Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Academic Article uri icon

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.

published proceedings

  • Nat Biotechnol

altmetric score

  • 46.07

author list (cited authors)

  • Dong, Y., Xie, M., Jiang, Y. u., Xiao, N., Du, X., Zhang, W., ... Wang, W.

citation count

  • 373

complete list of authors

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

publication date

  • February 2013