Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India.
Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.
BMC Genomics. 2019 Jul 29;20(1):617. doi: 10.1186/s12864-019-5980-y.
Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun.
We generated ≈300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. Repeat sequences constitute around 43.66% of the assembly. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle.
Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations.
米图恩（Bos frontalis），又称野黄牛，是一种濒危的牛科动物，属于牛族，2n=58 XX 染色体，分布在印度、中国、缅甸、不丹和孟加拉国的热带雨林地区。然而，该物种的起源仍存在争议，其基因组结构的信息也很少。我们相信，其全基因组序列数据和组装的可用性将极大地解决这个问题，并有助于生成包括米图恩的系统发育地位在内的许多信息。最近，公布了中国原产的野黄牛的第一个基因组组装。然而，改进的参考基因组组装仍将有助于理解在不同地理位置饲养的米图恩群体的遗传变异，并构建一个优越的共识组装。因此，我们对来自印度的成年雌性米图恩进行了全基因组深度测序，组装并注释了其基因组，并进行了广泛的生物信息学分析，以生成米图恩的优质从头基因组组装。
我们从全基因组深度测序平台生成了约 300 吉字节（Gb）的原始读数，并使用混合组装策略对序列数据进行组装，根据 BUSCO 分析，约 96%的序列被成功组装。最终的基因组组装总长度为 3.0 Gb，包含 5015 个支架，N50 值为 1 Mb。重复序列约占组装的 43.66%。米图恩与牛的基因组比对表明，它们的基因组如预期的那样高度保守。基因注释鉴定了米图恩基因组中存在的 28044 个蛋白质编码基因。与其他物种相比，米图恩的基因直系同源物显示出高度的相似性，而与牛相比，米图恩特有的编码序列较少。
我们在这里提供了印度米图恩的第一个从头草案基因组组装，与之前公布的野黄牛基因组相比，该组装具有更好的覆盖度、更少的碎片化、更好的注释，并且构成了一个相当完整的组装。这个全面的组装在很大程度上揭示了米图恩的基因组结构，并将为研究社区提供一个参考基因组组装，以阐明米图恩在其不同地理位置的进化历史。
