Scaffolding a Caenorhabditis nematode genome with RNA-seq.
Identifieur interne : 001F27 ( PubMed/Curation ); précédent : 001F26; suivant : 001F28Scaffolding a Caenorhabditis nematode genome with RNA-seq.
Auteurs : Ali Mortazavi [États-Unis] ; Erich M. Schwarz ; Brian Williams ; Lorian Schaeffer ; Igor Antoshechkin ; Barbara J. Wold ; Paul W. SternbergSource :
- Genome research [ 1549-5469 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Complementary.
- genetics : Caenorhabditis, Conserved Sequence, Genome.
- methods : Genomics, Sequence Analysis, DNA.
- Animals, Base Sequence, Molecular Sequence Data, Phylogeny, Sequence Alignment, Software.
Abstract
Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)(+) cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.
DOI: 10.1101/gr.111021.110
PubMed: 20980554
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Sternberg</name></author></analytic><series><title level="j">Genome research</title><idno type="eISSN">1549-5469</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Caenorhabditis (genetics)</term><term>Conserved Sequence (genetics)</term><term>DNA, Complementary (genetics)</term><term>Genome (genetics)</term><term>Genomics (methods)</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire (génétique)</term><term>Alignement de séquences</term><term>Analyse de séquence d'ADN ()</term><term>Animaux</term><term>Caenorhabditis (génétique)</term><term>Données de séquences moléculaires</term><term>Génome (génétique)</term><term>Génomique ()</term><term>Logiciel</term><term>Phylogénie</term><term>Séquence conservée (génétique)</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Complementary</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Caenorhabditis</term><term>Conserved Sequence</term><term>Genome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN complémentaire</term><term>Caenorhabditis</term><term>Génome</term><term>Séquence conservée</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Alignment</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Données de séquences moléculaires</term><term>Génomique</term><term>Logiciel</term><term>Phylogénie</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)(+) cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20980554</PMID><DateCompleted><Year>2011</Year><Month>03</Month><Day>16</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1549-5469</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>12</Issue><PubDate><Year>2010</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res.</ISOAbbreviation></Journal><ArticleTitle>Scaffolding a Caenorhabditis nematode genome with RNA-seq.</ArticleTitle><Pagination><MedlinePgn>1740-7</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1101/gr.111021.110</ELocationID><Abstract><AbstractText>Efficient sequencing of animal and plant genomes by next-generation technology should allow many neglected organisms of biological and medical importance to be better understood. As a test case, we have assembled a draft genome of Caenorhabditis sp. 3 PS1010 through a combination of direct sequencing and scaffolding with RNA-seq. We first sequenced genomic DNA and mixed-stage cDNA using paired 75-nt reads from an Illumina GAII. A set of 230 million genomic reads yielded an 80-Mb assembly, with a supercontig N50 of 5.0 kb, covering 90% of 429 kb from previously published genomic contigs. Mixed-stage poly(A)(+) cDNA gave 47.3 million mappable 75-mers (including 5.1 million spliced reads), which separately assembled into 17.8 Mb of cDNA, with an N50 of 1.06 kb. By further scaffolding our genomic supercontigs with cDNA, we increased their N50 to 9.4 kb, nearly double the average gene size in C. elegans. We predicted 22,851 protein-coding genes, and detected expression in 78% of them. Multigenome alignment and data filtering identified 2672 DNA elements conserved between PS1010 and C. elegans that are likely to encode regulatory sequences or previously unknown ncRNAs. Genomic and cDNA sequencing followed by joint assembly is a rapid and useful strategy for biological analysis.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mortazavi</LastName><ForeName>Ali</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schwarz</LastName><ForeName>Erich M</ForeName><Initials>EM</Initials></Author><Author ValidYN="Y"><LastName>Williams</LastName><ForeName>Brian</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Schaeffer</LastName><ForeName>Lorian</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Antoshechkin</LastName><ForeName>Igor</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Wold</LastName><ForeName>Barbara J</ForeName><Initials>BJ</Initials></Author><Author 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States</Country></Grant><Grant><GrantID>U01 HG003162</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><Agency>Howard Hughes Medical Institute</Agency><Country>United States</Country></Grant><Grant><GrantID>HG003162</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM084389</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>10</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genome 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