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Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach
- Source :
- Animation de l'axe technologique génomique de Biogenouest, Animation de l'axe technologique génomique de Biogenouest, Plateforme Génomique Santé Biogenouest®. FRA., Apr 2011, Rennes, France, Gene, Gene, Elsevier, 2012, 500 (1), pp.32-39. ⟨10.1016/j.gene.2012.03.053⟩, Gene 1 (500), 32-39. (2012), Gene, 2012, 500 (1), pp.32-39. ⟨10.1016/j.gene.2012.03.053⟩
- Publication Year :
- 2011
- Publisher :
- HAL CCSD, 2011.
-
Abstract
- International audience; 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 3 million quality sequences with an average size of 328 bp, representing more than 1 Gb 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/).
- Subjects :
- Gills
Male
muscle
animal diseases
[SDV]Life Sciences [q-bio]
0302 clinical medicine
poisson
Biologie de la reproduction
banque de données
[MATH]Mathematics [math]
ComputingMilieux_MISCELLANEOUS
Genetics
Animal biology
salmonidae
0303 health sciences
Differential display
Reproductive Biology
oncorhynchus mykiss
Contig
[SDV.BA]Life Sciences [q-bio]/Animal biology
Brain
High-Throughput Nucleotide Sequencing
General Medicine
Organ Specificity
cerveau
testicule
Female
expression des gènes
endocrine system
animal structures
salmonid
Computational biology
Biology
digestive system
DNA sequencing
03 medical and health sciences
Complementary DNA
Biologie animale
séquençage
genomics
Animals
[INFO]Computer Science [cs]
14. Life underwater
Gonads
Gene
030304 developmental biology
Whole genome sequencing
fish
cDNA library
urogenital system
Gene Expression Profiling
génome
ovaire
[SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology
Sequence Analysis, DNA
branchie
rainbow-trout
transcriptome
next-generation sequencing
Rainbow trout
030217 neurology & neurosurgery
truite arc en ciel
Subjects
Details
- Language :
- English
- ISSN :
- 03781119 and 18790038
- Database :
- OpenAIRE
- Journal :
- Animation de l'axe technologique génomique de Biogenouest, Animation de l'axe technologique génomique de Biogenouest, Plateforme Génomique Santé Biogenouest®. FRA., Apr 2011, Rennes, France, Gene, Gene, Elsevier, 2012, 500 (1), pp.32-39. ⟨10.1016/j.gene.2012.03.053⟩, Gene 1 (500), 32-39. (2012), Gene, 2012, 500 (1), pp.32-39. ⟨10.1016/j.gene.2012.03.053⟩
- Accession number :
- edsair.doi.dedup.....85835312d1a108594802b44bf1ced694