Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China.
PLoS One. 2013 Jul 25;8(7):e67456. doi: 10.1371/journal.pone.0067456. Print 2013.
The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait.
Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated.
De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta.
刀蛏（Sinonovacula constricta）是一种底栖性潮间带双壳贝类，具有重要的商业价值。尽管其经济重要性很高，但对其转录组的了解却很少。新一代测序技术为生成大量序列提供了快速高效的工具，这些序列可用于描述转录组、开发有效的分子标记和鉴定与生长相关的基因，生长是一个关键的繁殖特征。
从刀蛏的套膜、鳃、肝、虹吸管、性腺和肌肉足组织中分离出总 RNA。使用 454 焦磷酸测序技术对 S. constricta 进行高通量深度测序，共获得 859,313 条高质量读数，平均读长为 489bp。对这些读数进行聚类和组装，生成了 16,323 条 contigs 和 131,346 条 singletons，平均长度分别为 1,376bp 和 458bp。基于转录组测序，有 14,615 条序列与已知基因编码的 147,669 个预测蛋白有显著匹配。随后，鉴定出了先前未知的与生长相关的基因。共发现 13,563 个微卫星（SSRs）和 13,634 个高置信度单核苷酸多态性（SNP）位点，其中近一半得到了验证。
在 454 GS FLX 平台上对刀蛏 S. constricta 转录组进行从头测序，生成了大量的 ESTs。鉴定出候选生长因子和大量的 SSRs 和 SNPs。这些结果将对 S. constricta 的遗传研究产生影响。
