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Journal articles
Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach
Aurélie Le Cam
1
Julien Bobe
1
Olivier Bouchez
2
Cédric Cabau
3
Olivier Kah
4
Christophe Klopp
5
Jean-Jacques Lareyre
1
Isabelle Le Guen
1
Jérôme Lluch
2
Jérôme Montfort
1
Francois Moreews
6, 7
Barbara Nicol
8
Patrick Prunet
1
Pierre-Yves Rescan
1
Arianna Servili
9
Yann Guiguen
1
7
GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Aurélie Le Cam 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : aurelie-le-cam
Julien Bobe 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : julien-bobe ORCID : https://orcid.org/0000-0002-9355-8227
Olivier Bouchez 2
Author
Cédric Cabau 3
Author IdHAL : cedric-cabau ORCID : https://orcid.org/0000-0001-8560-4003
Olivier Kah 4
Author
Christophe Klopp 5
Author IdHAL : 0000-0001-7126-5477 ORCID : https://orcid.org/0000-0001-7126-5477
Jean-Jacques Lareyre 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : jean-jacques-lareyre ORCID : https://orcid.org/0000-0003-0747-0024
Isabelle Le Guen 1
Author IdHAL : isabelle-leguen ORCID : https://orcid.org/0000-0001-6091-5366
Jérôme Lluch 2
Author
Jérôme Montfort 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : jerome-montfort
Francois Moreews 6, 7
Author
Barbara Nicol 8
Author
Patrick Prunet 1
Author
Pierre-Yves Rescan 1
Author IdHAL : pierre-yves-rescan ORCID : https://orcid.org/0000-0002-4688-0977
Arianna Servili 9
Author IdHAL : arianna-servili ORCID : https://orcid.org/0000-0002-6813-7500
Yann Guiguen 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : yann-guiguen ORCID : https://orcid.org/0000-0001-5464-6219
1
LPGP - Laboratoire de Physiologie et Génomique des Poissons (France)
- INRA - Institut National de la Recherche Agronomique : UR1037 (France)
- Biosit : Biologie - Santé - Innovation Technologique - Structure Fédérative de Recherche en Biologie et Santé de Rennes (Université Rennes 1 - Campus Santé Villejean - 2, avenue Professeur Léon Bernard 35043 Rennes cedex - France)
2
GENOTOUL - Génopole Toulouse Midi-Pyrénées [Auzeville] (Chemin de Borde-Rouge Auzeville - France)
- INRA - Institut National de la Recherche Agronomique (France)
- INSA Toulouse - Institut National des Sciences Appliquées - Toulouse (135, avenue de Rangueil - 31077 Toulouse cedex 4 - France)
- UT3 - Université Toulouse III - Paul Sabatier (118 route de Narbonne - 31062 Toulouse - France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
- ENVT - Ecole Nationale Vétérinaire de Toulouse (23 chemin des Capelles
31076 Toulouse
Cedex - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- INSERM - Institut National de la Santé et de la Recherche Médicale (101, rue de Tolbiac, 75013 Paris - France)
- Toulouse INP - Institut National Polytechnique (Toulouse) (France)
- Université Fédérale Toulouse Midi-Pyrénées (41 Allée Jules Guesde, 31000 Toulouse - France)
3
Unité de recherches Avicoles (Nouzilly - France)
4
ICM - Interactions cellulaires et moléculaires (Campus de Beaulieu, 263 avenue du Général Leclerc CS 74205 35042 RENNES CEDEX - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- CNRS - Centre National de la Recherche Scientifique : UMR6026 (France)
5
UBIA - Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (24 Chemin de Borde Rouge BP 52627 - 31326 Castanet-Tolosan Cedex - France)
7
GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)
- Inria Rennes – Bretagne Atlantique (Campus de beaulieu
35042 Rennes cedex - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE (France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
- INSA Rennes - Institut National des Sciences Appliquées - Rennes (20, avenue des Buttes de Coësmes - CS 70839 - 35708 Rennes cedex 7 - France)
- UBS - Université de Bretagne Sud (BP 92116 - 56321 Lorient cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6074 (France)
- ENS Rennes - École normale supérieure - Rennes (Campus de Ker Lann - avenue Robert Schuman - 35170 Bruz - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- Télécom Bretagne (Technopôle Brest-Iroise CS 83818 29238 BREST Cedex 3 - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- CentraleSupélec (3, rue Joliot Curie, Plateau de Moulon, 91192 GIF-SUR-YVETTE Cedex - France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
8
IGDR - Institut de Génétique et Développement de Rennes (Faculté de Médecine - CS 34317 2 Av du Professeur Léon Bernard 35043 RENNES CEDEX - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6061 (France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
9
Department of Biology [Univ. of Cadiz] (Faculty of Marine and Environmental Sciences University of Cadiz E-11510 PUERTO REAL - Spain)
- University of Cadiz (Spain)
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 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/).
Document type :
Journal articles
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https://hal.inria.fr/hal-00753316
Contributor : Francois Moreews <>
Submitted on : Monday, November 19, 2012 - 9:37:48 AM
Last modification on : Thursday, January 14, 2021 - 11:29:07 AM
Contributor : Francois Moreews <>
Submitted on : Monday, November 19, 2012 - 9:37:48 AM
Last modification on : Thursday, January 14, 2021 - 11:29:07 AM
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Identifiers
- HAL Id : hal-00753316, version 1
- DOI : 10.1016/j.gene.2012.03.053
- PUBMED : 22465513
Collections
CNRS | INRIA | IRISA | IGDR | UNIV-RENNES1 | IRSET | INRA | BIOSIT | IRISA-D7 | LPGP | INSTITUT-TELECOM | UR1-UFR-SVE | INSA-TOULOUSE | UR1-UFR-ISTIC | UNIV-RENNES | INSA-GROUPE | UNIV-TLSE3 | INRAE | INSA-RENNES
Citation
Aurélie Le Cam, Julien Bobe, Olivier Bouchez, Cédric Cabau, Olivier Kah, et al.. Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach. Gene, Elsevier, 2012, 500 (1), pp.32-39. ⟨10.1016/j.gene.2012.03.053⟩. ⟨hal-00753316⟩
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