Haplotype-Phased Genome Assembly of Virulent Phytophthora ramorum Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation.
Identifieur interne : 000485 ( Main/Exploration ); précédent : 000484; suivant : 000486Haplotype-Phased Genome Assembly of Virulent Phytophthora ramorum Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation.
Auteurs : Mathu Malar C [Inde] ; Jennifer D. Yuzon [États-Unis] ; Subhadeep Das [Inde] ; Abhishek Das [Inde] ; Arijit Panda [Inde] ; Samrat Ghosh [Inde] ; Brett M. Tyler [États-Unis] ; Takao Kasuga [États-Unis] ; Sucheta Tripathy [Inde]Source :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2019.
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Abstract
Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for P. ramorum, we performed long-read sequencing of highly aggressive P. ramorum isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of 21 and 25 Crinkler effectors and 393 and 394 RXLR effector genes from two haplotypes. Of these, 24 and 25 RXLR effectors were newly predicted from haplotypes A and B, respectively. In addition, seven new paralogs of effector Avh207 were found in contig 54, not reported earlier. Comparison of the ND886 assembly with Pr102 V1 assembly suggests that several repeat-rich smaller scaffolds within the Pr102 V1 assembly were possibly misassembled; these regions are fully encompassed now in ND886 contigs. Our analysis further reveals that Pr102 is a heterokaryon with multiple nuclear types in the sequences corresponding to contig 10 of ND886 assembly.
DOI: 10.1094/MPMI-08-18-0222-R
PubMed: 30794480
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Tyler</name><affiliation wicri:level="2"><nlm:affiliation>5Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-7303, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>5Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-7303</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></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>3Department of Plant Pathology, University of California, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>3Department of Plant Pathology, University of California, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>4USDA-ARS, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>4USDA-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>1Computational 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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032</wicri:regionArea><wicri:noRegion>700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad</wicri:regionArea><wicri:noRegion>Ghaziabad</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30794480</idno><idno type="pmid">30794480</idno><idno type="doi">10.1094/MPMI-08-18-0222-R</idno><idno type="wicri:Area/Main/Corpus">000541</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000541</idno><idno type="wicri:Area/Main/Curation">000541</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000541</idno><idno type="wicri:Area/Main/Exploration">000541</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Haplotype-Phased Genome Assembly of Virulent <i>Phytophthora ramorum</i> Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation.</title><author><name sortKey="Malar C, Mathu" sort="Malar C, Mathu" uniqKey="Malar C M" first="Mathu" last="Malar C">Mathu Malar C</name><affiliation wicri:level="1"><nlm:affiliation>1Computational 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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032</wicri:regionArea><wicri:noRegion>700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad</wicri:regionArea><wicri:noRegion>Ghaziabad</wicri:noRegion></affiliation></author><author><name sortKey="Yuzon, Jennifer D" sort="Yuzon, Jennifer D" uniqKey="Yuzon J" first="Jennifer D" last="Yuzon">Jennifer D. Yuzon</name><affiliation wicri:level="2"><nlm:affiliation>3Department of Plant Pathology, University of California, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>3Department of Plant Pathology, University of California, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>4USDA-ARS, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>4USDA-ARS, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Das, Subhadeep" sort="Das, Subhadeep" uniqKey="Das S" first="Subhadeep" last="Das">Subhadeep Das</name><affiliation wicri:level="1"><nlm:affiliation>1Computational 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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032</wicri:regionArea><wicri:noRegion>700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad</wicri:regionArea><wicri:noRegion>Ghaziabad</wicri:noRegion></affiliation></author><author><name sortKey="Das, Abhishek" sort="Das, Abhishek" uniqKey="Das A" first="Abhishek" last="Das">Abhishek Das</name><affiliation wicri:level="1"><nlm:affiliation>1Computational 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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032</wicri:regionArea><wicri:noRegion>700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad</wicri:regionArea><wicri:noRegion>Ghaziabad</wicri:noRegion></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>1Computational 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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032</wicri:regionArea><wicri:noRegion>700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad</wicri:regionArea><wicri:noRegion>Ghaziabad</wicri:noRegion></affiliation></author><author><name sortKey="Ghosh, Samrat" sort="Ghosh, Samrat" uniqKey="Ghosh S" first="Samrat" last="Ghosh">Samrat Ghosh</name><affiliation wicri:level="1"><nlm:affiliation>1Computational 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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032</wicri:regionArea><wicri:noRegion>700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad</wicri:regionArea><wicri:noRegion>Ghaziabad</wicri:noRegion></affiliation></author><author><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. Tyler</name><affiliation wicri:level="2"><nlm:affiliation>5Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-7303, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>5Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-7303</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></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>3Department of Plant Pathology, University of California, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>3Department of Plant Pathology, University of California, Davis, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>4USDA-ARS, Davis, CA, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>4USDA-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>1Computational 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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032</wicri:regionArea><wicri:noRegion>700032</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad</wicri:regionArea><wicri:noRegion>Ghaziabad</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>DNA Copy Number Variations (MeSH)</term><term>Genome, Protozoan (genetics)</term><term>Haplotypes (MeSH)</term><term>Phytophthora (genetics)</term><term>Polymorphism, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Génome de protozoaire (génétique)</term><term>Haplotypes (MeSH)</term><term>Phytophthora (génétique)</term><term>Polymorphisme génétique (MeSH)</term><term>Variations de nombre de copies de segment d'ADN (MeSH)</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" xml:lang="en"><term>DNA Copy Number Variations</term><term>Haplotypes</term><term>Polymorphism, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Haplotypes</term><term>Polymorphisme génétique</term><term>Variations de nombre de copies de segment d'ADN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Phytophthora ramorum</i> is a destructive pathogen that causes sudden oak death disease. The genome sequence of <i>P. ramorum</i> isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for <i>P. ramorum</i>, we performed long-read sequencing of highly aggressive <i>P. ramorum</i> isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of 21 and 25 Crinkler effectors and 393 and 394 RXLR effector genes from two haplotypes. Of these, 24 and 25 RXLR effectors were newly predicted from haplotypes A and B, respectively. In addition, seven new paralogs of effector Avh207 were found in contig 54, not reported earlier. Comparison of the ND886 assembly with Pr102 V1 assembly suggests that several repeat-rich smaller scaffolds within the Pr102 V1 assembly were possibly misassembled; these regions are fully encompassed now in ND886 contigs. Our analysis further reveals that Pr102 is a heterokaryon with multiple nuclear types in the sequences corresponding to contig 10 of ND886 assembly.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">30794480</PMID><DateCompleted><Year>2019</Year><Month>08</Month><Day>01</Day></DateCompleted><DateRevised><Year>2019</Year><Month>08</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>32</Volume><Issue>8</Issue><PubDate><Year>2019</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>Haplotype-Phased Genome Assembly of Virulent <i>Phytophthora ramorum</i> Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation.</ArticleTitle><Pagination><MedlinePgn>1047-1060</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-08-18-0222-R</ELocationID><Abstract><AbstractText><i>Phytophthora ramorum</i> is a destructive pathogen that causes sudden oak death disease. The genome sequence of <i>P. ramorum</i> isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for <i>P. ramorum</i>, we performed long-read sequencing of highly aggressive <i>P. ramorum</i> isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of 21 and 25 Crinkler effectors and 393 and 394 RXLR effector genes from two haplotypes. Of these, 24 and 25 RXLR effectors were newly predicted from haplotypes A and B, respectively. In addition, seven new paralogs of effector Avh207 were found in contig 54, not reported earlier. Comparison of the ND886 assembly with Pr102 V1 assembly suggests that several repeat-rich smaller scaffolds within the Pr102 V1 assembly were possibly misassembled; these regions are fully encompassed now in ND886 contigs. Our analysis further reveals that Pr102 is a heterokaryon with multiple nuclear types in the sequences corresponding to contig 10 of ND886 assembly.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Malar C</LastName><ForeName>Mathu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuzon</LastName><ForeName>Jennifer D</ForeName><Initials>JD</Initials><AffiliationInfo><Affiliation>3Department of Plant Pathology, University of California, Davis, CA, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>4USDA-ARS, Davis, CA, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Das</LastName><ForeName>Subhadeep</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Das</LastName><ForeName>Abhishek</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Panda</LastName><ForeName>Arijit</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ghosh</LastName><ForeName>Samrat</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tyler</LastName><ForeName>Brett M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>5Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-7303, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kasuga</LastName><ForeName>Takao</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>3Department of Plant Pathology, University of California, Davis, CA, U.S.A.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>4USDA-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>1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>06</Month><Day>10</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="D056915" MajorTopicYN="Y">DNA Copy Number Variations</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018503" MajorTopicYN="Y">Genome, Protozoan</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="Y">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="Y">Polymorphism, Genetic</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N"> diseases</Keyword><Keyword MajorTopicYN="N">genomics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>2</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>8</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>2</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30794480</ArticleId><ArticleId IdType="doi">10.1094/MPMI-08-18-0222-R</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Inde</li><li>États-Unis</li></country><region><li>Californie</li><li>Oregon</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="Das, Abhishek" sort="Das, Abhishek" uniqKey="Das A" first="Abhishek" last="Das">Abhishek Das</name><name sortKey="Das, Abhishek" sort="Das, Abhishek" uniqKey="Das A" first="Abhishek" last="Das">Abhishek Das</name><name sortKey="Das, Subhadeep" sort="Das, Subhadeep" uniqKey="Das S" first="Subhadeep" last="Das">Subhadeep Das</name><name sortKey="Das, Subhadeep" sort="Das, Subhadeep" uniqKey="Das S" first="Subhadeep" last="Das">Subhadeep Das</name><name sortKey="Ghosh, Samrat" sort="Ghosh, Samrat" uniqKey="Ghosh S" first="Samrat" last="Ghosh">Samrat Ghosh</name><name sortKey="Ghosh, Samrat" sort="Ghosh, Samrat" uniqKey="Ghosh S" first="Samrat" last="Ghosh">Samrat Ghosh</name><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 D" sort="Yuzon, Jennifer D" uniqKey="Yuzon J" first="Jennifer D" last="Yuzon">Jennifer D. 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="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. Tyler</name><name sortKey="Yuzon, Jennifer D" sort="Yuzon, Jennifer D" uniqKey="Yuzon J" first="Jennifer D" last="Yuzon">Jennifer D. Yuzon</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Haplotype-Phased Genome Assembly of Virulent Phytophthora ramorum Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation.
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