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. © 2013 Nature America, Inc. All rights reserved.
Publication Title
Nature Biotechnology
Recommended Citation
Wang, W., Dong, Y., Xie, M., Jiang, Y., Xiao, N., Du, X., Zhang, W., Tosser-Klopp, G., Wang, J., Yang, S., Liang, J., Chen, W., Chen, J., Zeng, P., Hou, Y., Bian, C., Pan, S., Li, Y., Liu, X., Wang, W., Servin, B., Sayre, B., Zhu, B., Sweeney, D., Moore, R., Nie, W., Shen, Y., Zhao, R., Zhang, G., Li, J., Faraut, T., Womack, J., & Zhang, Y. (2013). Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology, 31 (2), 135-141. https://doi.org/10.1038/nbt.2478
