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- Title
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus).
- 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
- 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.
- Subjects
GOAT genetics; ANIMAL genome mapping; NUCLEOTIDE sequence; CHROMOSOMES; SCAFFOLD proteins; TRANSCRIPTION factors; COMPARATIVE studies
- Publication
Nature Biotechnology, 2013, Vol 31, Issue 2, p135
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt.2478