sheep Raw sequence reads. Mongolian sheep,Hu sheep and Tan sheep

We report genome characterization of three native Chinese domestic sheep breeds discovering 3,537,483 SNPs and 47,890 InDels using whole genome resequencing. The present study emphasizes the genetic diversity, extending our previous study. The genomic regions related to reproductive processes and immune system process of the stress responses according to GO analysis. Altogether, we found reproductive related genes (BMPR1B, BMP15, GDF9 and MTNR1A) and immune related genes (PGLYRP2, TRIM15, TRIM40, SOCS7 and TFAM) in the three sheep breeds. Our results provide a valuable resource of the genomic information for identifying genes associated with important economic traits in sheep and for understanding the genetic characteristics of adaptation to different ecological environments.