Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Apartado Oficial 11510 Puerto Real, Cádiz, Spain.
Mar Biotechnol (NY). 2012 Aug;14(4):423-35. doi: 10.1007/s10126-011-9422-3. Epub 2011 Dec 14.
Gilthead seabream (Sparus aurata) is a teleost belonging to the family Sparidae with a high economical relevance in the Mediterranean countries. Although genomic tools have been developed in this species in order to investigate its physiology at the molecular level and consequently its culture, genomic information on post-embryonic development is still scarce. In this study, we have investigated the transcriptome of a marine teleost during the larval stage (from hatching to 60 days after hatching) by the use of 454 pyrosequencing technology. We obtained a total of 68,289 assembled contigs, representing putative transcripts, belonging to 54,606 different clusters. Comparison against all S. aurata expressed sequenced tags (ESTs) from the NCBI database revealed that up to 34,722 contigs, belonging to about 61% of gene clusters, are sequences previously not described. Contigs were annotated through an iterative Blast pipeline by comparison against databases such as NCBI RefSeq from Danio rerio, SwissProt or NCBI teleost ESTs. Our results indicate that we have enriched the number of annotated sequences for this species by more than 50% compared with previously existing databases for the gilthead seabream. Gene Ontology analysis of these novel sequences revealed that there is a statistically significant number of transcripts with key roles in larval development, differentiation, morphology, and growth. Finally, all information has been made available online through user-friendly interfaces such as GBrowse and a Blast server with a graphical frontend.
真鲷（Sparus aurata）是鲈形目鲷科的一种鱼类，在地中海国家具有重要的经济意义。尽管已经为该物种开发了基因组工具，以研究其分子水平的生理学，从而研究其养殖，但关于胚胎后发育的基因组信息仍然很少。在这项研究中，我们使用 454 焦磷酸测序技术研究了海洋鱼类在幼体阶段（从孵化到孵化后 60 天）的转录组。我们总共获得了 68289 个组装的连续体，代表了 54606 个不同聚类的假定转录本。与 NCBI 数据库中所有 Sparus aurata 表达序列标签（EST）的比较表明，多达 34722 个连续体，属于约 61%的基因聚类，是以前未描述的序列。通过与 NCBI RefSeq 数据库中的 Danio rerio、SwissProt 或 NCBI 硬骨鱼 EST 等数据库进行迭代 Blast 比较，对连续体进行注释。我们的结果表明，与真鲷以前存在的数据库相比，我们通过这种方法为该物种注释序列的数量增加了 50%以上。对这些新序列的基因本体论分析表明，有大量具有幼虫发育、分化、形态和生长关键作用的转录本。最后，所有信息都通过 GBrowse 等用户友好的界面和带有图形前端的 Blast 服务器在线提供。
