Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles BMC Genomics Year : 2006

Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries

Abstract

Background: Within 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. Results: We 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. Conclusion: Due 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.

Domains

Genetics
Fichier principal
Vignette du fichier
2006_Govoroun_BMCGenomics_1.pdf (301.58 Ko) Télécharger le fichier
Origin Publisher files allowed on an open archive
Loading...

Dates and versions

hal-02659940 , version 1 (30-05-2020)

Identifiers

Cite

Marina Govoroun, Florence Le Gac, Yann Guiguen. Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries. BMC Genomics, 2006, 7, pp.1-8. ⟨10.1186/1471-2164-7-196⟩. ⟨hal-02659940⟩
9 View
40 Download

Altmetric

Share

Gmail Mastodon Facebook X LinkedIn More