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dc.contributor.author
Blavet, Nicolas
dc.contributor.author
Charif, Delphine
dc.contributor.author
Oger-Desfeux, Christine
dc.contributor.author
Marais, Gabriel A.B.
dc.contributor.author
Widmer, Alex
dc.date.accessioned
2018-10-09T08:42:41Z
dc.date.available
2017-06-09T13:26:07Z
dc.date.available
2018-10-09T08:42:41Z
dc.date.issued
2011-07
dc.identifier.other
10.1186/1471-2164-12-376
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/39007
dc.identifier.doi
10.3929/ethz-b-000039007
dc.description.abstract
Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
BioMed Central
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/2.0/
dc.subject
cDNA library
en_US
dc.subject
database
en_US
dc.subject
EST
en_US
dc.subject
SNP
en_US
dc.subject
Silene
en_US
dc.title
Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 2.0 Generic
ethz.journal.title
BMC Genomics
ethz.journal.volume
12
en_US
ethz.pages.start
376
en_US
ethz.size
11 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.nebis
004256340
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.date.deposited
2017-06-09T13:26:38Z
ethz.source
ECIT
ethz.identifier.importid
imp59364e59b729537663
ethz.ecitpid
pub:62783
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-12T14:38:54Z
ethz.rosetta.lastUpdated
2018-12-03T00:46:47Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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