De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope

Abstract

Roan antelope (Hippotragus equinus) is the second-largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Despite being listed as "Least Concern" across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although the roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the first de novo assembly and annotation of the whole-genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single-nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.

Keywords: Hippotragus equinus; de novo genome assembly; 10X Genomics Chromium; Bovidae; genomic diversity; roan antelope.

Figure 1

Roan antelope distribution and sampling. (A) Roan antelope (Hippotragus equinus). Photo by Raquel Godinho; (B) Geographic distribution of roan antelope subspecies according to Ansell (1972) and current species distribution, following IUCN SSC Antelope Specialist Group (2017). The geographic location of the five samples used in this study for whole-genome re-sequencing is represented by dark dots labelled with sample identifications (as in Table 1).

Figure 2

Synteny blocks between roan antelope and the domestic cow genomes. Synteny between roan scaffolds larger than 10 Kb and the domestic cow chromosomes (29 autosomes and the X). Scaffolds were ordered to obtain the best pairwise alignment blocks between the two genomes which are visualized using colored lines.

Figure 3

Intraspecific variation in roan antelope. (A) Bar chart comparing the number of quality-filtered alternative homozygous and heterozygous single-nucleotide variants (millions of SNVs) among the five re-sequenced wild individuals. (B) Plot of principal component analysis (PCA) for the same individuals. PC1 and PC2 show the first and second axes with corresponding percentage of explained variance. Circles identify each individual and colors correspond to the respective subspecies, following Figure 1.