Marine Biotechnology Division, Central Marine Fisheries Research Institute, Kochi, 682 018, Kerala, India.
Mangalore University, Mangalagangotri, Mangalore, 574 199, Karnataka, India.
Sci Rep. 2020 Sep 22;10(1):15438. doi: 10.1038/s41598-020-72194-1.
The Indian black clam Villorita cyprinoides (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of Villorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of V. cyprinoides using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to Corbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs, rrnS and rrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered V. cyprinoides and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of V. cyprinoides and C. fluminea, analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus Villorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.
印度黑蛤 Villorita cyprinoides（Cyrenidae 科）是一种具有水产养殖重要性的商业开采物种，其在印度的蛤类渔业中贡献超过 70%，仅分布于印度半岛。目前，关于 Villorita 的信息非常稀少，特别是在分子数据方面。本研究旨在提供关于线粒体基因组结构的综合知识，并评估 Cyrenidae 的系统发育地位。这导致了使用下一代测序技术报告了 V. cyprinoides 的第一个完整线粒体基因组。该 A+T 环状线粒体基因组长 15880bp，包含 13 个蛋白质编码基因（PCGs），包括 ATP8（在几种双壳类动物中缺失），22 个转移 RNA 和两个核糖体 RNA 基因，位于重链上，以顺时针方向排列，基因顺序类似于 Corbicula fluminea。从来自超目 Imparidentia 的 47 个代表物种的串联多基因序列（12 个 PCGs、rrnS 和 rrnL 以及两个核基因（组蛋白 H3、18S rRNA）推断的分子系统发育，将 V. cyprinoides 和 Cyrenid 蛤聚类到一个单系群中，支持 Cyrenidae 的单系性。随后的线粒体基因顺序分析证实了 V. cyprinoides 和 C. fluminea 的密切关系，与系统发育结果类似。使用验证的化石数据进行校准的多基因树拓扑结构揭示了 Cyrenid 蛤在晚三叠世至早侏罗世期间的起源和多样化。本研究获得的数据将对隐种鉴定、双壳类动物线粒体基因组的分子特征以及 Villorita 属的线粒体进化历史有显著的贡献。此外，完整的线粒体基因组可以帮助开发潜在的标记，用于评估黑蛤种群的遗传健康。
