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Draft genome of the gayal, Bos frontalis

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, an...

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Autores principales: Wang, Ming-Shan, Zeng, Yan, Wang, Xiao, Nie, Wen-Hui, Wang, Jin-Huan, Su, Wei-Ting, Otecko, Newton O, Xiong, Zi-Jun, Wang, Sheng, Qu, Kai-Xing, Yan, Shou-Qing, Yang, Min-Min, Wang, Wen, Dong, Yang, Wu, Dong-Dong, Zhang, Ya-Ping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710521/
https://www.ncbi.nlm.nih.gov/pubmed/29048483
http://dx.doi.org/10.1093/gigascience/gix094
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author Wang, Ming-Shan
Zeng, Yan
Wang, Xiao
Nie, Wen-Hui
Wang, Jin-Huan
Su, Wei-Ting
Otecko, Newton O
Xiong, Zi-Jun
Wang, Sheng
Qu, Kai-Xing
Yan, Shou-Qing
Yang, Min-Min
Wang, Wen
Dong, Yang
Wu, Dong-Dong
Zhang, Ya-Ping
author_facet Wang, Ming-Shan
Zeng, Yan
Wang, Xiao
Nie, Wen-Hui
Wang, Jin-Huan
Su, Wei-Ting
Otecko, Newton O
Xiong, Zi-Jun
Wang, Sheng
Qu, Kai-Xing
Yan, Shou-Qing
Yang, Min-Min
Wang, Wen
Dong, Yang
Wu, Dong-Dong
Zhang, Ya-Ping
author_sort Wang, Ming-Shan
collection PubMed
description 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.
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spelling pubmed-57105212017-12-07 Draft genome of the gayal, Bos frontalis Wang, Ming-Shan Zeng, Yan Wang, Xiao Nie, Wen-Hui Wang, Jin-Huan Su, Wei-Ting Otecko, Newton O Xiong, Zi-Jun Wang, Sheng Qu, Kai-Xing Yan, Shou-Qing Yang, Min-Min Wang, Wen Dong, Yang Wu, Dong-Dong Zhang, Ya-Ping Gigascience Data Note 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. Oxford University Press 2017-10-05 /pmc/articles/PMC5710521/ /pubmed/29048483 http://dx.doi.org/10.1093/gigascience/gix094 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Wang, Ming-Shan
Zeng, Yan
Wang, Xiao
Nie, Wen-Hui
Wang, Jin-Huan
Su, Wei-Ting
Otecko, Newton O
Xiong, Zi-Jun
Wang, Sheng
Qu, Kai-Xing
Yan, Shou-Qing
Yang, Min-Min
Wang, Wen
Dong, Yang
Wu, Dong-Dong
Zhang, Ya-Ping
Draft genome of the gayal, Bos frontalis
title Draft genome of the gayal, Bos frontalis
title_full Draft genome of the gayal, Bos frontalis
title_fullStr Draft genome of the gayal, Bos frontalis
title_full_unstemmed Draft genome of the gayal, Bos frontalis
title_short Draft genome of the gayal, Bos frontalis
title_sort draft genome of the gayal, bos frontalis
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710521/
https://www.ncbi.nlm.nih.gov/pubmed/29048483
http://dx.doi.org/10.1093/gigascience/gix094
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