Genomic Variability of Phytophthora palmivora Isolates from Different Oil Palm Cultivation Regions in Colombia.
Identifieur interne : 000175 ( Main/Exploration ); précédent : 000174; suivant : 000176Genomic Variability of Phytophthora palmivora Isolates from Different Oil Palm Cultivation Regions in Colombia.
Auteurs : Juanita Gil [Colombie] ; Mariana Herrera [Colombie] ; Jorge Duitama [Colombie] ; Greicy Sarria [Colombie] ; Silvia Restrepo [Colombie] ; Hernán Mauricio Romero [Colombie]Source :
- Phytopathology [ 0031-949X ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
- Wicri :
- geographic : Colombie.
English descriptors
- KwdEn :
- MESH :
- geographic : Colombia, South America.
- Genomics, Phytophthora, Plant Diseases.
Abstract
Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete Phytophthora palmivora, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for P. palmivora, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of P. palmivora with oil palm and could be further exploited as tools for the development of effective strategies for disease control.
DOI: 10.1094/PHYTO-06-19-0209-R
PubMed: 32314947
Affiliations:
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Romero</name><affiliation wicri:level="1"><nlm:affiliation>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá</wicri:regionArea><wicri:noRegion>Bogotá</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Universidad Nacional de Colombia, Carrera 45 No. 26-85, 111321, Bogotá, DC, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Department of Biology, Universidad Nacional de Colombia, Carrera 45 No. 26-85, 111321, Bogotá, DC</wicri:regionArea><wicri:noRegion>DC</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno 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xml:lang="fr">Colombie</country><wicri:regionArea>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá</wicri:regionArea><wicri:noRegion>Bogotá</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Systems and Computing Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Systems and Computing Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá</wicri:regionArea><wicri:noRegion>Bogotá</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Biological Sciences Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Biological Sciences Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, 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xml:lang="fr">Colombie</country><wicri:regionArea>Systems and Computing Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá</wicri:regionArea><wicri:noRegion>Bogotá</wicri:noRegion></affiliation></author><author><name sortKey="Sarria, Greicy" sort="Sarria, Greicy" uniqKey="Sarria G" first="Greicy" last="Sarria">Greicy Sarria</name><affiliation wicri:level="1"><nlm:affiliation>Pests and Diseases Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Pests and Diseases Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá</wicri:regionArea><wicri:noRegion>Bogotá</wicri:noRegion></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>Biological Sciences Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Biological Sciences Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá</wicri:regionArea><wicri:noRegion>Bogotá</wicri:noRegion></affiliation></author><author><name sortKey="Romero, Hernan Mauricio" sort="Romero, Hernan Mauricio" uniqKey="Romero H" first="Hernán Mauricio" last="Romero">Hernán Mauricio Romero</name><affiliation wicri:level="1"><nlm:affiliation>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá</wicri:regionArea><wicri:noRegion>Bogotá</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Universidad Nacional de Colombia, Carrera 45 No. 26-85, 111321, Bogotá, DC, Colombia.</nlm:affiliation><country xml:lang="fr">Colombie</country><wicri:regionArea>Department of Biology, Universidad Nacional de Colombia, Carrera 45 No. 26-85, 111321, Bogotá, DC</wicri:regionArea><wicri:noRegion>DC</wicri:noRegion></affiliation></author></analytic><series><title level="j">Phytopathology</title><idno type="ISSN">0031-949X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Colombia (MeSH)</term><term>Genomics (MeSH)</term><term>Phytophthora (MeSH)</term><term>Plant Diseases (MeSH)</term><term>South America (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amérique du Sud (MeSH)</term><term>Colombie (MeSH)</term><term>Génomique (MeSH)</term><term>Maladies des plantes (MeSH)</term><term>Phytophthora (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Colombia</term><term>South America</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genomics</term><term>Phytophthora</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Amérique du Sud</term><term>Colombie</term><term>Génomique</term><term>Maladies des plantes</term><term>Phytophthora</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Colombie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete <i>Phytophthora palmivora</i>, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for <i>P. palmivora</i>, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of <i>P. palmivora</i> with oil palm and could be further exploited as tools for the development of effective strategies for disease control.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">32314947</PMID><DateCompleted><Year>2020</Year><Month>09</Month><Day>03</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><Volume>110</Volume><Issue>9</Issue><PubDate><Year>2020</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Genomic Variability of <i>Phytophthora palmivora</i> Isolates from Different Oil Palm Cultivation Regions in Colombia.</ArticleTitle><Pagination><MedlinePgn>1553-1564</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-06-19-0209-R</ELocationID><Abstract><AbstractText>Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete <i>Phytophthora palmivora</i>, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for <i>P. palmivora</i>, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of <i>P. palmivora</i> with oil palm and could be further exploited as tools for the development of effective strategies for disease control.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gil</LastName><ForeName>Juanita</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá, Colombia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Systems and Computing Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Biological Sciences Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Herrera</LastName><ForeName>Mariana</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Duitama</LastName><ForeName>Jorge</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Systems and Computing Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sarria</LastName><ForeName>Greicy</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Pests and Diseases Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Restrepo</LastName><ForeName>Silvia</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9016-1040</Identifier><AffiliationInfo><Affiliation>Biological Sciences Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Romero</LastName><ForeName>Hernán Mauricio</ForeName><Initials>HM</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-0760-2296</Identifier><AffiliationInfo><Affiliation>Biology and Breeding Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, 111121, Bogotá, Colombia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biology, Universidad Nacional de Colombia, Carrera 45 No. 26-85, 111321, Bogotá, DC, Colombia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phytopathology</MedlineTA><NlmUniqueID>9427222</NlmUniqueID><ISSNLinking>0031-949X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D003105" MajorTopicYN="N" Type="Geographic">Colombia</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="Y">Phytophthora</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013020" MajorTopicYN="N" Type="Geographic">South America</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">allelic variants</Keyword><Keyword MajorTopicYN="N">genetics and resistance</Keyword><Keyword MajorTopicYN="N">genome assembly</Keyword><Keyword MajorTopicYN="N">mycology</Keyword><Keyword MajorTopicYN="N">techniques</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32314947</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-06-19-0209-R</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Colombie</li></country></list><tree><country name="Colombie"><noRegion><name sortKey="Gil, Juanita" sort="Gil, Juanita" uniqKey="Gil J" first="Juanita" last="Gil">Juanita Gil</name></noRegion><name sortKey="Duitama, Jorge" sort="Duitama, Jorge" uniqKey="Duitama J" first="Jorge" last="Duitama">Jorge Duitama</name><name sortKey="Gil, Juanita" sort="Gil, Juanita" uniqKey="Gil J" first="Juanita" last="Gil">Juanita Gil</name><name sortKey="Gil, Juanita" sort="Gil, Juanita" uniqKey="Gil J" first="Juanita" last="Gil">Juanita Gil</name><name sortKey="Herrera, Mariana" sort="Herrera, Mariana" uniqKey="Herrera M" first="Mariana" last="Herrera">Mariana Herrera</name><name sortKey="Restrepo, Silvia" sort="Restrepo, Silvia" uniqKey="Restrepo S" first="Silvia" last="Restrepo">Silvia Restrepo</name><name sortKey="Romero, Hernan Mauricio" sort="Romero, Hernan Mauricio" uniqKey="Romero H" first="Hernán Mauricio" last="Romero">Hernán Mauricio Romero</name><name sortKey="Romero, Hernan Mauricio" sort="Romero, Hernan Mauricio" uniqKey="Romero H" first="Hernán Mauricio" last="Romero">Hernán Mauricio Romero</name><name sortKey="Sarria, Greicy" sort="Sarria, Greicy" uniqKey="Sarria G" first="Greicy" last="Sarria">Greicy Sarria</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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