Draft Genome Resource for the Ex-types of Phytophthora ramorum, P. kernoviae, and P. melonis, Species of Regulatory Concern, Using Ultra-Long Read MinION Nanopore Sequencing.
Identifieur interne : 000236 ( Main/Exploration ); précédent : 000235; suivant : 000237Draft Genome Resource for the Ex-types of Phytophthora ramorum, P. kernoviae, and P. melonis, Species of Regulatory Concern, Using Ultra-Long Read MinION Nanopore Sequencing.
Auteurs : Subodh K. Srivastava [États-Unis] ; Z Gloria Abad [États-Unis] ; Leandra M. Knight [États-Unis] ; Kurt Zeller [États-Unis] ; Vessela Mavrodieva [États-Unis] ; Mark Nakhla [États-Unis]Source :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phytophthora.
- parasitologie : Maladies des plantes.
- Cartographie de contigs, Génome, Polymorphisme de nucléotide simple, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- MESH :
- genetics : Phytophthora.
- parasitology : Plant Diseases.
- Contig Mapping, Genome, High-Throughput Nucleotide Sequencing, Nanopore Sequencing, Polymorphism, Single Nucleotide.
Abstract
Phytophthora ramorum, P. kernoviae, and P. melonis are each species of current regulatory concern in the United States, the United Kingdom, and other areas of the world. Ex-type material are cultures and duplicates of the type that was used to describe each species and that are deposited in additional culture collections. Using these type specimens as references is essential to designing correct molecular identification and diagnostic systems. Here, we report a whole genome sequence for the Ex-type material of P. ramorum, P. kernoviae, and P. melonis generated using high-throughput sequencing via the MinION third generation platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of P. ramorum, P. kernoviae, and P. melonis (1,322, 545, and 2,091 contigs, respectively). The ab initio prediction of genes from these species reveals that there are 16,838, 12,793, and 34,580 genes in P. ramorum, P. kernoviae, and P. melonis, respectively. Of the 34,580 P. melonis genes, 10,164 genes were conserved among all three of these Phytophthora species which may include pathogenicity genes. We compared the ex-type of P. ramorum EU1 lineage assembly with another selected isolate of EU1 available at the National Center for Biotechnology Information and found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; the comparison with the EU2 lineage genome isolate revealed 441,859 SNPs genome-wide. This genome resource of the ex-types of P. ramorum, and P. kernoviae is a significant contribution as these species are among the most important pathogens of regulatory concern in different regions of the world.
DOI: 10.1094/MPMI-12-19-0342-A
PubMed: 32129709
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Srivastava</name><affiliation wicri:level="2"><nlm:affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Abad, Z Gloria" sort="Abad, Z Gloria" uniqKey="Abad Z" first="Z Gloria" last="Abad">Z Gloria Abad</name><affiliation wicri:level="2"><nlm:affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Knight, Leandra M" sort="Knight, Leandra M" uniqKey="Knight L" first="Leandra M" last="Knight">Leandra M. Knight</name><affiliation wicri:level="2"><nlm:affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Zeller, Kurt" sort="Zeller, Kurt" uniqKey="Zeller K" first="Kurt" last="Zeller">Kurt Zeller</name><affiliation wicri:level="2"><nlm:affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Mavrodieva, Vessela" sort="Mavrodieva, Vessela" uniqKey="Mavrodieva V" first="Vessela" last="Mavrodieva">Vessela Mavrodieva</name><affiliation wicri:level="2"><nlm:affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Nakhla, Mark" sort="Nakhla, Mark" uniqKey="Nakhla M" first="Mark" last="Nakhla">Mark Nakhla</name><affiliation wicri:level="2"><nlm:affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author></analytic><series><title level="j">Molecular plant-microbe interactions : MPMI</title><idno type="ISSN">0894-0282</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Contig Mapping (MeSH)</term><term>Genome (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Nanopore Sequencing (MeSH)</term><term>Phytophthora (genetics)</term><term>Plant Diseases (parasitology)</term><term>Polymorphism, Single Nucleotide (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cartographie de contigs (MeSH)</term><term>Génome (MeSH)</term><term>Maladies des plantes (parasitologie)</term><term>Phytophthora (génétique)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Contig Mapping</term><term>Genome</term><term>High-Throughput Nucleotide Sequencing</term><term>Nanopore Sequencing</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie de contigs</term><term>Génome</term><term>Polymorphisme de nucléotide simple</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Phytophthora ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i> are each species of current regulatory concern in the United States, the United Kingdom, and other areas of the world. Ex-type material are cultures and duplicates of the type that was used to describe each species and that are deposited in additional culture collections. Using these type specimens as references is essential to designing correct molecular identification and diagnostic systems. Here, we report a whole genome sequence for the Ex-type material of <i>P. ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i> generated using high-throughput sequencing via the MinION third generation platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of <i>P. ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i> (1,322, 545, and 2,091 contigs, respectively). The <i>ab initio</i> prediction of genes from these species reveals that there are 16,838, 12,793, and 34,580 genes in <i>P. ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i>, respectively. Of the 34,580 P. <i>melonis</i> genes, 10,164 genes were conserved among all three of these <i>Phytophthora</i> species which may include pathogenicity genes. We compared the ex-type of <i>P. ramorum</i> EU1 lineage assembly with another selected isolate of EU1 available at the National Center for Biotechnology Information and found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; the comparison with the EU2 lineage genome isolate revealed 441,859 SNPs genome-wide. This genome resource of the ex-types of <i>P. ramorum</i>, and <i>P. kernoviae</i> is a significant contribution as these species are among the most important pathogens of regulatory concern in different regions of the world.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">32129709</PMID><DateCompleted><Year>2020</Year><Month>09</Month><Day>04</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>04</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>33</Volume><Issue>6</Issue><PubDate><Year>2020</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>Draft Genome Resource for the Ex-types of <i>Phytophthora ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i>, Species of Regulatory Concern, Using Ultra-Long Read MinION Nanopore Sequencing.</ArticleTitle><Pagination><MedlinePgn>794-797</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-12-19-0342-A</ELocationID><Abstract><AbstractText><i>Phytophthora ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i> are each species of current regulatory concern in the United States, the United Kingdom, and other areas of the world. Ex-type material are cultures and duplicates of the type that was used to describe each species and that are deposited in additional culture collections. Using these type specimens as references is essential to designing correct molecular identification and diagnostic systems. Here, we report a whole genome sequence for the Ex-type material of <i>P. ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i> generated using high-throughput sequencing via the MinION third generation platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of <i>P. ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i> (1,322, 545, and 2,091 contigs, respectively). The <i>ab initio</i> prediction of genes from these species reveals that there are 16,838, 12,793, and 34,580 genes in <i>P. ramorum</i>, <i>P. kernoviae</i>, and <i>P. melonis</i>, respectively. Of the 34,580 P. <i>melonis</i> genes, 10,164 genes were conserved among all three of these <i>Phytophthora</i> species which may include pathogenicity genes. We compared the ex-type of <i>P. ramorum</i> EU1 lineage assembly with another selected isolate of EU1 available at the National Center for Biotechnology Information and found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; the comparison with the EU2 lineage genome isolate revealed 441,859 SNPs genome-wide. This genome resource of the ex-types of <i>P. ramorum</i>, and <i>P. kernoviae</i> is a significant contribution as these species are among the most important pathogens of regulatory concern in different regions of the world.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Srivastava</LastName><ForeName>Subodh K</ForeName><Initials>SK</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-0845-0199</Identifier><AffiliationInfo><Affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Abad</LastName><ForeName>Z Gloria</ForeName><Initials>ZG</Initials><AffiliationInfo><Affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Knight</LastName><ForeName>Leandra M</ForeName><Initials>LM</Initials><AffiliationInfo><Affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zeller</LastName><ForeName>Kurt</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mavrodieva</LastName><ForeName>Vessela</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nakhla</LastName><ForeName>Mark</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Plant Microbe Interact</MedlineTA><NlmUniqueID>9107902</NlmUniqueID><ISSNLinking>0894-0282</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020451" MajorTopicYN="N">Contig Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000081414" MajorTopicYN="Y">Nanopore Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">3G HTS</Keyword><Keyword MajorTopicYN="N">MinION ONT ultra–long read sequencing</Keyword><Keyword MajorTopicYN="N">Phytophthora</Keyword><Keyword MajorTopicYN="N">ex-type</Keyword><Keyword MajorTopicYN="N">genome</Keyword><Keyword MajorTopicYN="N">high throughput sequencing</Keyword><Keyword MajorTopicYN="N">third generation high throughput sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>3</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>3</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32129709</ArticleId><ArticleId IdType="doi">10.1094/MPMI-12-19-0342-A</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Caroline du Nord</li><li>Maryland</li></region></list><tree><country name="États-Unis"><region name="Maryland"><name sortKey="Srivastava, Subodh K" sort="Srivastava, Subodh K" uniqKey="Srivastava S" first="Subodh K" last="Srivastava">Subodh K. Srivastava</name></region><name sortKey="Abad, Z Gloria" sort="Abad, Z Gloria" uniqKey="Abad Z" first="Z Gloria" last="Abad">Z Gloria Abad</name><name sortKey="Knight, Leandra M" sort="Knight, Leandra M" uniqKey="Knight L" first="Leandra M" last="Knight">Leandra M. Knight</name><name sortKey="Knight, Leandra M" sort="Knight, Leandra M" uniqKey="Knight L" first="Leandra M" last="Knight">Leandra M. Knight</name><name sortKey="Mavrodieva, Vessela" sort="Mavrodieva, Vessela" uniqKey="Mavrodieva V" first="Vessela" last="Mavrodieva">Vessela Mavrodieva</name><name sortKey="Nakhla, Mark" sort="Nakhla, Mark" uniqKey="Nakhla M" first="Mark" last="Nakhla">Mark Nakhla</name><name sortKey="Srivastava, Subodh K" sort="Srivastava, Subodh K" uniqKey="Srivastava S" first="Subodh K" last="Srivastava">Subodh K. Srivastava</name><name sortKey="Zeller, Kurt" sort="Zeller, Kurt" uniqKey="Zeller K" first="Kurt" last="Zeller">Kurt Zeller</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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