Goat Genome Assembly

The domestic goat is one of the most important livestock. Here we report its high quality reference genome generated by combining Illumina sequencing and a new whole genome mapping system based on optical mapping technology. The N50 size of contigs, scaffolds, and super-scaffolds for the assembly are 18.7 kb, 3.06 Mb, and 16.3 Mb, respectively. Supper-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and this assembly is well supported by radiation hybrid map of chromosome 1. We annotated 22,175 protein-coding genes, most of which are recovered by RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat revealed 51 genes that were significantly differentially expressed between the two types of hair follicles. This study provides a high quality reference genome for goats, and shows that whole genome mapping technology can be used in de novo assemblies of large genomes.