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.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.forename: Min
authors.initials: M
authors.lastname: Xie
authors.forename: Yu
authors.initials: Y
authors.lastname: Jiang
authors.forename: Nianqing
authors.initials: N
authors.lastname: Xiao
authors.forename: Xiaoyong
authors.initials: X
authors.lastname: Du
authors.forename: Wenguang
authors.initials: W
authors.lastname: Zhang
authors.forename: Gwenola
authors.initials: G
authors.lastname: Tosser-Klopp
authors.forename: Jinhuan
authors.initials: J
authors.lastname: Wang
authors.forename: Shuang
authors.initials: S
authors.lastname: Yang
authors.forename: Jie
authors.initials: J
authors.lastname: Liang
authors.forename: Wenbin
authors.initials: W
authors.lastname: Chen
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.forename: Peng
authors.initials: P
authors.lastname: Zeng
authors.forename: Yong
authors.initials: Y
authors.lastname: Hou
authors.forename: Chao
authors.initials: C
authors.lastname: Bian
authors.forename: Shengkai
authors.initials: S
authors.lastname: Pan
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Li
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Wenliang
authors.initials: W
authors.lastname: Wang
authors.forename: Bertrand
authors.initials: B
authors.lastname: Servin
authors.forename: Brian
authors.initials: B
authors.lastname: Sayre
authors.forename: Bin
authors.initials: B
authors.lastname: Zhu
authors.forename: Deacon
authors.initials: D
authors.lastname: Sweeney
authors.forename: Rich
authors.initials: R
authors.lastname: Moore
authors.forename: Wenhui
authors.initials: W
authors.lastname: Nie
authors.forename: Yongyi
authors.initials: Y
authors.lastname: Shen
authors.forename: Ruoping
authors.initials: R
authors.lastname: Zhao
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.forename: Jinquan
authors.initials: J
authors.lastname: Li
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
authors.forename: James
authors.initials: J
authors.lastname: Womack
authors.forename: Yaping
authors.initials: Y
authors.lastname: Zhang
authors.forename: James
authors.initials: J
authors.lastname: Kijas
authors.forename: Noelle
authors.initials: N
authors.lastname: Cockett
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.forename: Shuhong
authors.initials: S
authors.lastname: Zhao
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle; D002681:China; D002874:Chromosome Mapping; D005260:Female; D016678:Genome; D015894:Genome, Human; D006041:Goats / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D026801:Synteny / Q000235:genetics