Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing
Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing
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DOI：
10.1186/1471-2164-13-181
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发表时间：
2012-05-11
期刊：
影响因子：
4.4
通讯作者：
Johnston, Ian A.
中科院分区：
文献类型：
--
作者：
de la Serrana, Daniel Garcia;Estevez, Alicia;Johnston, Ian A.
背景：金头鲷（Sparus aurata L.）发生在地中海周围和沿着东大西洋海岸从英国到塞内加尔。它能耐受各种温度和盐度，经常在微咸的沿海泻湖和河口地区发现，特别是在其生命周期的早期。吉尔黑德海鲷在地中海广泛种植，年产量为125，000公吨。在这里，我们提出了一个从头组装的快速骨骼肌转录组的金头鲷使用454读，并确定基因旁系同源物，剪接变异体和微卫星重复。骨骼肌的注释转录组将有助于理解与这一经济重要物种的生产相关的性状的遗传和分子基础。从成鱼的快速肌节中产生了大约270万个mRNA序列数据的读数（约2公斤）和幼鱼（类似于0.09kg），其已经被喂食至饱足、禁食3-5d或转移到低温（11摄氏度）或高温（33摄氏度）3-5d。Newbler v2.5组装产生43，461个>100 bp的同工酶。通过搜索蛋白质和基因本体数据库注释的序列的数量为10，465。注释的同工酶的平均覆盖度为x40，含有5655个独特的基因ID和785个编码含有58-1536个氨基酸的蛋白质的全长cDNA。基于使用来自GenBank的200个全长cDNA的验证，发现v2.5组装具有良好的质量。来自参考转录组的注释的同工酶可归因于344个KEGG途径图谱。我们确定了26个基因旁系同源物（其中20个是硬骨鱼特异性的）和43个剪接变体，其中12个缺失了可能影响其生物学功能的功能域。许多关键的转录因子，信号分子和结构蛋白的肌肉发生和肌肉生长所必需的已被确定。生理状态影响的读数映射到isotigs的数量，反映了基因表达的变化之间的treatment.Conclusions：我们已经产生了一个全面的快速骨骼肌转录组的金头鲷，这将提供一个资源，SNP发现基因的生产性状的商业利益和表达研究的增长和适应。
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 (similar to 2 kg) and juvenile fish (similar to 0.09 kg) that had been either fed to satiation, fasted for 3-5d or transferred to low (11 degrees C) or high (33 degrees 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.