FN Archimer Export Format PT J TI De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray BT AF BENZEKRI, Hicham ARMESTO, Paula COUSIN, Xavier ROVIRA, Mireia CRESPO, Diego ALEJANDRO MERLO, Manuel MAZURAIS, David BAUTISTA, Rocio GUERRERO-FERNANDEZ, Dario FERNANDEZ-POZO, Noe PONCE, Marian INFANTE, Carlos ZAMBONINO-INFANTE, Jose Luis NIDELET, Sabine GUT, Marta REBORDINOS, Laureana PLANAS, Josep V. BEGOUT, Marie-Laure GONZALO CLAROS, M. MANCHADO, Manuel AS 1:1,2;2:3;3:4,5;4:6,7;5:6,7;6:8;7:9;8:2;9:2;10:1;11:3;12:10;13:9;14:11;15:12;16:8;17:6,7;18:4;19:1,2;20:3; FF 1:;2:;3:;4:;5:;6:;7:PDG-RBE-PFOM-ARN;8:;9:;10:;11:;12:;13:PDG-RBE-PFOM-ARN;14:;15:;16:;17:;18:PDG-RBE-HGS-LRHLR;19:;20:; C1 Univ Malaga, Fac Ciencias, Dept Bioquim & Biol Mol, E-29071 Malaga, Spain. Univ Malaga, Plataforma Andaluza Bioinformat, Malaga 29590, Spain. Consejeria Agr & Pesca, IFAPA, IFAPA Ctr El Toruno, Cadiz 11500, Spain. IFREMER, Lab Ecotoxicol, F-17137 Lhoumeau, France. INRA LPGP, F-35042 Rennes, France. Univ Barcelona, Fac Biol, Deptt Fisiol & Immunol, E-08028 Barcelona, Spain. Univ Barcelona IBUB, Inst Biomed, Barcelona 08028, Spain. Univ Cadiz, Fac Ciencias Mar & Ambientales, Genet Lab, Cadiz 11510, Spain. IFREMER, Unit Funct Physiol Marine Organisms, UMR LEMAR 6539, F-29280 Plouzane, France. Fitoplanton Marino, Cadiz 11500, Spain. Inst Genom Fonct, MGX Montpellier GenomiX, F-34094 Montpellier, France. Ctr Nacl Anal Genom, Barcelona 08028, Spain. C2 UNIV MALAGA, SPAIN UNIV MALAGA, SPAIN IFAPA, SPAIN IFREMER, FRANCE INRA, FRANCE UNIV BARCELONA, SPAIN UNIV BARCELONA, SPAIN UNIV CADIZ, SPAIN IFREMER, FRANCE FITOPLANCTON MARINO, SPAIN INST GENOM FONCT, FRANCE CTR NACL ANAL GENOM, SPAIN SI LA ROCHELLE BREST SE PDG-RBE-BE-LBEX PDG-RBE-PFOM-ARN PDG-RBE-HGS-LRHLR IN WOS Ifremer jusqu'en 2018 copubli-france copubli-p187 copubli-europe IF 3.986 TC 61 UR https://archimer.ifremer.fr/doc/00238/34918/33626.pdf LA English DT Article DE ;Soles;Transcriptome;Microarray;Orthology;Molecular markers;SoleaDB AB Background Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution. Results A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB. Conclusions Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species. PY 2014 PD NOV SO Bmc Genomics SN 1471-2164 PU Biomed Central Ltd VL 15 UT 000345250500001 DI 10.1186/1471-2164-15-952 ID 34918 ER EF