Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies.
Identifieur interne : 000302 ( Main/Exploration ); précédent : 000301; suivant : 000303Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies.
Auteurs : Ramadan A. Arafa [Égypte, Japon] ; Said M. Kamel [Égypte] ; Mohamed T. Rakha [Égypte] ; Nour Elden K. Soliman [Égypte] ; Olfat M. Moussa [Égypte] ; Kenta Shirasawa [Japon]Source :
- PloS one [ 1932-6203 ] ; 2020.
Descripteurs français
- KwdFr :
- ADN mitochondrial (génétique), Analyse de séquence d'ADN (MeSH), Fongicides industriels (pharmacologie), Gènes fongiques du type conjugant (génétique), Génotype (MeSH), Lycopersicon esculentum (microbiologie), Maladies des plantes (génétique), Maladies des plantes (microbiologie), Phytophthora infestans (croissance et développement), Phytophthora infestans (génétique), Répétitions microsatellites (génétique), Solanum tuberosum (microbiologie), Séquençage nucléotidique à haut débit (MeSH).
- MESH :
- croissance et développement : Phytophthora infestans.
- génétique : ADN mitochondrial, Gènes fongiques du type conjugant, Maladies des plantes, Phytophthora infestans, Répétitions microsatellites.
- microbiologie : Lycopersicon esculentum, Maladies des plantes, Solanum tuberosum.
- pharmacologie : Fongicides industriels.
- Analyse de séquence d'ADN, Génotype, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- DNA, Mitochondrial (genetics), Fungicides, Industrial (pharmacology), Genes, Mating Type, Fungal (genetics), Genotype (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Lycopersicon esculentum (microbiology), Microsatellite Repeats (genetics), Phytophthora infestans (genetics), Phytophthora infestans (growth & development), Plant Diseases (genetics), Plant Diseases (microbiology), Sequence Analysis, DNA (MeSH), Solanum tuberosum (microbiology).
- MESH :
- chemical , genetics : DNA, Mitochondrial.
- chemical , pharmacology : Fungicides, Industrial.
- genetics : Genes, Mating Type, Fungal, Microsatellite Repeats, Phytophthora infestans, Plant Diseases.
- growth & development : Phytophthora infestans.
- microbiology : Lycopersicon esculentum, Plant Diseases, Solanum tuberosum.
- Genotype, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
Abstract
Phytophthora infestans (Mont.) de Bary, a hemibiotrophic oomycete, has caused severe epidemics of late blight in tomato and potato crops around the world since the Irish Potato Famine in the 1840s. Breeding of late blight resistant cultivars is one of the most effective strategies to overcome this disruptive disease. However, P. infestans is able to break down host resistance and acquire resistance to various fungicides, possibly because of the existence of high genetic variability among P. infestans isolates via sexual and asexual reproduction. Therefore, to manage this disease, it is important to understand the genetic divergence of P. infestans isolates. In this study, we analyzed the genomes of P. infestans isolates collected from Egypt and Japan using various molecular approaches including the mating type assay and genotyping simple sequence repeats, mitochondria DNA, and effector genes. We also analyzed genome-wide single nucleotide polymorphisms using double-digest restriction-site associated DNA sequencing and whole genome resequencing (WGRS). The isolates were classified adequately using high-resolution genome-wide approaches. Moreover, these analyses revealed new clusters of P. infestans isolates in the Egyptian population. Monitoring the genetic divergence of P. infestans isolates as well as breeding of resistant cultivars would facilitate the elimination of the late blight disease.
DOI: 10.1371/journal.pone.0221604
PubMed: 31961875
PubMed Central: PMC6974037
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Breeding of late blight resistant cultivars is one of the most effective strategies to overcome this disruptive disease. However, P. infestans is able to break down host resistance and acquire resistance to various fungicides, possibly because of the existence of high genetic variability among P. infestans isolates via sexual and asexual reproduction. Therefore, to manage this disease, it is important to understand the genetic divergence of P. infestans isolates. In this study, we analyzed the genomes of P. infestans isolates collected from Egypt and Japan using various molecular approaches including the mating type assay and genotyping simple sequence repeats, mitochondria DNA, and effector genes. We also analyzed genome-wide single nucleotide polymorphisms using double-digest restriction-site associated DNA sequencing and whole genome resequencing (WGRS). The isolates were classified adequately using high-resolution genome-wide approaches. Moreover, these analyses revealed new clusters of P. infestans isolates in the Egyptian population. Monitoring the genetic divergence of P. infestans isolates as well as breeding of resistant cultivars would facilitate the elimination of the late blight disease.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31961875</PMID><DateCompleted><Year>2020</Year><Month>04</Month><Day>01</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>01</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>1</Issue><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Analysis of the lineage of Phytophthora infestans isolates using mating type assay, traditional markers, and next generation sequencing technologies.</ArticleTitle><Pagination><MedlinePgn>e0221604</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0221604</ELocationID><Abstract><AbstractText>Phytophthora infestans (Mont.) de Bary, a hemibiotrophic oomycete, has caused severe epidemics of late blight in tomato and potato crops around the world since the Irish Potato Famine in the 1840s. Breeding of late blight resistant cultivars is one of the most effective strategies to overcome this disruptive disease. However, P. infestans is able to break down host resistance and acquire resistance to various fungicides, possibly because of the existence of high genetic variability among P. infestans isolates via sexual and asexual reproduction. Therefore, to manage this disease, it is important to understand the genetic divergence of P. infestans isolates. In this study, we analyzed the genomes of P. infestans isolates collected from Egypt and Japan using various molecular approaches including the mating type assay and genotyping simple sequence repeats, mitochondria DNA, and effector genes. We also analyzed genome-wide single nucleotide polymorphisms using double-digest restriction-site associated DNA sequencing and whole genome resequencing (WGRS). The isolates were classified adequately using high-resolution genome-wide approaches. Moreover, these analyses revealed new clusters of P. infestans isolates in the Egyptian population. Monitoring the genetic divergence of P. infestans isolates as well as breeding of resistant cultivars would facilitate the elimination of the late blight disease.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Arafa</LastName><ForeName>Ramadan A</ForeName><Initials>RA</Initials><AffiliationInfo><Affiliation>Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kamel</LastName><ForeName>Said M</ForeName><Initials>SM</Initials><AffiliationInfo><Affiliation>Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rakha</LastName><ForeName>Mohamed T</ForeName><Initials>MT</Initials><AffiliationInfo><Affiliation>Department of Horticulture, Faculty of Agriculture, University of Kafrelsheikh, Kafr El-Sheikh, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Soliman</LastName><ForeName>Nour Elden K</ForeName><Initials>NEK</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Moussa</LastName><ForeName>Olfat M</ForeName><Initials>OM</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shirasawa</LastName><ForeName>Kenta</ForeName><Initials>K</Initials><Identifier Source="ORCID">0000-0001-7880-6221</Identifier><AffiliationInfo><Affiliation>Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>01</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004272">DNA, Mitochondrial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005659">Fungicides, Industrial</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004272" MajorTopicYN="N">DNA, Mitochondrial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005659" MajorTopicYN="N">Fungicides, Industrial</DescriptorName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D049770" MajorTopicYN="N">Genes, Mating Type, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="Y">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018551" MajorTopicYN="N">Lycopersicon esculentum</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011198" MajorTopicYN="N">Solanum tuberosum</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>08</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>12</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>1</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>1</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31961875</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0221604</ArticleId><ArticleId IdType="pii">PONE-D-19-22233</ArticleId><ArticleId IdType="pmc">PMC6974037</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Fungal Biol. 2017 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