De novowhole-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. Although 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 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 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.

Blue turns to grey - Palaeogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus)

“…In both analyses, the scimitar-horned oryx ( Oryx dammah , SB20612, Humble et al 2020) was used as the outgroup (not shown). Roan and sable antelope raw data are from Gonçalves et al (2021) and Koepfli et al (2019). Photo credits: see fig.…”

“…We used published raw sequencing read data of three roan ( Hippotragus equinus ) (Gonçalves et al 2021), eight sable antelopes ( Hippotragus niger ) (Koepfli et al 2019) from contemporary samples, and the scimitar-horned oryx ( Oryx dammah ) (Humble et al 2020) (supplementary table S4) in our analyses. The reads for these samples were treated in the same way as described above with the exception that merged and unmerged reads were both mapped, that the maximum overlap parameter in FLASH v1.2.11 was adjusted according to sequencing cycle length and that no rescaling was performed.…”

“…Similarly, we avoided further phylogenetic biases by using trees with strong branch supports (bootstrap support >90) and low rate variation among lineages (CoV in root-to-tip length <0.1; Vankan et al 2022). We used the following individuals: the early Holocene blue antelope (NBC RB4 D3), the roan antelope (10954, Gonçalves et al 2021), the sable antelope (SB2152, Koepfli et al 2019) and the scimitar-horned oryx (SB20612, Humble et al 2020) as outgroup. As input files we used the fasta files generated with Consensify (see above) but including only transversions.…”

“…As outgroup the scimitar-horned oryx was used (Humble et al 2020). Roan and sable antelope raw data are from Gonçalves et al (2021) and Koepfli et al (2019). Photo credits: NBC RB4 D3: J.T.…”

“…We constructed a neighbour-joining tree using the nuclear genome data from the two blue, three roan (Gonçalves et al 2021) and eight sable antelopes (Koepfli et al 2019), along with the scimitar-horned oryx (SB20612, Humble et al 2020) as outgroup to examine the dominant phylogenetic signal. The rescaled bam files from mapDamage for the fossil and historical blue antelope specimens as well as the bam files for all contemporary individuals were used as input files.…”