Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing
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Publication date
2012-05-11ISSN
1471-2164
Abstract
Background: The gilthead sea bream (Sparus aurata L.) occurs around the Mediterranean and along Eastern Atlantic
coasts from Great Britain to Senegal. It is tolerant of a wide range of temperatures and salinities and is often found in
brackish coastal lagoons and estuarine areas, particularly early in its life cycle. Gilthead sea bream are extensively
cultivated in the Mediterranean with an annual production of 125,000 metric tonnes. Here we present a de novo
assembly of the fast skeletal muscle transcriptome of gilthead sea bream using 454 reads and identify gene paralogues,
splice variants and microsatellite repeats. An annotated transcriptome of the skeletal muscle will facilitate
understanding of the genetic and molecular basis of traits linked to production in this economically important species.
Results: Around 2.7 million reads of mRNA sequence data were generated from the fast myotomal of adult fish
(~2 kg) and juvenile fish (~0.09 kg) that had been either fed to satiation, fasted for 3-5d or transferred to low (11°C) or
high (33°C) temperatures for 3-5d. Newbler v2.5 assembly resulted in 43,461 isotigs >100 bp. The number of
sequences annotated by searching protein and gene ontology databases was 10,465. The average coverage of the
annotated isotigs was x40 containing 5655 unique gene IDs and 785 full-length cDNAs coding for proteins containing
58–1536 amino acids. The v2.5 assembly was found to be of good quality based on validation using 200 full-length
cDNAs from GenBank. Annotated isotigs from the reference transcriptome were attributable to 344 KEGG pathway
maps. We identified 26 gene paralogues (20 of them teleost-specific) and 43 splice variants, of which 12 had functional
domains missing that were likely to affect their biological function. Many key transcription factors, signaling molecules
and structural proteins necessary for myogenesis and muscle growth have been identified. Physiological status affected
the number of reads that mapped to isotigs, reflecting changes in gene expression between treatments.
Conclusions: We have produced a comprehensive fast skeletal muscle transcriptome for the gilthead sea bream,
which will provide a resource for SNP discovery in genes with a large effect on production traits of commercial interest
and for expression studies of growth and adaptation.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
637 - Produce of domestic (farmyard) animals and game
Pages
17
Publisher
BMC
Is part of
BMC Genomics
Citation
García de la Serrana, Daniel, Alicia Estévez, Karl B. Andrée, and Ian A. Johnston. 2012. “Fast Skeletal Muscle Transcriptome of the Gilthead Sea Bream (Sparus Aurata) Determined by Next Generation Sequencing.” BMC Genomics 13 (1): 181. doi:10.1186/1471-2164-13-181.
Grant agreement number
EC/FP7/222719/EU/Building a biological knowledge-base on fish lifecycles for competitive, sustainable European aquaculture/LIFECYCLE
Program
Aqüicultura
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2850]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/