Detection of alternative splice and gene duplication by RNA sequencing in Japanese flounder, Paralichthys olivaceus.
Detection of alternative splice and gene duplication by RNA sequencing in Japanese flounder, Paralichthys olivaceus.
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DOI：
10.1534/g3.114.012138
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发表时间：
2014-11-05
期刊：
影响因子：
--
通讯作者：
Zhang Q
中科院分区：
文献类型：
--
作者：
Wang W;Wang J;You F;Ma L;Yang X;Gao J;He Y;Qi J;Yu H;Wang Z;Wang X;Wu Z;Zhang Q
牙鲆(Paralichthys Olivaceus)是中国重要的经济鱼类之一。性二态，特别是两性之间不同的生长速度和体型，使这种鱼成为研究进化中的基本问题和水产养殖中的应用主题的这种二态的机制的一个很好的模型。然而，缺乏“组学”数据阻碍了这一进程。最近出现的RNA测序技术为进一步研究非模式物种的基因组特征提供了一个强大的工具。在这里，我们使用Illumina测序法对一个双单倍体日本比目鱼个体进行了从头转录组测序。一条成对末端测序的单通道产生了超过2700万个读数。这些片段被组装成107,318个非冗余转录本，其中一半(51,563个；48.1%)被blastx注释到公共蛋白质数据库中。在Trity软件中实现的甲壳蛋白共检测到1051个具有潜在选择性剪接的基因。通过克隆和Sanger测序，随机挑选的10个基因中有4个确实包含选择性剪接。值得注意的是，使用加倍的单倍体日本比目鱼个体可以让我们分析基因重复。总共从1859个基因中检测到3940个“单核苷酸多态”，可能发生了基因重复。本研究为牙鲆的结构和功能基因组学研究奠定了基础。
Japanese flounder (Paralichthys olivaceus) is one of the economic important fish in China. Sexual dimorphism, especially the different growth rates and body sizes between two sexes, makes this fish a good model to investigate mechanisms responsible for such dimorphism for both fundamental questions in evolution and applied topics in aquaculture. However, the lack of “omics” data has hindered the process. The recent advent of RNA-sequencing technology provides a robust tool to further study characteristics of genomes of nonmodel species. Here, we performed de novo transcriptome sequencing for a double haploid Japanese flounder individual using Illumina sequencing. A single lane of paired-end sequencing produced more than 27 million reads. These reads were assembled into 107,318 nonredundant transcripts, half of which (51,563; 48.1%) were annotated by blastx to public protein database. A total of 1051 genes that had potential alternative splicings were detected by Chrysalis implemented in Trinity software. Four of 10 randomly picked genes were verified truly containing alternative splicing by cloning and Sanger sequencing. Notably, using a doubled haploid Japanese flounder individual allow us to analyze gene duplicates. In total, 3940 “single-nucleotide polymorphisms” were detected form 1859 genes, which may have happened gene duplicates. This study lays the foundation for structural and functional genomics studies in Japanese flounder.
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