Draft genome of the milu (Elaphurus davidianus)

Abstract

Background: Milu, also known as Père David's deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena, we constructed a draft genome of the species.

Findings: In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of a male milu deer using an Illumina HiSeq 2000 platform. Assembly yielded a final genome with a scaffold N50 size of 3.03 megabases (Mb) and a 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, 1335 miRNA, 1441 snRNA, and 893 tRNA sequences in the milu genome. The divergence time between E. davidianus and Bos taurus 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, which will provide a valuable resource for studying the species' demographic history of severe bottleneck and the genetic mechanism(s) of special phenotypic evolution.

Figure 1:

Photo of 2 fighting Père David's deer in Dafeng Milu National Reserves, Jiangsu, China. A red wound was spotted on the body of the deer to the right, and winning such fights generally increases mating chances.

Figure 2:

Phylogenetic relationships and genomic comparisons. (A) A Venn diagram of the orthologues shared among Elaphurus davidianus, Equus caballus, Capra hircus, Bos taurus, and Homo sapiens. Each number represents a gene family number, and the sum of the numbers in the green, yellow, brown, red, and blue areas indicate total numbers of the gene families in milu, horse, human, goat, and cattle genomes, respectively. (B) Divergence time estimates for the 5 species generated using MCMCtree and the 4-fold degenerate sites; the dots correspond to calibration points, and the divergence times were obtained from http://www.timetree.org/; blue nodal bars indicate 95% confidence intervals.