Doğan Özgül, Schrödl Michael, Chen Zeyuan
Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey.
SNSB-Bavarian State Collection of Zoology, Munich, Germany.
PeerJ. 2020 Feb 21;8:e8603. doi: 10.7717/peerj.8603. eCollection 2020.
Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for and and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for and (AGN). Phylogenetic analyses confirmed the position of within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of and (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth's most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (, , , , and ) detected by the branch-specific aBSREL approach and three genes (, and ) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of and of clusters for the genus . Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.
柄眼目是腹足纲中物种最为丰富的目之一，包括陆生蜗牛和蛞蝓，其中一些在经济方面具有重要意义，可作为人类食物、农业害虫、寄生虫载体或因其具有入侵性。尽管它们具有高度的多样性和重要性，但柄眼目的内部系统发育一直存在争议。迄今为止，仅对34个柄眼目物种的线粒体基因组进行了测序。在此，我们使用下一代测序技术对一种入侵性害虫蛞蝓——莫氏嗜黏液蛞蝓（1855年，柄眼目：阿勇蛞蝓科）的完整线粒体基因组进行了测序、分析，并与其他柄眼目物种进行了比较。莫氏嗜黏液蛞蝓的线粒体基因组长度为14,547 bp，包含13个蛋白质编码基因、两个rRNA基因、22个tRNA基因和一个控制区，A + T含量为70.20%。除了COX1和ND5外，所有蛋白质编码基因（PCGs）均以ATN密码子起始，且均以TAR或T-stop密码子结束。除了tRNA-Ser(AGN)和tRNA-Glu外，所有tRNA均折叠成三叶草叶形二级结构。系统发育分析证实了莫氏嗜黏液蛞蝓在阿勇蛞蝓总科中的位置，恢复了阿勇蛞蝓总科与正形蛞蝓总科之间的姐妹群关系，并支持柄眼目中除了旋蜗牛总科外所有目前公认的总科的单系性。柄眼目的初始分化时间估计为1.3855亿年前，对应于早白垩世。莫氏嗜黏液蛞蝓与林地嗜黏液蛞蝓（林奈，1758年）的分化时间估计为1524万年前，对应于地球最近的一次全球变暖事件——中新世气候适宜期。此外，还进行了选择分析，以研究不同选择力对柄眼目线粒体基因组形成的作用。尽管纯化选择是塑造柄眼目线粒体基因组的主要选择力，但通过分支特异性aBSREL方法检测到的6个基因（COX1、COX2、COX3、ND4、ND5和CYTB）以及通过基于密码子的BEB、FUBAR和MEME方法检测到的3个基因（ATP6、ND2和ND3）受到了多样化选择。柄眼目物种线粒体PCGs上的正选择替换似乎适应了环境条件，并影响线粒体ATP的产生或对活性氧效应的保护。使用MLGO对柄眼目线粒体基因组重排进行的比较分析显示，柄眼目具有保守性；例外情况指的是几个分支的潜在近裔性状，包括阿勇蛞蝓属的tRNA基因簇和rRNA基因簇的重排顺序。一般来说，tRNA基因倾向于重排，串联重复随机丢失、转换和倒位是塑造柄眼目线粒体基因组的最基本机制。
