TY - JOUR T1 - 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 A1 - Benzekri,Hicham A1 - Armesto,Paula A1 - Cousin,Xavier A1 - Rovira,Mireia A1 - Crespo,Diego A1 - Alejandro Merlo,Manuel A1 - Mazurais,David A1 - Bautista,Rocio A1 - Guerrero-Fernandez,Dario A1 - Fernandez-Pozo,Noe A1 - Ponce,Marian A1 - Infante,Carlos A1 - Zambonino-Infante,Jose Luis A1 - Nidelet,Sabine A1 - Gut,Marta A1 - Rebordinos,Laureana A1 - Planas,Josep V. A1 - Begout,Marie-Laure A1 - Gonzalo Claros,M. A1 - Manchado,Manuel AD - Univ Malaga, Fac Ciencias, Dept Bioquim & Biol Mol, E-29071 Malaga, Spain. AD - Univ Malaga, Plataforma Andaluza Bioinformat, Malaga 29590, Spain. AD - Consejeria Agr & Pesca, IFAPA, IFAPA Ctr El Toruno, Cadiz 11500, Spain. AD - IFREMER, Lab Ecotoxicol, F-17137 Lhoumeau, France. AD - INRA LPGP, F-35042 Rennes, France. AD - Univ Barcelona, Fac Biol, Deptt Fisiol & Immunol, E-08028 Barcelona, Spain. AD - Univ Barcelona IBUB, Inst Biomed, Barcelona 08028, Spain. AD - Univ Cadiz, Fac Ciencias Mar & Ambientales, Genet Lab, Cadiz 11510, Spain. AD - IFREMER, Unit Funct Physiol Marine Organisms, UMR LEMAR 6539, F-29280 Plouzane, France. AD - Fitoplanton Marino, Cadiz 11500, Spain. AD - Inst Genom Fonct, MGX Montpellier GenomiX, F-34094 Montpellier, France. AD - Ctr Nacl Anal Genom, Barcelona 08028, Spain. UR - https://archimer.ifremer.fr/doc/00238/34918/ DO - 10.1186/1471-2164-15-952 KW - Soles KW - Transcriptome KW - Microarray KW - Orthology KW - Molecular markers KW - SoleaDB N2 - 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. Y1 - 2014/11 PB - Biomed Central Ltd JF - Bmc Genomics SN - 1471-2164 VL - 15 ID - 34918 ER -