ArticleBMC genomics2006
Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 3 of them syntheses that pooled it.
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37 citing papers in PubMed, 3 syntheses or guidelines pooled it, 87 citations in OpenAlex.
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- Comparative genome mapping between Chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (O. mykiss) based on homologous microsatellite loci.G3 (Bethesda, Md.) · 2013Article
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- Analysis of the Asian seabass transcriptome based on expressed sequence tags.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
- Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes.BMC genomics · 2011Article
- Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate.BMC genomics · 2011Article
- A first generation integrated map of the rainbow trout genome.BMC genomics · 2011Article
- EST-based identification of genes expressed in skeletal muscle of the mandarin fish (Siniperca chuatsi).Genomics, proteomics & bioinformatics · 2011Article
- Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches.BMC genomics · 2010Article
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- Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWithin the framework of a genomics project on livestock species (AGENAE), we initiated a high-throughput DNA sequencing program of Expressed Sequence Tags (ESTs) in rainbow trout, Oncorhynchus mykiss.
resultsWe constructed three cDNA libraries including one highly complex pooled-tissue library. These libraries were normalized and subtracted to reduce clone redundancy. ESTs sequences were produced, and 96,472 ESTs corresponding to high quality sequence reads were released on the international database, currently representing 42.5% of the overall sequence knowledge in this species. All these EST sequences and other publicly available ESTs in rainbow trout have been included on a publicly available Website (SIGENAE) and have been clustered into a total of 52,930 clusters of putative transcripts groups, including 24,616 singletons. 57.1% of these 52,930 clusters are represented by at least one Agenae EST and 14,343 clusters (27.1%) are only composed by Agenae ESTs. Sequence analysis also reveals that normalization and especially subtraction were effective in decreasing redundancy, and that the pooled-tissue library was representative of the initial tissue complexity.
conclusionDue to present work on the construction of rainbow trout normalized cDNA libraries and their extensive sequencing, along with other large scale sequencing programs, rainbow trout is now one of the major fish models in term of EST sequences available in a public database, just after Zebrafish, Danio rerio. This information is now used for the selection of a non redundant set of clones for producing DNA micro-arrays in order to examine global gene expression.
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