title: 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.
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.
authors.forename: Hicham
authors.initials: H
authors.lastname: Benzekri
authors.forename: Paula
authors.initials: P
authors.lastname: Armesto
authors.forename: Xavier
authors.initials: X
authors.lastname: Cousin
authors.forename: Mireia
authors.initials: M
authors.lastname: Rovira
authors.forename: Diego
authors.initials: D
authors.lastname: Crespo
authors.forename: Manuel Alejandro
authors.initials: MA
authors.lastname: Merlo
authors.forename: David
authors.initials: D
authors.lastname: Mazurais
authors.forename: Rocío
authors.initials: R
authors.lastname: Bautista
authors.forename: Darío
authors.initials: D
authors.lastname: Guerrero-Fernández
authors.forename: Noe
authors.initials: N
authors.lastname: Fernandez-Pozo
authors.forename: Marian
authors.initials: M
authors.lastname: Ponce
authors.forename: Carlos
authors.initials: C
authors.lastname: Infante
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Zambonino
authors.forename: Sabine
authors.initials: S
authors.lastname: Nidelet
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.forename: Laureana
authors.initials: L
authors.lastname: Rebordinos
authors.forename: Josep V
authors.initials: JV
authors.lastname: Planas
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Bégout
authors.forename: M Gonzalo
authors.initials: MG
authors.lastname: Claros
authors.affiliation: IFAPA Centro El Toruño, IFAPA, Consejeria de Agricultura y Pesca, 11500 El Puerto de Santa María, Cádiz, Spain. manuel.manchado@juntadeandalucia.es.
authors.forename: Manuel
authors.initials: M
authors.lastname: Manchado
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003459:Crystallins; D030541:Databases, Genetic; D005412:Flatfishes / Q000235:genetics*; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards; D010802:Phylogeny; D015203:Reproducibility of Results; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D003459:Crystallins