoplasmic effectors. Genes encoding cytoplasmic effectors include 791 genes with an RxLR domain (the largest number known so far in a <i>Phytophthora</i> species) and 16 with a Crinkler (CRN) domain. We detected homologs of previously described avirulence gene (Avr) present in <i>Phytophthora</i> spp., such as Avr1, Avr3b, Avr4, and Avrblb1, suggesting a high level of effector gene conservation among <i>Phytophthora</i> species. Nonetheless, fewer CRN effectors were obtained in <i>P. betacei</i> compared to all other <i>Phytophthora</i> species analyzed. The comparison between <i>P. infestans</i> and <i>P. betacei</i> effector profiles shows unique features in <i>P. betacei</i> that might be involved in pathogenesis and host preference. Indeed, 402 unique predicted effector genes were detected in <i>P. betacei</i>, corresponding to 197 apoplastic effector genes, 203 RxLR cytoplasmic effector genes, and 2 effector genes with CRN domain. This is the first characterization of the effector profile of <i>P. betacei</i> and the broadest comparison of predicted effector repertoires in the genus <i>Phytophthora</i> following a standardized prediction pipeline. The resultant <i>P. betacei</i> putative effector repertoire provides a reasonable set of proteins whose experimental validation could lead to understand the specific virulence factors responsible for the host specificity of this species.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32582295</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-8021</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in genetics</Title><ISOAbbreviation>Front Genet</ISOAbbreviation></Journal><ArticleTitle>Effector Repertoire of <i>Phytophthora betacei</i>: In Search of Possible Virulence Factors Responsible for Its Host Specificity.</ArticleTitle><Pagination><MedlinePgn>579</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fgene.2020.00579</ELocationID><Abstract><AbstractText><i>Phytophthora betacei</i> is an oomycete plant pathogen closely related to <i>Phytophthora infestans.</i> It infects tree tomato (<i>Solanum betaceum</i>) in northern South America, but is, under natural conditions, unable to infect potatoes or tomatoes, the main hosts of its sister species <i>P. infestans</i>. We characterized, and compared the effector repertoires of <i>P. betacei</i> and other <i>Phytophthora</i> species. To this end, we used <i>in silico</i> approaches to predict and describe the repertoire of secreted proteins in <i>Phytophthora</i> species and determine unique and core effectors. <i>P. betacei</i> has the largest proteome and secretome of all <i>Phytophthora</i> species evaluated. We identified between 450 and 1933 candidate effector genes in <i>Phytophthora ramorum, Phytophthora sojae, Phytophthora cactorum, Phytophthora parasitica, Phytophthora palmivora, P. infestans</i>, and <i>P. betacei</i> genomes. The <i>P. betacei</i> predicted secretome contains 5653 proteins, 1126 of which are apoplastic effectors and 807cytoplasmic effectors. Genes encoding cytoplasmic effectors include 791 genes with an RxLR domain (the largest number known so far in a <i>Phytophthora</i> species) and 16 with a Crinkler (CRN) domain. We detected homologs of previously described avirulence gene (Avr) present in <i>Phytophthora</i> spp., such as Avr1, Avr3b, Avr4, and Avrblb1, suggesting a high level of effector gene conservation among <i>Phytophthora</i> species. Nonetheless, fewer CRN effectors were obtained in <i>P. betacei</i> compared to all other <i>Phytophthora</i> species analyzed. The comparison between <i>P. infestans</i> and <i>P. betacei</i> effector profiles shows unique features in <i>P. betacei</i> that might be involved in pathogenesis and host preference. Indeed, 402 unique predicted effector genes were detected in <i>P. betacei</i>, corresponding to 197 apoplastic effector genes, 203 RxLR cytoplasmic effector genes, and 2 effector genes with CRN domain. This is the first characterization of the effector profile of <i>P. betacei</i> and the broadest comparison of predicted effector repertoires in the genus <i>Phytophthora</i> following a standardized prediction pipeline. The resultant <i>P. betacei</i> putative effector repertoire provides a reasonable set of proteins whose experimental validation could lead to understand the specific virulence factors responsible for the host specificity of this species.</AbstractText><CopyrightInformation>Copyright © 2020 Rojas-Estevez, Urbina-Gómez, Ayala-Usma, Guayazan-Palacios, Mideros, Bernal, Cardenas and Restrepo.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rojas-Estevez</LastName><ForeName>Paola</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Urbina-Gómez</LastName><ForeName>David A</ForeName><Initials>DA</Initials><AffiliationInfo><Affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ayala-Usma</LastName><ForeName>David A</ForeName><Initials>DA</Initials><AffiliationInfo><Affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Laboratorio de Biología Computacional y Ecología Microbiana, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guayazan-Palacios</LastName><ForeName>Natalia</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mideros</LastName><ForeName>Maria Fernanda</ForeName><Initials>MF</Initials><AffiliationInfo><Affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bernal</LastName><ForeName>Adriana J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Laboratorio de Interacciones Moleculares de Microorganismos en Agricultura, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cardenas</LastName><ForeName>Martha</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Restrepo</LastName><ForeName>Silvia</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Genet</MedlineTA><NlmUniqueID>101560621</NlmUniqueID><ISSNLinking>1664-8021</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora betacei</Keyword><Keyword MajorTopicYN="N">comparative genomics</Keyword><Keyword MajorTopicYN="N">effector genes</Keyword><Keyword MajorTopicYN="N">host specificity</Keyword><Keyword MajorTopicYN="N">oomycetes</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>05</Month><Day>11</Day></PubMedPubDate><PubMedPubDate 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Ayala-Usma</name><name sortKey="Bernal, Adriana J" sort="Bernal, Adriana J" uniqKey="Bernal A" first="Adriana J" last="Bernal">Adriana J. Bernal</name><name sortKey="Cardenas, Martha" sort="Cardenas, Martha" uniqKey="Cardenas M" first="Martha" last="Cardenas">Martha Cardenas</name><name sortKey="Guayazan Palacios, Natalia" sort="Guayazan Palacios, Natalia" uniqKey="Guayazan Palacios N" first="Natalia" last="Guayazan-Palacios">Natalia Guayazan-Palacios</name><name sortKey="Mideros, Maria Fernanda" sort="Mideros, Maria Fernanda" uniqKey="Mideros M" first="Maria Fernanda" last="Mideros">Maria Fernanda Mideros</name><name sortKey="Restrepo, Silvia" sort="Restrepo, Silvia" uniqKey="Restrepo S" first="Silvia" last="Restrepo">Silvia Restrepo</name><name sortKey="Rojas Estevez, Paola" sort="Rojas Estevez, Paola" uniqKey="Rojas Estevez P" first="Paola" last="Rojas-Estevez">Paola Rojas-Estevez</name><name sortKey="Urbina G Mez, David A" sort="Urbina G Mez, David A" uniqKey="Urbina G Mez D" first="David A" last="Urbina-G Mez">David A. 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