Fast skeletal muscle transcriptome of the gilthead sea bream (Sparus aurata) determined by next generation sequencing.

BMC Genomics
Daniel Garcia de la SerranaIan A Johnston

Abstract

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. 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 annotat...Continue Reading

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Citations

Jan 4, 2013·PloS One·Daniel Garcia de la serranaIan A Johnston
Apr 16, 2014·Genome Biology and Evolution·Daniel Garcia de la SerranaIan A Johnston
Feb 28, 2016·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·Daniel Garcia de la SerranaIan A Johnston
Jul 28, 2013·Marine Biotechnology·Carlos Frederico Ceccon LanesIgor Babiak
Nov 2, 2015·Molecular Genetics and Genomics : MGG·Jiayu ZhuGongshe Yang
Oct 14, 2014·Marine Genomics·Costas S TsigenopoulosGeorgios Kotoulas
Jun 19, 2013·General and Comparative Endocrinology·Florbela A VieiraD M Power
Mar 4, 2020·The Journal of Heredity·Andrew P AndersonAdam G Jones
Jul 2, 2019·Frontiers in Endocrinology·Marco António Campinho
May 26, 2020·Fungal Biology·Reza Zolfaghari EmamehReza Falak
Apr 3, 2019·Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology·P HarishD Garcia de la Serrana
Aug 27, 2021·Metabolites·Alessandra RenziniLuca Madaro

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Methods Mentioned

BETA
454 sequencing
electrophoresis
PCR

Software Mentioned

PhylM
InterProScan
- Toolkit - Cell - Biology
blastp
Inparanoid
Annot BLAST
Blast2GO
GS Reference Mapper
Isotig
Essembl

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