Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)
Yang Dong
(1, 2)
,
Min Xie
(3)
,
Yu Jiang
(1, 4)
,
Nianqing Xiao
(5)
,
Xiaoyong Du
(6)
,
Wenguang Zhang
(1, 7)
,
Gwenola Tosser-Klopp
(8)
,
Jinhuan Wang
(1)
,
Shuang Yang
(3)
,
Jie Liang
(3)
,
Wenbin Chen
(3)
,
Jing Chen
(3)
,
Peng Zeng
(3)
,
Yong Hou
(3)
,
Chao Bian
(3)
,
Shengkai Pan
(3)
,
Yuxiang Li
(3)
,
Xin Liu
(3)
,
Wenliang Wang
(3)
,
Bertrand Servin
(8)
,
Brian Sayre
(9)
,
Bin Zhu
(5)
,
Deacon Sweeney
(5)
,
Rich Moore
(5)
,
Wenhui Nie
(1)
,
Yongyi Shen
(1, 2)
,
Ruoping Zhao
(1)
,
Guojie Zhang
(3)
,
Jinquan Li
(7)
,
Thomas Faraut
(8)
,
James Womack
(10)
,
Yaping Zhang
(1)
,
James Kijas
(4)
,
Noelle Cockett
(11)
,
Xun Xu
(1, 2, 3)
,
Shuhong Zhao
(6)
,
Jun Wang
(3)
,
Wen Wang
(1)
1
CAS -
Chinese Academy of Sciences
2 UCAS - University of Chinese Academy of Sciences [Beijing]
3 BGI - Beijing Genomics Institute [Shenzhen]
4 Livestock Industries
5 OpGen Inc.
6 HZAU - Huazhong Agricultural University [Wuhan]
7 IMAU - Inner Mongolia Agricultural University
8 LGC - Laboratoire de Génétique Cellulaire
9 Virginia State University
10 Texas A&M University System
11 USU - Utah State University
2 UCAS - University of Chinese Academy of Sciences [Beijing]
3 BGI - Beijing Genomics Institute [Shenzhen]
4 Livestock Industries
5 OpGen Inc.
6 HZAU - Huazhong Agricultural University [Wuhan]
7 IMAU - Inner Mongolia Agricultural University
8 LGC - Laboratoire de Génétique Cellulaire
9 Virginia State University
10 Texas A&M University System
11 USU - Utah State University
Gwenola Tosser-Klopp
- Fonction : Auteur
- PersonId : 737163
- IdHAL : gwenola-tosser
- ORCID : 0000-0003-0550-4673
- IdRef : 067312497
Xin Liu
- Fonction : Auteur
- PersonId : 758866
- ORCID : 0000-0003-3256-2940
Bertrand Servin
- Fonction : Auteur
- PersonId : 183571
- IdHAL : bertrand-servin
- ORCID : 0000-0001-5141-0913
- IdRef : 079704646
Thomas Faraut
- Fonction : Auteur
- PersonId : 749003
- IdHAL : thomas-faraut
- ORCID : 0000-0001-5156-3434
Xun Xu
- Fonction : Auteur
- PersonId : 801031
- ORCID : 0000-0002-5338-5173
Résumé
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.