Phylogenetic implications of the whole mitochondrial genome provide insight into geographic distribution and morphological relationships of Bos spp.

Bos genus includes 8 species namely Bos frontalis, Bos gaurus, Bos grunniens, Bos indicus, Bos javanicus, Bos mutus, Bos primigenius, Bos taurus is one of the world's most numerous mammals. Their habitats vary greatly depending on the particular species. Mitochondrial genomics is considered an essential tool for identifying species and monitoring populations in need of conservation. In the current study, we report the first complete mitochondrial DNA of Vietnamese gaur using Oxford Nanopore long-read sequencing technology. In addition, we performed a comparative analysis using the complete mitochondrial genome of 34 other Bos species. In combination with genetic distance and geographic information, our study indicates distinctive haplotype patterns of mitochondrion in South and Southeast Asia in comparison with East Asia and Europe. We also strongly suggest that, unlike using partial sequences, the complete mitochondrial genome may be better for population genetic assessment of Bos spp. Last but not least, we demonstrated a simple experimental setup of the ONT platform could be feasible for large-scale population genetic evaluations of wild animals. Altogether, our study provides pieces of evidence to emphasize the necessity of using whole mitochondrial DNA for phylogenetic implication by long-read sequencing methods.

牛属（Bos genus）共包含8个物种，分别为大额牛（Bos frontalis）、印度野牛（Bos gaurus）、牦牛（Bos grunniens）、瘤牛（Bos indicus）、爪哇野牛（Bos javanicus）、野牦牛（Bos mutus）、原牛（Bos primigenius）以及家牛（Bos taurus），其中家牛是全球现存数量最多的哺乳动物之一。其栖息环境因物种不同而存在显著差异。线粒体基因组学（mitochondrial genomics）被视作物种鉴定与濒危保护种群监测的核心技术工具。本研究首次利用牛津纳米孔长读长测序（Oxford Nanopore long-read sequencing）技术，获得了越南印度野牛的完整线粒体DNA序列。此外，本研究结合其余34个牛属物种的完整线粒体基因组开展了比较分析。结合遗传距离与地理分布信息，本研究发现，相较于东亚与欧洲种群，南亚及东南亚地区的线粒体单倍型模式具有显著特异性。本研究同时提出，相较于使用部分基因序列，完整线粒体基因组或许更适用于牛属物种种群遗传学评估。最后，本研究证实，采用简易的牛津纳米孔（ONT）平台实验方案，即可实现野生动物的大规模种群遗传学评估。综上，本研究通过长读长测序方法获取完整线粒体DNA，为其在系统发育推断中的应用必要性提供了实证依据。