Updated Assembly of Phytophthora ramorum pr102 Isolate Incorporating Long Reads from PacBio Sequencing.
Identifieur interne : 000350 ( Main/Exploration ); précédent : 000349; suivant : 000351Updated Assembly of Phytophthora ramorum pr102 Isolate Incorporating Long Reads from PacBio Sequencing.
Auteurs : Mathu Malar C [Inde] ; Jennifer David Yuzon [États-Unis] ; Arijit Panda [Inde] ; Takao Kasuga [États-Unis] ; Sucheta Tripathy [Inde]Source :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Génome de protozoaire, Phytophthora.
- parasitologie : Maladies des plantes, Quercus.
- Analyse de séquence d'ADN, Californie.
English descriptors
- KwdEn :
- MESH :
- geographic : California.
- genetics : Genome, Protozoan, Phytophthora.
- parasitology : Plant Diseases, Quercus.
- Sequence Analysis, DNA.
Abstract
The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.
DOI: 10.1094/MPMI-05-19-0147-A
PubMed: 31306082
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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wicri:level="1"><nlm:affiliation>Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Academy of Scientific and Innovative Research (AcSIR), New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Yuzon, Jennifer David" sort="Yuzon, Jennifer David" uniqKey="Yuzon J" first="Jennifer David" last="Yuzon">Jennifer David Yuzon</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Panda, Arijit" sort="Panda, Arijit" uniqKey="Panda A" first="Arijit" last="Panda">Arijit Panda</name><affiliation wicri:level="1"><nlm:affiliation>Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032</wicri:regionArea><wicri:noRegion>Kolkata 700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Academy of Scientific and Innovative Research (AcSIR), New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Kasuga, Takao" sort="Kasuga, Takao" uniqKey="Kasuga T" first="Takao" last="Kasuga">Takao Kasuga</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Pathology, University of California, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Pathology, University of California, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Tripathy, Sucheta" sort="Tripathy, Sucheta" uniqKey="Tripathy S" first="Sucheta" last="Tripathy">Sucheta Tripathy</name><affiliation wicri:level="1"><nlm:affiliation>Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032</wicri:regionArea><wicri:noRegion>Kolkata 700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Academy of Scientific and Innovative Research (AcSIR), New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular plant-microbe interactions : MPMI</title><idno type="ISSN">0894-0282</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>California (MeSH)</term><term>Genome, Protozoan (genetics)</term><term>Phytophthora (genetics)</term><term>Plant Diseases (parasitology)</term><term>Quercus (parasitology)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Californie (MeSH)</term><term>Génome de protozoaire (génétique)</term><term>Maladies des plantes (parasitologie)</term><term>Phytophthora (génétique)</term><term>Quercus (parasitologie)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>California</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Protozoan</term><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Génome de protozoaire</term><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Maladies des plantes</term><term>Quercus</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Plant Diseases</term><term>Quercus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Californie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The NA1 clonal lineage of <i>Phytophthora ramorum</i> is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">31306082</PMID><DateCompleted><Year>2019</Year><Month>10</Month><Day>31</Day></DateCompleted><DateRevised><Year>2019</Year><Month>10</Month><Day>31</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>32</Volume><Issue>11</Issue><PubDate><Year>2019</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>Updated Assembly of <i>Phytophthora ramorum</i> pr102 Isolate Incorporating Long Reads from PacBio Sequencing.</ArticleTitle><Pagination><MedlinePgn>1472-1474</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-05-19-0147-A</ELocationID><Abstract><AbstractText>The NA1 clonal lineage of <i>Phytophthora ramorum</i> is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Malar C</LastName><ForeName>Mathu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuzon</LastName><ForeName>Jennifer David</ForeName><Initials>JD</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, CA, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>USDA-ARS, Davis, CA, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Panda</LastName><ForeName>Arijit</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kasuga</LastName><ForeName>Takao</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, University of California, Davis, CA, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>USDA-ARS, Davis, CA, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tripathy</LastName><ForeName>Sucheta</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-0611-8088</Identifier><AffiliationInfo><Affiliation>Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>09</Month><Day>27</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="D002140" MajorTopicYN="N" Type="Geographic">California</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018503" MajorTopicYN="Y">Genome, Protozoan</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="Y">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029963" MajorTopicYN="N">Quercus</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phytophthora ramorum</Keyword><Keyword MajorTopicYN="N">gaps</Keyword><Keyword MajorTopicYN="N">long read assembly</Keyword><Keyword MajorTopicYN="N">repeats</Keyword><Keyword MajorTopicYN="N">sudden oak death</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>7</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>7</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31306082</ArticleId><ArticleId IdType="doi">10.1094/MPMI-05-19-0147-A</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Inde</li><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><country name="Inde"><noRegion><name sortKey="Malar C, Mathu" sort="Malar C, Mathu" uniqKey="Malar C M" first="Mathu" last="Malar C">Mathu Malar C</name></noRegion><name sortKey="Malar C, Mathu" sort="Malar C, Mathu" uniqKey="Malar C M" first="Mathu" last="Malar C">Mathu Malar C</name><name sortKey="Panda, Arijit" sort="Panda, Arijit" uniqKey="Panda A" first="Arijit" last="Panda">Arijit Panda</name><name sortKey="Panda, Arijit" sort="Panda, Arijit" uniqKey="Panda A" first="Arijit" last="Panda">Arijit Panda</name><name sortKey="Tripathy, Sucheta" sort="Tripathy, Sucheta" uniqKey="Tripathy S" first="Sucheta" last="Tripathy">Sucheta Tripathy</name><name sortKey="Tripathy, Sucheta" sort="Tripathy, Sucheta" uniqKey="Tripathy S" first="Sucheta" last="Tripathy">Sucheta Tripathy</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Yuzon, Jennifer David" sort="Yuzon, Jennifer David" uniqKey="Yuzon J" first="Jennifer David" last="Yuzon">Jennifer David Yuzon</name></region><name sortKey="Kasuga, Takao" sort="Kasuga, Takao" uniqKey="Kasuga T" first="Takao" last="Kasuga">Takao Kasuga</name><name sortKey="Kasuga, Takao" sort="Kasuga, Takao" uniqKey="Kasuga T" first="Takao" last="Kasuga">Takao Kasuga</name><name sortKey="Yuzon, Jennifer David" sort="Yuzon, Jennifer David" uniqKey="Yuzon J" first="Jennifer David" last="Yuzon">Jennifer David Yuzon</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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