Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Wen Wang; Yang Dong; Min Xie; Yu Jiang; Nianqing Xiao; Xiaoyong Du; Wenguang Zhang; Gwenola Tosser-Klopp; Jinhuan Wang; Shuang Yang; Jie Liang; Wenbin Chen; Jing Chen; Peng Zeng; Yong Hou; Chao Bian; Shengkai Pan; Yuxiang Li; Xin Liu; Wenliang Wang; Bertrand Servin; Brian Sayre; Bin Zhu; Deacon Sweeney; Rich Moore; Wenhui Nie; Yongyi Shen; Ruoping Zhao; Guojie Zhang; Jinquan Li; Thomas Faraut; James Womack; Yaping Zhang; James Kijas; Noelle Cockett; Xun Xu; Shuhong Zhao; Jun Wang

doi:10.1038/nbt.2478

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Wen Wang, Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, Wenguang Zhang, Gwenola Tosser-Klopp, Jinhuan Wang, Shuang Yang, Jie Liang, Wenbin Chen, Jing Chen, Peng Zeng, Yong Hou, Chao Bian, Shengkai Pan, Yuxiang Li, Xin Liu, Wenliang WangBertrand Servin, Brian Sayre, Bin Zhu, Deacon Sweeney, Rich Moore, Wenhui Nie, Yongyi Shen, Ruoping Zhao, Guojie Zhang, Jinquan Li, Thomas Faraut, James Womack, Yaping Zhang, James Kijas, Noelle Cockett, Xun Xu, Shuhong Zhao, Jun Wang

Research output: Contribution to journal › Article › peer-review

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Abstract

We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing (scaffold N50 = 3.06 Mb, super-scaffold N50 = 16.3 Mb). Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and the assembly is well supported by two radiation hybrid maps of chromosome 1. We annotate 22,175 protein-coding genes, most of which were recovered in the RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles. This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes.

Original language	English
Pages (from-to)	135-141
Number of pages	7
Journal	Nature Biotechnology
Volume	31
Issue number	2
DOIs	https://doi.org/10.1038/nbt.2478
State	Published - Feb 2013
Externally published	Yes

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Wang, W., Dong, Y., Xie, M., Jiang, Y., Xiao, N., Du, X., Zhang, W., Tosser-Klopp, G., Wang, J., Yang, S., Liang, J., Chen, W., Chen, J., Zeng, P., Hou, Y., Bian, C., Pan, S., Li, Y., Liu, X., ... Wang, J. (2013). Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology, 31(2), 135-141. https://doi.org/10.1038/nbt.2478

@article{f3e03c415ba64f018735d14eb836c78d,

title = "Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)",

abstract = "We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing (scaffold N50 = 3.06 Mb, super-scaffold N50 = 16.3 Mb). Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and the assembly is well supported by two radiation hybrid maps of chromosome 1. We annotate 22,175 protein-coding genes, most of which were recovered in the RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles. This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes.",

author = "Wen Wang and Yang Dong and Min Xie and Yu Jiang and Nianqing Xiao and Xiaoyong Du and Wenguang Zhang and Gwenola Tosser-Klopp and Jinhuan Wang and Shuang Yang and Jie Liang and Wenbin Chen and Jing Chen and Peng Zeng and Yong Hou and Chao Bian and Shengkai Pan and Yuxiang Li and Xin Liu and Wenliang Wang and Bertrand Servin and Brian Sayre and Bin Zhu and Deacon Sweeney and Rich Moore and Wenhui Nie and Yongyi Shen and Ruoping Zhao and Guojie Zhang and Jinquan Li and Thomas Faraut and James Womack and Yaping Zhang and James Kijas and Noelle Cockett and Xun Xu and Shuhong Zhao and Jun Wang",

year = "2013",

month = feb,

doi = "10.1038/nbt.2478",

language = "英语",

volume = "31",

pages = "135--141",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Research",

number = "2",

}

Wang, W, Dong, Y, Xie, M, Jiang, Y, Xiao, N, Du, X, Zhang, W, Tosser-Klopp, G, Wang, J, Yang, S, Liang, J, Chen, W, Chen, J, Zeng, P, Hou, Y, Bian, C, Pan, S, Li, Y, Liu, X, Wang, W, Servin, B, Sayre, B, Zhu, B, Sweeney, D, Moore, R, Nie, W, Shen, Y, Zhao, R, Zhang, G, Li, J, Faraut, T, Womack, J, Zhang, Y, Kijas, J, Cockett, N, Xu, X, Zhao, S & Wang, J 2013, 'Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)', Nature Biotechnology, vol. 31, no. 2, pp. 135-141. https://doi.org/10.1038/nbt.2478

TY - JOUR

T1 - Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

AU - Wang, Wen

AU - Dong, Yang

AU - Xie, Min

AU - Jiang, Yu

AU - Xiao, Nianqing

AU - Du, Xiaoyong

AU - Zhang, Wenguang

AU - Tosser-Klopp, Gwenola

AU - Wang, Jinhuan

AU - Yang, Shuang

AU - Liang, Jie

AU - Chen, Wenbin

AU - Chen, Jing

AU - Zeng, Peng

AU - Hou, Yong

AU - Bian, Chao

AU - Pan, Shengkai

AU - Li, Yuxiang

AU - Liu, Xin

AU - Wang, Wenliang

AU - Servin, Bertrand

AU - Sayre, Brian

AU - Zhu, Bin

AU - Sweeney, Deacon

AU - Moore, Rich

AU - Nie, Wenhui

AU - Shen, Yongyi

AU - Zhao, Ruoping

AU - Zhang, Guojie

AU - Li, Jinquan

AU - Faraut, Thomas

AU - Womack, James

AU - Zhang, Yaping

AU - Kijas, James

AU - Cockett, Noelle

AU - Xu, Xun

AU - Zhao, Shuhong

AU - Wang, Jun

PY - 2013/2

Y1 - 2013/2

N2 - We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing (scaffold N50 = 3.06 Mb, super-scaffold N50 = 16.3 Mb). Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and the assembly is well supported by two radiation hybrid maps of chromosome 1. We annotate 22,175 protein-coding genes, most of which were recovered in the RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles. This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes.

AB - We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing (scaffold N50 = 3.06 Mb, super-scaffold N50 = 16.3 Mb). Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and the assembly is well supported by two radiation hybrid maps of chromosome 1. We annotate 22,175 protein-coding genes, most of which were recovered in the RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles. This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes.

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U2 - 10.1038/nbt.2478

DO - 10.1038/nbt.2478

M3 - 文章

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AN - SCOPUS:84873595859

SN - 1087-0156

VL - 31

SP - 135

EP - 141

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 2

ER -

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

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