黄河口与长江口近江牡蛎的比较转录组分析

A Comparative Transcriptional Analysis of Crassostrea ariakensis from Yellow River and Yangtze River Estuaries

为进一步开发近江牡蛎Crassostreaariakensis的基因资源,探究黄河口与长江口近江牡蛎的遗传差异,采用Illumina HiSeq 4000测序平台对东营垦利和南通海门的近江牡蛎进行高通量转录组测序。对测序数据进行拼接后分别得到83680条和71269条unigene,并对unigene进行了基因功能注释和正选择基因的富集分析。结果表明,同源基因经筛选得到正选择基因259个,GO (Gene Ontology)功能分析中共涉及到967个相关功能类别,其中有关到生物学过程的分类条目占比最多,为590项。总体上看,与细胞器、代谢过程、结合以及催化活性相关的类别占主导地位。KEGG( Kyoto Encyclopedia of Genes and Genomes)富集分析表明,共涉及48个代谢通路,其中与核糖体、细胞凋亡相关的通路占比最大。上述结果不仅加深了对黄河口以及长江口近江牡蛎基因表达水平差异的认识,同时也为今后进行近江牡蛎各类遗传学分析和一些关键基因的克隆以及具体功能分析提供了基础数据。

Crassostrea ariakensis inhabits a wide range of latitudes. In order to further develop the genetic resource of C. ariakensis, and explore the genetic difference of C. ariakensis between Yellow River and Yangtze River Estuaries, RNA-seq and bioinformatics analysis were conducted to compare the transcriptome of C. ariakensis from Kenli, Dongying and Haimen, Nantong. A total of 49,258,106 and 39,345,510 clean reads were generated from C. ariakensisin Kenli and Haimen, respectively. After de novo assembly, we received 83,680 and 71,269 unigenes, respectively. The complete sets of unigenes were queried against seven public annotation databases. Then the orthologous analysis and positive selection analysis were conducted to identify the positively selected genes. In total, 259 pairs of unigenes were identified with the Ka/Ks ratio > 1. The functional description of the GO (Gene ontology) and analysis of metabolic pathways of KEGG (Kyoto encyclopedia of genes and genomes) revealed that the positively selected genes were mainly enriched in the pathways relating to organelle, metabolism, ribosome and apoptosis. This study not only enhanced our understanding to gene differential expression of C. ariakensis in Yellow River Estuary and Yangtze River Estuary, but also provided basic gene resources for cloning, functional analysis and molecular genetic marker development of C. ariakensis.