title: Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach.
abstract: Rainbow trout, Oncorhynchus mykiss, is an important aquaculture species worldwide and, in addition to being of commercial interest, it is also a research model organism of considerable scientific importance. Because of the lack of a whole genome sequence in that species, transcriptomic analyses of this species have often been hindered. Using next-generation sequencing (NGS) technologies, we sought to fill these informational gaps. Here, using Roche 454-Titanium technology, we provide new tissue-specific cDNA repertoires from several rainbow trout tissues. Non-normalized cDNA libraries were constructed from testis, ovary, brain and gill rainbow trout tissue samples, and these different libraries were sequenced in 10 separate half-runs of 454-Titanium. Overall, we produced a total of 3million quality sequences with an average size of 328bp, representing more than 1Gb of expressed sequence information. These sequences have been combined with all publicly available rainbow trout sequences, resulting in a total of 242,187 clusters of putative transcript groups and 22,373 singletons. To identify the predominantly expressed genes in different tissues of interest, we developed a Digital Differential Display (DDD) approach. This approach allowed us to characterize the genes that are predominantly expressed within each tissue of interest. Of these genes, some were already known to be tissue-specific, thereby validating our approach. Many others, however, were novel candidates, demonstrating the usefulness of our strategy and of such tissue-specific resources. This new sequence information, acquired using NGS 454-Titanium technology, deeply enriched our current knowledge of the expressed genes in rainbow trout through the identification of an increased number of tissue-specific sequences. This identification allowed a precise cDNA tissue repertoire to be characterized in several important rainbow trout tissues. The rainbow trout contig browser can be accessed at the following publicly available web site (http://www.sigenae.org/).
authors.affiliation: INRA, UR1037 LPGP Fish Physiology and Genomics, F-35000 Rennes, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Le Cam
authors.forename: Julien
authors.initials: J
authors.lastname: Bobe
authors.forename: Olivier
authors.initials: O
authors.lastname: Bouchez
authors.forename: Cédric
authors.initials: C
authors.lastname: Cabau
authors.forename: Olivier
authors.initials: O
authors.lastname: Kah
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Lareyre
authors.forename: Isabelle
authors.initials: I
authors.lastname: Le Guen
authors.forename: Jérôme
authors.initials: J
authors.lastname: Lluch
authors.forename: Jérôme
authors.initials: J
authors.lastname: Montfort
authors.forename: Francois
authors.initials: F
authors.lastname: Moreews
authors.forename: Barbara
authors.initials: B
authors.lastname: Nicol
authors.forename: Patrick
authors.initials: P
authors.lastname: Prunet
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Rescan
authors.forename: Arianna
authors.initials: A
authors.lastname: Servili
authors.forename: Yann
authors.initials: Y
authors.lastname: Guiguen
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling; D005880:Gills / Q000378:metabolism; D006066:Gonads / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D017686:Oncorhynchus mykiss / Q000235:genetics*; D009928:Organ Specificity; D017422:Sequence Analysis, DNA