Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts.
Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts.
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DOI：
10.1186/1471-2164-14-178
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发表时间：
2013-03-15
期刊：
影响因子：
4.4
通讯作者：
Pérez-Sánchez J
中科院分区：
文献类型：
--
作者：
Calduch-Giner JA;Bermejo-Nogales A;Benedito-Palos L;Estensoro I;Ballester-Lozano G;Sitjà-Bobadilla A;Pérez-Sánchez J
金头鲷（Sparus aurata）是地中海地区养殖的主要鱼类，是一个有趣的研究模型。然而，对于这种非常有价值的物种来说，转录组和基因组数据仍然稀缺。转录组数据库是通过从头组装来自 mRNA 公共存储库的金头鲷序列和表达序列标签集合以及来自骨骼肌 (1)、肠道 (1)、头肾 (2) 和血液 (1) 五个 cDNA 454 标准化文库的新高质量读数来构建的。新的 454 个标准化文库的测序产生了 2,945,914 个高质量读数，从头全局组装产生了 125,263 个独特序列，平均长度为 727 nt。针对蛋白质和核苷酸数据库的 Blast 分析注释了编码 21,384 个基因描述的 63,880 个序列，这些序列在开放阅读框的同聚物区域进行冗余和移码，并托管在 http://www.nutrigroup-iats.org/seabreamdb。在带注释的基因描述中，16,177 个被映射到 Ingenuity Pathway Analysis (IPA) 数据库中，10,899 个符合功能分析条件，在 372 个 IPA 经典路径中代表了 341 个。在核苷酸金头鲷数据库中通过 Blast 搜索随机选择的棘鱼转录本的高代表性证明了其蛋白质编码转录本的高覆盖率。新组装的金头鲷转录组代表了该物种基因组资源的进步，因为它可能包含超过75%的活跃转录基因，构成了协助功能基因组学和未来基因组计划研究的宝贵工具。
The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of gilthead sea bream sequences derived from public repositories of mRNA and collections of expressed sequence tags together with new high-quality reads from five cDNA 454 normalized libraries of skeletal muscle (1), intestine (1), head kidney (2) and blood (1). Sequencing of the new 454 normalized libraries produced 2,945,914 high-quality reads and the de novo global assembly yielded 125,263 unique sequences with an average length of 727 nt. Blast analysis directed to protein and nucleotide databases annotated 63,880 sequences encoding for 21,384 gene descriptions, that were curated for redundancies and frameshifting at the homopolymer regions of open reading frames, and hosted at http://www.nutrigroup-iats.org/seabreamdb. Among the annotated gene descriptions, 16,177 were mapped in the Ingenuity Pathway Analysis (IPA) database, and 10,899 were eligible for functional analysis with a representation in 341 out of 372 IPA canonical pathways. The high representation of randomly selected stickleback transcripts by Blast search in the nucleotide gilthead sea bream database evidenced its high coverage of protein-coding transcripts. The newly assembled gilthead sea bream transcriptome represents a progress in genomic resources for this species, as it probably contains more than 75% of actively transcribed genes, constituting a valuable tool to assist studies on functional genomics and future genome projects.
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影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
DOI：
10.1093/bioinformatics/btq365
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Balzer S;Malde K;Lanzén A;Sharma A;Jonassen I
通讯作者：
Jonassen I
影响因子：
46.9
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
通讯作者：
Pallen, Mark J.
影响因子：
4.4
作者：
de la Serrana, Daniel Garcia;Estevez, Alicia;Johnston, Ian A.
通讯作者：
Johnston, Ian A.
影响因子：
4.4
作者：
Meyer E;Aglyamova GV;Wang S;Buchanan-Carter J;Abrego D;Colbourne JK;Willis BL;Matz MV
通讯作者：
Matz MV