Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity.
Identifieur interne : 000533 ( Main/Exploration ); précédent : 000532; suivant : 000534Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity.
Auteurs : Chenming Cui [États-Unis] ; John H. Herlihy [États-Unis] ; Aureliano Bombarely [États-Unis] ; John M. Mcdowell [États-Unis] ; David C. Haak [États-Unis]Source :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2019.
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Abstract
Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in >1.25 million reads with an N50 of 13 kb. The resulting assembly is 95.2 Mbp in 424 scaffolds with an N50 length of 313 kb. This assembly is approximately 30 Mbp bigger than the current reference genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 97.4% complete orthologs (19.2% duplicated). Evolutionary analysis supports a recent whole-genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.
DOI: 10.1094/MPMI-04-19-0103-TA
PubMed: 31479390
Affiliations:
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Mcdowell</name><affiliation wicri:level="2"><nlm:affiliation>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061</wicri:regionArea><placeName><region type="state">Virginie</region></placeName></affiliation></author><author><name sortKey="Haak, David C" sort="Haak, David C" uniqKey="Haak D" first="David C" last="Haak">David C. Haak</name><affiliation wicri:level="2"><nlm:affiliation>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061</wicri:regionArea><placeName><region type="state">Virginie</region></placeName></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>Genome Size (MeSH)</term><term>Genome, Protozoan (genetics)</term><term>Genomics (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Phytophthora (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Génome de protozoaire (génétique)</term><term>Génomique (MeSH)</term><term>Phytophthora (génétique)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Taille du génome (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>Genome Size</term><term>Genomics</term><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Génomique</term><term>Séquençage nucléotidique à haut débit</term><term>Taille du génome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. <i>Phytophthora capsici</i> is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, <i>P. capsici</i> has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in >1.25 million reads with an N<sub>50</sub> of 13 kb. The resulting assembly is 95.2 Mbp in 424 scaffolds with an N<sub>50</sub> length of 313 kb. This assembly is approximately 30 Mbp bigger than the current reference genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 97.4% complete orthologs (19.2% duplicated). Evolutionary analysis supports a recent whole-genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">31479390</PMID><DateCompleted><Year>2019</Year><Month>11</Month><Day>21</Day></DateCompleted><DateRevised><Year>2019</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>32</Volume><Issue>12</Issue><PubDate><Year>2019</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>Draft Assembly of <i>Phytophthora capsici</i> from Long-Read Sequencing Uncovers Complexity.</ArticleTitle><Pagination><MedlinePgn>1559-1563</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-04-19-0103-TA</ELocationID><Abstract><AbstractText>Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. <i>Phytophthora capsici</i> is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, <i>P. capsici</i> has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in >1.25 million reads with an N<sub>50</sub> of 13 kb. The resulting assembly is 95.2 Mbp in 424 scaffolds with an N<sub>50</sub> length of 313 kb. This assembly is approximately 30 Mbp bigger than the current reference genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 97.4% complete orthologs (19.2% duplicated). Evolutionary analysis supports a recent whole-genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cui</LastName><ForeName>Chenming</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Herlihy</LastName><ForeName>John H</ForeName><Initials>JH</Initials><AffiliationInfo><Affiliation>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bombarely</LastName><ForeName>Aureliano</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McDowell</LastName><ForeName>John M</ForeName><Initials>JM</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-9070-4874</Identifier><AffiliationInfo><Affiliation>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Haak</LastName><ForeName>David C</ForeName><Initials>DC</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-3692-3152</Identifier><AffiliationInfo><Affiliation>School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>10</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="D059646" MajorTopicYN="N">Genome Size</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018503" MajorTopicYN="Y">Genome, Protozoan</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="Y">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="Y">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">MinION</Keyword><Keyword MajorTopicYN="N">genomics</Keyword><Keyword MajorTopicYN="N">metabolomics</Keyword><Keyword MajorTopicYN="N">miniasm</Keyword><Keyword MajorTopicYN="N">nanopore sequencing</Keyword><Keyword MajorTopicYN="N">oomycete</Keyword><Keyword MajorTopicYN="N">pathogen</Keyword><Keyword MajorTopicYN="N">proteomics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31479390</ArticleId><ArticleId IdType="doi">10.1094/MPMI-04-19-0103-TA</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Virginie</li></region></list><tree><country name="États-Unis"><region name="Virginie"><name sortKey="Cui, Chenming" sort="Cui, Chenming" uniqKey="Cui C" first="Chenming" last="Cui">Chenming Cui</name></region><name sortKey="Bombarely, Aureliano" sort="Bombarely, Aureliano" uniqKey="Bombarely A" first="Aureliano" last="Bombarely">Aureliano Bombarely</name><name sortKey="Haak, David C" sort="Haak, David C" uniqKey="Haak D" first="David C" last="Haak">David C. Haak</name><name sortKey="Herlihy, John H" sort="Herlihy, John H" uniqKey="Herlihy J" first="John H" last="Herlihy">John H. Herlihy</name><name sortKey="Mcdowell, John M" sort="Mcdowell, John M" uniqKey="Mcdowell J" first="John M" last="Mcdowell">John M. Mcdowell</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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