Sun Shao'e, Li Qi, Kong Lingfeng, Yu Hong
Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
Sci Rep. 2016 Sep 22;6:33794. doi: 10.1038/srep33794.
We present the complete mitochondrial genomes (mitogenomes) of Trisidos kiyoni and Potiarca pilula, both important species from the family Arcidae (Arcoida: Arcacea). Typical bivalve mtDNA features were described, such as the relatively conserved gene number (36 and 37), a high A + T content (62.73% and 61.16%), the preference for A + T-rich codons, and the evidence of non-optimal codon usage. The mitogenomes of Arcidae species are exceptional for their extraordinarily large and variable sizes and substantial gene rearrangements. The mitogenome of T. kiyoni (19,614 bp) and P. pilula (28,470 bp) are the two smallest Arcidae mitogenomes. The compact mitogenomes are weakly associated with gene number and primarily reflect shrinkage of the non-coding regions. The varied size in Arcidae mitogenomes reflect a dynamic history of expansion. A significant positive correlation is observed between mitogenome size and the combined length of cox1-3, the lengths of Cytb, and the combined length of rRNAs (rrnS and rrnL) (P < 0.001). Both protein coding genes (PCGs) and tRNA rearrangements is observed in P. pilula and T. kiyoni mitogenomes. This analysis imply that the complicated gene rearrangement in mitochondrial genome could be considered as one of key characters in inferring higher-level phylogenetic relationship of Arcidae.
我们展示了紫石房蛤（Trisidos kiyoni）和扁玉螺（Potiarca pilula）的完整线粒体基因组（线粒体基因组），这两种都是蚶科（蚶总科：蚶科）的重要物种。描述了典型的双壳类线粒体DNA特征，如相对保守的基因数量（36个和37个）、高A+T含量（62.73%和61.16%）、对富含A+T密码子的偏好以及非最佳密码子使用的证据。蚶科物种的线粒体基因组以其异常大且可变的大小以及大量的基因重排而异常。紫石房蛤的线粒体基因组（19,614 bp）和扁玉螺的线粒体基因组（28,470 bp）是蚶科中两个最小的线粒体基因组。紧凑的线粒体基因组与基因数量的关联较弱，主要反映了非编码区的收缩。蚶科线粒体基因组大小的变化反映了其动态的扩张历史。线粒体基因组大小与cox1 - 3的总长度、细胞色素b的长度以及rRNA（rrnS和rrnL）的总长度之间存在显著的正相关（P < 0.001）。在扁玉螺和紫石房蛤的线粒体基因组中均观察到蛋白质编码基因（PCGs）和tRNA的重排。该分析表明，线粒体基因组中复杂的基因重排可被视为推断蚶科高级系统发育关系的关键特征之一。
