Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
BMC Genomics. 2018 May 10;19(1):354. doi: 10.1186/s12864-018-4717-7.
Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes.
In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the O was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNA gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome.
The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
线粒体 DNA 序列长期以来一直被用于系统发育研究。然而，对于蛇线粒体基因组基因排列模式的变化，关注较少。在这里，我们分析了来自 14 个科的 65 种蛇的完整线粒体基因组序列和结构，并研究了它们的结构模式、组织和进化。我们的目的是进一步探讨蛇类线粒体基因组的进化意义和可能的重排机制。
总共检测到 11 种线粒体基因排列模式（I 型、II 型、III 型、III-A 型、III-B 型、III-B1 型、III-C 型、III-D 型、III-E 型、III-F 型、III-G 型），线粒体基因组重排是蛇类的主要趋势，尤其是在盲蛇目中。在蛇类线粒体基因组中，重排主要涉及三个过程，基因丢失、易位和复制。在盲蛇目中，O 基因在 Typhlopidae 和 Leptotyphlopidae 中丢失了几次，但在真盲蛇目中仍然是一个原始特征。控制区的重复和 tRNA 基因的易位是真盲蛇目线粒体基因组的两个明显特征。在三个科的七个不同谱系中，P假 Pro（P）的独立和随机复制以不同大小出现，表明 P*的存在是线粒体基因组中的一个多态事件。
WANCY tRNA 基因簇和控制区及其相邻片段是线粒体基因组重排的热点。重复控制区的维持可能是蛇类线粒体基因组结构多样性的来源。
