Key Laboratory of Marine Bio-resource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
Genome. 2010 Dec;53(12):1041-52. doi: 10.1139/G10-096.
Extraordinary variation has been found in mitochondrial (mt) genome inheritance, gene content and arrangement among bivalves. However, only few bivalve mt genomes have been comparatively analyzed to infer their evolutionary scenarios. In this study, the complete mt genome of the venerid Paphia euglypta (Bivalvia: Veneridae) was firstly studied and, secondly, it was comparatively analyzed with other venerids (e.g., Venerupis philippinarum and Meretrix petechialis) to better understand the mt genome evolution within a family. Though several common features such as the AT content, codon usage of protein-coding genes, and AT/GC skew are shared by the three venerids, a high level of variability is observed in genome size, gene content, gene order, arrangements and primary sequence of nucleotides or amino acids. Most of the gene rearrangement can be explained by the "tandem duplication and random loss" model. From the observed rearrangement patterns, we speculate that block interchange between adjacent genes may be common in the evolution of mt genomes in venerids. Furthermore, this study presents several new findings in mt genome annotation of V. philippinarum and M. petechialis, and hence we have reannotated the genome of these two species as: (1) the ORF of the formerly annotated cox2 gene in V. philippinarum is deduced by using a truncated "T" codon and a second cox2 gene is identified; (2) the trnS-AGN gene is identified and marked in the mt genome of both venerids. Thus, this study demonstrated a high variability of mt genomes in the Veneridae, and showed the importance of comparative mt genome analysis to interpret the evolution of the bivalve mt genome.
双壳类动物的线粒体（mt）基因组在遗传、基因内容和排列上存在显著差异。然而，仅有少数双壳类动物的 mt 基因组被进行了比较分析，以推断其进化情况。本研究首次对帘蛤科的鲍 Paphia euglypta 的完整 mt 基因组进行了研究，并与其他帘蛤科动物（如菲律宾帘蛤和西施舌）进行了比较分析，以更好地了解该科内 mt 基因组的进化。尽管这三种帘蛤科动物具有一些共同特征，如 AT 含量、蛋白质编码基因的密码子使用、以及 AT/GC 倾斜，但在基因组大小、基因内容、基因顺序、排列和核苷酸或氨基酸的一级序列方面存在高度的可变性。大多数基因重排可以用“串联重复和随机丢失”模型来解释。从观察到的重排模式来看，我们推测相邻基因之间的块交换可能在帘蛤科 mt 基因组的进化中很常见。此外，本研究在菲律宾帘蛤和西施舌的 mt 基因组注释中提出了一些新的发现，因此我们重新注释了这两个物种的基因组：（1）菲律宾帘蛤原注释 cox2 基因的 ORF 通过使用截断的“T”密码子推断得出，并鉴定出第二个 cox2 基因；（2）在这两种帘蛤科动物的 mt 基因组中鉴定并标记了 trnS-AGN 基因。因此，本研究表明帘蛤科 mt 基因组具有高度的变异性，并展示了比较 mt 基因组分析在解释双壳类动物 mt 基因组进化中的重要性。
