Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
Mar Biotechnol (NY). 2012 Feb;14(1):69-78. doi: 10.1007/s10126-011-9389-0. Epub 2011 May 21.
The clam Meretrix meretrix (Mollusca: Bivalvia) is an important commercial species in China. The deficiency of genomic and transcriptomic data is becoming the bottleneck of further researches on its complex and unique developmental processes. To improve this situation, in this study, a large-scale RNA sequencing was conducted on M. meretrix on larval stages. In particular, mRNAs of trochophore, D-veliger, pediveliger, and postlarva were purified, reverse transcribed, and sequenced through 454 sequencing technology. A total of 704,671 reads were obtained and assembled into 124,737 unique sequences (35,205 contigs and 89,532 singletons). Further analysis showed that 118,075 (94.66%) of these sequences were low-expression-level transcripts. Fifteen thousand two hundred fifteen (12.20%) of the unique sequences were annotated by searching against Uniprot Protein Knowledgebase, while the others (109,522, 87.80%) were left as novel sequences. Gene ontology analysis of the annotated sequences showed that most of them were assigned to certain gene ontology terms. By analyzing the depth of each unique sequence, a preliminary quantification analysis was conducted. An amount of sequences that showed a dramatic transcript discrepancy among the four larval stages were screened, which were related to development, growth, shell formation, and immune responses etc. As the first attempt on large-scale RNA sequencing of marine bivalve larvae, this work would enrich the knowledge of larval development of marine bivalves and provide fundamental support for further researches.
中国的西施舌（软体动物：双壳纲）是一种重要的商业物种。基因组和转录组数据的缺乏正成为进一步研究其复杂而独特的发育过程的瓶颈。为了改善这种情况，本研究对西施舌幼虫期进行了大规模的 RNA 测序。特别是，通过 454 测序技术，纯化、反转录和测序了担轮幼虫、D 型面盘幼虫、足囊幼虫和幼贝的 mRNA。共获得 704671 条reads，组装成 124737 个独特序列（35205 个 contigs 和 89532 个 singletons）。进一步分析表明，这些序列中 118075 个（94.66%）为低表达水平的转录本。15215 个（12.20%）独特序列通过与 Uniprot 蛋白质知识库的比对进行注释，而其余序列（109522 个，87.80%）则被标记为新序列。对注释序列的基因本体论分析表明，它们大多数被分配到特定的基因本体论术语中。通过分析每个独特序列的深度，进行了初步的定量分析。筛选出在四个幼虫期表现出显著转录差异的大量序列，这些序列与发育、生长、壳形成和免疫反应等有关。作为对海洋双壳类幼虫大规模 RNA 测序的首次尝试，这项工作将丰富海洋双壳类幼虫发育的知识，并为进一步的研究提供基础支持。
