School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
Institute of Ecosystem Study (ISE), Italian National Research Council, Sassari, Italy.
Sci Rep. 2016 Feb 1;6:20096. doi: 10.1038/srep20096.
The Pheretima complex within the Megascolecidae family is a major earthworm group. Recently, the systematic status of the Pheretima complex based on morphology was challenged by molecular studies. In this study, we carry out the first comparative mitogenomic study in oligochaetes. The mitogenomes of 15 earthworm species were sequenced and compared with other 9 available earthworm mitogenomes, with the main aim to explore their phylogenetic relationships and test different analytical approaches on phylogeny reconstruction. The general earthworm mitogenomic features revealed to be conservative: all genes encoded on the same strand, all the protein coding loci shared the same initiation codon (ATG), and tRNA genes showed conserved structures. The Drawida japonica mitogenome displayed the highest A + T content, reversed AT/GC-skews and the highest genetic diversity. Genetic distances among protein coding genes displayed their maximum and minimum interspecific values in the ATP8 and CO1 genes, respectively. The 22 tRNAs showed variable substitution patterns between the considered earthworm mitogenomes. The inclusion of rRNAs positively increased phylogenetic support. Furthermore, we tested different trimming tools for alignment improvement. Our analyses rejected reciprocal monophyly among Amynthas and Metaphire and indicated that the two genera should be systematically classified into one.
巨蚓科中的正蚓属复合体是一类主要的蚯蚓群。最近，基于形态的正蚓属复合体的系统地位受到了分子研究的挑战。在这项研究中，我们进行了寡毛类动物的首次比较线粒体基因组研究。对 15 种蚯蚓物种的线粒体基因组进行了测序，并与其他 9 种已有的蚯蚓线粒体基因组进行了比较，主要目的是探讨它们的系统发育关系，并测试不同的分析方法在系统发育重建中的应用。一般的蚯蚓线粒体基因组特征表现出保守性：所有基因都在同一链上编码，所有蛋白质编码基因都使用相同的起始密码子（ATG），并且 tRNA 基因具有保守的结构。日本 Drawida 的线粒体基因组显示出最高的 A+T 含量、反转的 AT/GC 倾斜度和最高的遗传多样性。蛋白质编码基因之间的遗传距离在 ATP8 和 CO1 基因中分别显示出最大和最小的种间值。22 个 tRNA 在考虑的蚯蚓线粒体基因组之间表现出不同的替代模式。rRNA 的包含增加了系统发育支持。此外，我们还测试了不同的修剪工具来改进对齐。我们的分析结果拒绝了 Amynthas 和 Metaphire 之间的相互单系性，并表明这两个属应该被系统地归为一类。
