De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next‐generation sequencing techniques
Identifieur interne : 001202 ( Istex/Curation ); précédent : 001201; suivant : 001203De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next‐generation sequencing techniques
Auteurs : F. Angeloni [Pays-Bas] ; C. A. M. Wagemaker [Pays-Bas] ; M. S. M. Jetten [Pays-Bas] ; H. J. M. Op Den Camp [Pays-Bas] ; E. M. Janssen-Megens [Pays-Bas] ; K. Francoijs [Pays-Bas] ; H. G. Stunnenberg [Pays-Bas] ; N. J. Ouborg [Pays-Bas]Source :
- Molecular Ecology Resources [ 1755-098X ] ; 2011-07.
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Abstract
Next‐generation sequencing (NGS) technologies are increasingly applied in many organisms, including nonmodel organisms that are important for ecological and conservation purposes. Illumina and 454 sequencing are among the most used NGS technologies and have been shown to produce optimal results at reasonable costs when used together. Here, we describe the combined application of these two NGS technologies to characterize the transcriptome of a plant species of ecological and conservation relevance for which no genomic resource is available, Scabiosa columbaria. We obtained 528 557 reads from a 454 GS‐FLX run and a total of 28 993 627 reads from two lanes of an Illumina GAII single run. After read trimming, the de novo assembly of both types of reads produced 109 630 contigs. Both the contigs and the >75 bp remaining singletons were blasted against the Uniprot/Swissprot database, resulting in 29 676 and 10 515 significant hits, respectively. Based on sequence similarity with known gene products, these sequences represent at least 12 516 unique genes, most of which are well covered by contig sequences. In addition, we identified 4320 microsatellite loci, of which 856 had flanking sequences suitable for PCR primer design. We also identified 75 054 putative SNPs. This annotated sequence collection and the relative molecular markers represent a main genomic resource for S. columbaria which should contribute to future research in conservation and population biology studies. Our results demonstrate the utility of NGS technologies as starting point for the development of genomic tools in nonmodel but ecologically important species.
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DOI: 10.1111/j.1755-0998.2011.02990.x
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Ouborg</name><affiliation wicri:level="1"><mods:affiliation>Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Molecular Ecology, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands</mods:affiliation><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Molecular Ecology, Heyendaalseweg 135, 6525 AJ Nijmegen</wicri:regionArea></affiliation></author></analytic><monogr></monogr><series><title level="j">Molecular Ecology Resources</title><idno type="ISSN">1755-098X</idno><idno type="eISSN">1755-0998</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2011-07">2011-07</date><biblScope unit="volume">11</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="662">662</biblScope><biblScope unit="page" to="674">674</biblScope></imprint><idno type="ISSN">1755-098X</idno></series><idno type="istex">D926D53B3E45FA34E64D8BAC0091962D43587654</idno><idno type="DOI">10.1111/j.1755-0998.2011.02990.x</idno><idno type="ArticleID">MEN2990</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1755-098X</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>SNPs</term><term>Scabiosa columbaria</term><term>genetic resources</term><term>microsatellites</term><term>next‐generation sequencing</term><term>transcriptome characterization</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Next‐generation sequencing (NGS) technologies are increasingly applied in many organisms, including nonmodel organisms that are important for ecological and conservation purposes. Illumina and 454 sequencing are among the most used NGS technologies and have been shown to produce optimal results at reasonable costs when used together. Here, we describe the combined application of these two NGS technologies to characterize the transcriptome of a plant species of ecological and conservation relevance for which no genomic resource is available, Scabiosa columbaria. We obtained 528 557 reads from a 454 GS‐FLX run and a total of 28 993 627 reads from two lanes of an Illumina GAII single run. After read trimming, the de novo assembly of both types of reads produced 109 630 contigs. Both the contigs and the >75 bp remaining singletons were blasted against the Uniprot/Swissprot database, resulting in 29 676 and 10 515 significant hits, respectively. Based on sequence similarity with known gene products, these sequences represent at least 12 516 unique genes, most of which are well covered by contig sequences. In addition, we identified 4320 microsatellite loci, of which 856 had flanking sequences suitable for PCR primer design. We also identified 75 054 putative SNPs. This annotated sequence collection and the relative molecular markers represent a main genomic resource for S. columbaria which should contribute to future research in conservation and population biology studies. Our results demonstrate the utility of NGS technologies as starting point for the development of genomic tools in nonmodel but ecologically important species.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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