Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
Identifieur interne : 000133 ( Main/Exploration ); précédent : 000132; suivant : 000134Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
Auteurs : Dario Cantu [États-Unis] ; Manjula Govindarajulu ; Alex Kozik ; Meinan Wang ; Xianming Chen ; Kenji K. Kojima ; Jerzy Jurka ; Richard W. Michelmore ; Jorge DubcovskySource :
- PloS one [ 1932-6203 ] ; 2011.
Descripteurs français
- KwdFr :
- ADN fongique (génétique), Analyse de séquence d'ADN (méthodes), Basidiomycota (génétique), Cartographie de contigs (MeSH), Données de séquences moléculaires (MeSH), Ergostérol (biosynthèse), Gènes fongiques (génétique), Génome fongique (génétique), Maladies des plantes (microbiologie), Protéines fongiques (métabolisme), Synténie (génétique), Séquences répétées d'acides nucléiques (génétique), Triticum (microbiologie), Éléments transposables d'ADN (génétique).
- MESH :
- biosynthèse : Ergostérol.
- génétique : ADN fongique, Basidiomycota, Gènes fongiques, Génome fongique, Synténie, Séquences répétées d'acides nucléiques, Éléments transposables d'ADN.
- microbiologie : Maladies des plantes, Triticum.
- métabolisme : Protéines fongiques.
- méthodes : Analyse de séquence d'ADN.
- Cartographie de contigs, Données de séquences moléculaires.
English descriptors
- KwdEn :
- Basidiomycota (genetics), Contig Mapping (MeSH), DNA Transposable Elements (genetics), DNA, Fungal (genetics), Ergosterol (biosynthesis), Fungal Proteins (metabolism), Genes, Fungal (genetics), Genome, Fungal (genetics), Molecular Sequence Data (MeSH), Plant Diseases (microbiology), Repetitive Sequences, Nucleic Acid (genetics), Sequence Analysis, DNA (methods), Synteny (genetics), Triticum (microbiology).
- MESH :
- chemical , biosynthesis : Ergosterol.
- chemical , genetics : DNA Transposable Elements, DNA, Fungal.
- genetics : Basidiomycota, Genes, Fungal, Genome, Fungal, Repetitive Sequences, Nucleic Acid, Synteny.
- chemical , metabolism : Fungal Proteins.
- methods : Sequence Analysis, DNA.
- microbiology : Plant Diseases, Triticum.
- Contig Mapping, Molecular Sequence Data.
Abstract
BACKGROUND
The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST) is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS) has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130).
METHODOLOGY/PRINCIPAL FINDINGS
We obtained nearly 80 million high quality paired-end reads (>50x coverage) that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG) genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase.
CONCLUSIONS/SIGNIFICANCE
The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for rapid and efficient access to genomic sequence in non-model organisms.
DOI: 10.1371/journal.pone.0024230
PubMed: 21909385
PubMed Central: PMC3164196
Affiliations:
Links toward previous steps (curation, corpus...)
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In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS) has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130).</p></div><div type="abstract" xml:lang="en"><p><b>METHODOLOGY/PRINCIPAL FINDINGS</b></p><p>We obtained nearly 80 million high quality paired-end reads (>50x coverage) that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG) genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS/SIGNIFICANCE</b></p><p>The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for rapid and efficient access to genomic sequence in non-model organisms.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21909385</PMID><DateCompleted><Year>2012</Year><Month>01</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>8</Issue><PubDate><Year>2011</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.</ArticleTitle><Pagination><MedlinePgn>e24230</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0024230</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST) is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS) has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130).</AbstractText><AbstractText Label="METHODOLOGY/PRINCIPAL FINDINGS" NlmCategory="RESULTS">We obtained nearly 80 million high quality paired-end reads (>50x coverage) that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG) genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase.</AbstractText><AbstractText Label="CONCLUSIONS/SIGNIFICANCE" NlmCategory="CONCLUSIONS">The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for rapid and efficient access to genomic sequence in non-model organisms.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cantu</LastName><ForeName>Dario</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Plant Sciences, University of California Davis, Davis, California, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Govindarajulu</LastName><ForeName>Manjula</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Kozik</LastName><ForeName>Alex</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Meinan</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Xianming</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Kojima</LastName><ForeName>Kenji K</ForeName><Initials>KK</Initials></Author><Author ValidYN="Y"><LastName>Jurka</LastName><ForeName>Jerzy</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Michelmore</LastName><ForeName>Richard W</ForeName><Initials>RW</Initials></Author><Author ValidYN="Y"><LastName>Dubcovsky</LastName><ForeName>Jorge</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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IdType="pubmed">17332020</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><noCountry><name sortKey="Chen, Xianming" sort="Chen, Xianming" uniqKey="Chen X" first="Xianming" last="Chen">Xianming Chen</name><name sortKey="Dubcovsky, Jorge" sort="Dubcovsky, Jorge" uniqKey="Dubcovsky J" first="Jorge" last="Dubcovsky">Jorge Dubcovsky</name><name sortKey="Govindarajulu, Manjula" sort="Govindarajulu, Manjula" uniqKey="Govindarajulu M" first="Manjula" last="Govindarajulu">Manjula Govindarajulu</name><name sortKey="Jurka, Jerzy" sort="Jurka, Jerzy" uniqKey="Jurka J" first="Jerzy" last="Jurka">Jerzy Jurka</name><name sortKey="Kojima, Kenji K" sort="Kojima, Kenji K" uniqKey="Kojima K" first="Kenji K" last="Kojima">Kenji K. Kojima</name><name sortKey="Kozik, Alex" sort="Kozik, Alex" uniqKey="Kozik A" first="Alex" last="Kozik">Alex Kozik</name><name sortKey="Michelmore, Richard W" sort="Michelmore, Richard W" uniqKey="Michelmore R" first="Richard W" last="Michelmore">Richard W. Michelmore</name><name sortKey="Wang, Meinan" sort="Wang, Meinan" uniqKey="Wang M" first="Meinan" last="Wang">Meinan Wang</name></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Cantu, Dario" sort="Cantu, Dario" uniqKey="Cantu D" first="Dario" last="Cantu">Dario Cantu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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