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. 2017 Nov 1;6(11):1-7.
doi: 10.1093/gigascience/gix094.

Draft genome of the gayal, Bos frontalis

Ming-Shan Wang  1   2 , Yan Zeng  1   2 , Xiao Wang  1   2 , Wen-Hui Nie  1 , Jin-Huan Wang  1 , Wei-Ting Su  1 , Newton O Otecko  1   2 , Zi-Jun Xiong  1   3 , Sheng Wang  4 , Kai-Xing Qu  5 , Shou-Qing Yan  6 , Min-Min Yang  1   2 , Wen Wang  1   2 , Yang Dong  7   8 , Dong-Dong Wu  1   2 , Ya-Ping Zhang  1   2   9
Affiliations

Draft genome of the gayal, Bos frontalis

Ming-Shan Wang et al. Gigascience. .

Abstract

Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal.

Keywords: Bos frontalis; annotation; genome assembly; phylogeny.

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Figures

Figure 1:
Figure 1:
A picture showing a female gayal (Bos frontalis, provided by Kai-Xing Qu).
Figure 2:
Figure 2:
Karyotype of the gayal used for genome sequencing (provided by Wen-Hui Nie).
Figure 3:
Figure 3:
17-mer frequency distribution of sequencing reads.
Figure 4:
Figure 4:
Phylogenetic trees of gayal and other bovine species. (A) Tree constructed based on maximum likelihood method. (B) Tree constructed using Bayesian inference.
Figure 5:
Figure 5:
Maximum likelihood trees of gayal and other bovine species using whole complete mtDNA. IDs in parentheses are GenBank accession number.
Figure 6:
Figure 6:
Divergence time estimated between gayal and other bovine species.
See this image and copyright information in PMC

References

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