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

Research Article

Marta Gut¹  Diego Crespo²  Mireia Rovira²  Josep V Planas²  Noe Fernandez-Pozo³  M Gonzalo Claros⁴  Hicham Benzekri⁴  Carlos Infante⁵  Marian Ponce⁶  Paula Armesto⁶  Manuel Manchado⁶  Jose Luis Zambonino⁷  David Mazurais⁷  Marie-Laure Bégout⁸  Xavier Cousin⁹  Laureana Rebordinos^1,10  Manuel Alejandro Merlo^1,10  Sabine Nidelet^1,11  Rocío Bautista^1,12  Darío Guerrero-Fernández^1,12 

[1] Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, c/Baldiri Reixac 4, 08028, Barcelona, Spain;Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028, Barcelona, Spain;Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Campus de Teatinos s/n, Universidad de Málaga, 29071, Málaga, Spain;Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Campus de Teatinos s/n, Universidad de Málaga, 29071, Málaga, Spain;Plataforma Andaluza de Bioinformática, Universidad de Málaga, Edificio de Bioinnovación, C/ Severo Ochoa 34, 29590, Málaga, Spain;Fitoplanton Marino, S.L. Dársena Comercial s/n (Muelle Pesquero), 11500 El Puerto de Santa María, Cádiz, Spain;IFAPA Centro El Toruño, IFAPA, Consejeria de Agricultura y Pesca, 11500 El Puerto de Santa María, Cádiz, Spain;IFREMER, Unit of Functional Physiology of Marine Organisms, Ifremer, UMR 6539 LEMAR, 29280, Plouzané, France;Laboratoire d’Ecotoxicologie, Place Gaby Coll, IFREMER, BP 7, 17137, L’Houmeau, France;Laboratoire d’Ecotoxicologie, Place Gaby Coll, IFREMER, BP 7, 17137, L’Houmeau, France;INRA LPGP, Campus de Beaulieu, 35042, Rennes, France;Laboratorio de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Polígono del Río San Pedro, Puerto Real, 11510, Cádiz, Spain;MGX-Montpellier GenomiX c/o Institut de Genomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier, France;Plataforma Andaluza de Bioinformática, Universidad de Málaga, Edificio de Bioinnovación, C/ Severo Ochoa 34, 29590, Málaga, Spain;

关键词: Soles;    Transcriptome;    Microarray;    Orthology;    Molecular markers;    SoleaDB;   

DOI  :  10.1186/1471-2164-15-952

 received in 2014-04-30, accepted in 2014-10-15,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundSenegalese 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.ResultsA 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.ConclusionsTranscriptomes 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.

【 授权许可】

Unknown   
© Benzekri et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.