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

被引：392

作者：

Dong, Yang ^{[1
,2
]}

Xie, Min ^{[3
]}

Jiang, Yu ^{[1
,5
]}

Xiao, Nianqing ^{[10
]}

Du, Xiaoyong ^{[4
]}

Zhang, Wenguang ^{[1
,6
]}

Tosser-Klopp, Gwenola ^{[7
]}

Wang, Jinhuan ^{[1
]}

Yang, Shuang ^{[3
]}

Liang, Jie ^{[3
]}

Chen, Wenbin ^{[3
]}

Chen, Jing ^{[3
]}

Zeng, Peng ^{[3
]}

Hou, Yong ^{[3
]}

Bian, Chao ^{[3
]}

Pan, Shengkai ^{[3
]}

Li, Yuxiang ^{[3
]}

Liu, Xin ^{[3
]}

Wang, Wenliang ^{[3
]}

Servin, Bertrand ^{[7
]}

Sayre, Brian ^{[11
]}

Zhu, Bin ^{[10
]}

Sweeney, Deacon ^{[10
]}

Moore, Rich ^{[10
]}

Nie, Wenhui ^{[1
]}

Shen, Yongyi ^{[1
,2
]}

Zhao, Ruoping ^{[1
]}

Zhang, Guojie ^{[3
]}

Li, Jinquan ^{[6
]}

Faraut, Thomas ^{[7
]}

Womack, James ^{[9
]}

Zhang, Yaping ^{[1
]}

Kijas, James ^{[5
]}

Cockett, Noelle ^{[8
]}

Xu, Xun ^{[1
,2
,3
]}

Zhao, Shuhong ^{[4
]}

Wang, Jun ^{[3
]}

Wang, Wen ^{[1
]}

机构：

[1] Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming, Peoples R China

[2] Univ Chinese Acad Sci, Beijing, Peoples R China

[3] BGI Shenzhen, Shenzhen, Peoples R China

[4] Huazhong Agr Univ, Wuhan, Peoples R China

[5] CSIRO Livestock Ind, St Lucia, Qld, Australia

[6] Inner Mongolia Agr Univ, Hohhot, Peoples R China

[7] INRA, Lab Genet Cellulaire, F-31326 Castanet Tolosan, France

[8] Utah State Univ, Logan, UT 84322 USA

[9] Texas A&M Univ, College Stn, TX USA

[10] OpGen Inc, Gaithersburg, MD USA

[11] Virginia State Univ, Petersburg, VA 23806 USA

来源：

NATURE BIOTECHNOLOGY | 2013年 / 31卷 / 02期

基金：

中国国家自然科学基金;

关键词：

RETINOIC ACID; HAIR; CHROMOSOME; EVOLUTION; VALIDATION; ORIGINS; GROWTH; MILK; MAPS;

D O I：

10.1038/nbt.2478

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We report the similar to 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 >5x 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.

引用

页码：135 / 141

页数：7

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