De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a dat
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- 作者：Hicham Benzekri (1) (2)
Paula Armesto (3)
Xavier Cousin (4) (5)
Mireia Rovira (6)
Diego Crespo (6)
Manuel Alejandro Merlo (7)
David Mazurais (8)
Roc铆o Bautista (2)
Dar铆o Guerrero-Fern谩ndez (2)
Noe Fernandez-Pozo (1)
Marian Ponce (3)
Carlos Infante (9)
Jose Luis Zambonino (8)
Sabine Nidelet (10)
Marta Gut (11)
Laureana Rebordinos (7)
Josep V Planas (6)
Marie-Laure B茅gout (4)
M Gonzalo Claros (1) (2)
Manuel Manchado (3)
1. Departamento de Biolog铆a Molecular y Bioqu铆mica ; Facultad de Ciencias ; Universidad de M谩laga ; Campus de Teatinos s/n ; 29071 ; M谩laga ; Spain
2. Plataforma Andaluza de Bioinform谩tica ; Universidad de M谩laga ; Edificio de Bioinnovaci贸n ; C/ Severo Ochoa 34 ; 29590 ; M谩laga ; Spain
3. IFAPA Centro El Toru帽o ; IFAPA ; Consejeria de Agricultura y Pesca ; 11500 El Puerto de Santa Mar铆a ; C谩diz ; Spain
4. IFREMER ; Laboratoire d鈥橢cotoxicologie ; Place Gaby Coll ; BP 7 ; 17137 ; L鈥橦oumeau ; France
5. INRA LPGP ; Campus de Beaulieu ; 35042 ; Rennes ; France
6. Departament de Fisiologia i Immunologia ; Facultat de Biologia ; Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB) ; 08028 ; Barcelona ; Spain
7. Laboratorio de Gen茅tica. Facultad de Ciencias del Mar y Ambientales ; Universidad de C谩diz ; Pol铆gono del R铆o San Pedro ; Puerto Real ; 11510 ; C谩diz ; Spain
8. IFREMER ; Unit of Functional Physiology of Marine Organisms ; Ifremer ; UMR 6539 LEMAR ; 29280 ; Plouzan茅 ; France
9. Fitoplanton Marino ; S.L. D谩rsena Comercial s/n (Muelle Pesquero) ; 11500 El Puerto de Santa Mar铆a ; C谩diz ; Spain
10. MGX-Montpellier GenomiX c/o Institut de Genomique Fonctionnelle ; 141 rue de la Cardonille ; 34094 ; Montpellier ; France
11. Centro Nacional de An谩lisis Gen贸mico ; Parc Cient铆fic de Barcelona ; c/Baldiri Reixac 4 ; 08028 ; Barcelona ; Spain - 关键词：Soles ; Transcriptome ; Microarray ; Orthology ; Molecular markers ; SoleaDB
- 刊名：BMC Genomics
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：1
- 全文大小：2,282 KB
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- 出版者：BioMed Central
- ISSN：1471-2164
文摘
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.