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

Type Article
Date 2014-11
Language English
Author(s) Benzekri Hicham1, 2, Armesto Paula3, Cousin XavierORCID4, 5, Rovira Mireia6, 7, Crespo Diego6, 7, Alejandro Merlo Manuel8, Mazurais DavidORCID9, Bautista Rocio2, Guerrero-Fernandez Dario2, Fernandez-Pozo Noe1, Ponce Marian3, Infante Carlos10, Zambonino-Infante Jose LuisORCID9, Nidelet Sabine11, Gut Marta12, Rebordinos Laureana8, Planas Josep V.6, 7, Begout Marie-LaureORCID4, Gonzalo Claros M.1, 2, Manchado Manuel3
Affiliation(s) 1 : Univ Malaga, Fac Ciencias, Dept Bioquim & Biol Mol, E-29071 Malaga, Spain.
2 : Univ Malaga, Plataforma Andaluza Bioinformat, Malaga 29590, Spain.
3 : Consejeria Agr & Pesca, IFAPA, IFAPA Ctr El Toruno, Cadiz 11500, Spain.
4 : IFREMER, Lab Ecotoxicol, F-17137 Lhoumeau, France.
5 : INRA LPGP, F-35042 Rennes, France.
6 : Univ Barcelona, Fac Biol, Deptt Fisiol & Immunol, E-08028 Barcelona, Spain.
7 : Univ Barcelona IBUB, Inst Biomed, Barcelona 08028, Spain.
8 : Univ Cadiz, Fac Ciencias Mar & Ambientales, Genet Lab, Cadiz 11510, Spain.
9 : IFREMER, Unit Funct Physiol Marine Organisms, UMR LEMAR 6539, F-29280 Plouzane, France.
10 : Fitoplanton Marino, Cadiz 11500, Spain.
11 : Inst Genom Fonct, MGX Montpellier GenomiX, F-34094 Montpellier, France.
12 : Ctr Nacl Anal Genom, Barcelona 08028, Spain.
Source Bmc Genomics (1471-2164) (Biomed Central Ltd), 2014-11 , Vol. 15 , P. -
DOI 10.1186/1471-2164-15-952
WOS© Times Cited 53
Note Additional files : http://www.biomedcentral.com/1471-2164/15/952/additional
Keyword(s) Soles, Transcriptome, Microarray, Orthology, Molecular markers, SoleaDB
Abstract 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.
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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 (2014). 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. Bmc Genomics, 15, -. Publisher's official version : https://doi.org/10.1186/1471-2164-15-952 , Open Access version : https://archimer.ifremer.fr/doc/00238/34918/