Draft genome of the milu (Elaphurus davidianus)

Abstract Background: Milu, also known as Père David's deer (Elaphurus davidianus), had been widely distributed in East Asia but experienced a severe bottleneck (only 18 survived by the end of 19th century), and the current 4500 individual population was propagated from only 11 individuals reared by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. The draft genome reported in this study will provide valuable resources to investigate deeper into its evolutionary history and population dynamics of severely bottlenecked species. Findings: In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of the male milu deer using an Illumina HiSeq 2000 platform. Assembly gave a final genome with scaffold N50 of 3.03 megabases (Mb), and total length of 2.52 Gb. Moreover, we identified 20,125 protein-coding genes and 988.1 Mb of repetitive sequences. In addition, homology-based searches detected 280 rRNA, 1,335 miRNA, 1,441 snRNA and 893 tRNA sequences in the genome of E. davidianus. The divergence time between E. davidianus and the ancestors Bos taurus and Capra hircus, was estimated to be about 28.20 million years ago (Mya). We identified 167 species-specific genes and 293 expanded gene families in the milu lineage. Conclusions: We report the first reference genome of milu. The genome will provide a valuable resource for studying the species' demographic history and the population genetic dynamics for severely bottlenecked species.