Wu Na, Liu Jinlong, Wang Song, Guo Xianguang
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Genes (Basel). 2022 Jan 23;13(2):203. doi: 10.3390/genes13020203.
Intraspecific rearrangements of mitochondrial genomes are rarely reported in reptiles, even in vertebrates. The sunwatcher toad-headed agama, , can serve as an excellent model for investigating the dynamic mitogenome structure at intraspecific level. To date, seven subspecies of are well recognized, but little is known about the mitogenomic evolution among different subspecies. In this study, complete mitogenomes of subspecies II and were determined by next-generation sequencing, and another I retrieved from GenBank was compiled for comparative analysis. The nucleotide composition and the codon usage are similar to those previously published from toad-headed agamas. II and have 23 tRNA genes, including standard 22 tRNA genes and one extra ( duplication). Gene order and phylogenetic analyses in the genus support prevalent intraspecific gene rearrangement in and other congener species including , , and . Six different mitochondrial gene arrangements are observed in . Overall, the occurrence of rearrangements may result from multiple independent structural dynamic events. The split of the two subspecies in was dated at approximately 2.34 million years ago (Ma). Two types of gene rearrangements are found in the three mitogenomes of , and this intraspecific rearrangement phenomenon can be explained by the tandem duplication/random loss (TDRL) model. Post duplication, the alternative loss types can occur in 0.23-0.72 Ma, suggesting that the duplication and fixation of these rearrangements can occur quite quickly. These findings highlight the need for more mitogenomes at the population level in order to better understand the potentially rampant intraspecific mitogenomic reorganization in .
线粒体基因组的种内重排在爬行动物中鲜有报道，在脊椎动物中亦是如此。草原沙蜥（Phrynocephalus frontalis）可作为研究种内水平线粒体基因组动态结构的绝佳模型。迄今为止，草原沙蜥的七个亚种已得到广泛认可，但不同亚种间的线粒体基因组进化情况却知之甚少。在本研究中，通过二代测序测定了亚种II和亚种III的完整线粒体基因组，并从GenBank中检索了另一个亚种I进行比较分析。核苷酸组成和密码子使用情况与先前发表的草原沙蜥线粒体基因组相似。亚种II和亚种III有23个tRNA基因，包括标准的22个tRNA基因和一个额外的tRNA（重复）。草原沙蜥属内的基因顺序和系统发育分析支持草原沙蜥及其他同属物种（包括荒漠沙蜥、变色沙蜥和青海沙蜥）中普遍存在的种内基因重排现象。在草原沙蜥中观察到六种不同的线粒体基因排列方式。总体而言，重排的发生可能源于多个独立的结构动态事件。草原沙蜥两个亚种的分化时间约为234万年前（Ma）。在草原沙蜥的三个线粒体基因组中发现了两种类型的基因重排，这种种内重排现象可以用串联重复/随机丢失（TDRL）模型来解释。重复发生后，替代丢失类型可能发生在0.23 - 0.72 Ma之间，这表明这些重排的重复和固定可能发生得相当快。这些发现凸显了在种群水平上需要更多线粒体基因组来更好地理解草原沙蜥中潜在的猖獗种内线粒体基因组重组。
