SNP discovery and gene annotation in the surf clam Mesodesma donacium

The main objective of this research was to identify single-nucleotide polymorphisms (SNPs) from an Expressed Sequences Tags (EST) data set generated by 454 pyrosequencing in the soft clam Mesodesma donacium. A total of 180 159 ESTs were yielded from a M. donacium cDNA library. De novo assembly was performed using stringent calling parameters, producing 10 178 contigs and 41 765 singletons. Here, a total of 2594 SNPs were discovered related to 613 consensus sequences, achieving a frequency of 1 SNPs per 260 bp. SNP variants showed that A/G, A/T and C/T were the most abundant among the identified polymorphisms. We validated a total of 12 SNPs loci by HRMA for annotated genes such as heat shock protein-70 and the translation elongation factor 1-alpha. The Gene Ontology analysis regarding molecular function level revealed that sequences with SNPs were mainly classified to protein and nucleotide binding, as well hydrolase activity, ion binding and oxidoreductase activity. Further, biological...

本研究的核心目标是从软壳蛤（Mesodesma donacium）经454焦磷酸测序（454 pyrosequencing）获得的表达序列标签（Expressed Sequences Tags, EST）数据集内，挖掘单核苷酸多态性（single-nucleotide polymorphisms, SNPs）。本研究从该软壳蛤的cDNA文库中共计得到180159条EST序列。采用严格的组装参数开展从头组装（De novo assembly），最终生成10178条重叠群（contigs）与41765条单序列（singletons）。本研究共发现2594个与613条一致序列（consensus sequences）相关的SNPs位点，单核苷酸多态性的出现频率为每260 bp出现1个SNPs。SNPs变异类型分析显示，A/G、A/T与C/T为本次鉴定出的多态性位点中占比最高的三类变异。研究团队通过高分辨率熔解分析（HRMA）对12个位于已注释基因（如热休克蛋白70（heat shock protein-70）与翻译延伸因子1-α（translation elongation factor 1-alpha））内的SNPs位点进行了验证。基于分子功能层级的基因本体论（Gene Ontology）分析结果表明，携带SNPs的序列主要被归类为蛋白质结合、核苷酸结合、水解酶活性、离子结合以及氧化还原酶活性相关功能类别。此外，生物学……