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

作者：Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, Wenguang Zhang, Gwenola Tosser‐Klopp, Jinhuan Wang, Shuang Yang, Shuang Yang, Jie Liang, Wenbin Chen, Jing Chen, Peng Zeng, Yong Hou, Chao Bian, Shengkai Pan, Yuxiang Li, Xin Liu, Wenliang Wang, Wenliang Wang, Bertrand Servin, Brian L Sayre, Bin Zhu, Deacon Sweeney, Rich Moore, Wenhui Nie, Yongyi Shen, Ruoping Zhao, Guojie Zhang, Jinquan Li, Thomas Faraut, James E. Womack, Ya‐Ping Zhang, James Kijas, Noelle E. Cockett, Xun Xu, Shuhong Zhao, Jun Wang, Jun Wang, Wen Wang, Wen Wang · 发表于：Nature Biotechnology · 年份：2012 · DOI：10.1038/nbt.2478 · 被引用次数：547 · 研究领域：Genomics and Phylogenetic Studies、Genetic Mapping and Diversity in Plants and Animals、Genetic and phenotypic traits in livestock

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.