A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert

Abstract

Background: The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts.

Findings: Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions.

Conclusions: Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.

Figure 1:

A gemsbok (Oryx gazella) male at Etosha National Park (Namibia). Picture from Charles J Sharp QS: P170, Q54800218, Gemsbok (Oryx gazella) male, CC BY-SA 4.0.

Figure 2:

Overview of the approach to generate a chromosome-level gemsbok genome assembly. (A) Illumina paired-end and mate-pair reads were assembled into contigs (purple) and then into scaffolds (green) using SOAPdenovo (i). These scaffolds were merged into superscaffolds (orange) using Dovetail Chicago methodology (ii) [11]. Finally, Reference-Assisted Chromosome Assembly tool (RACA) [13] was applied to produce chromosomal fragments (blue) from the superscaffolds (iii). (B) To reveal potential chimeric scaffolds, we used the information provided by RACA to identify regions with low read coverage and no syntenic information (demarcated with a red box) in scaffolds (i) or in superscaffolds (iii). The HiRise scaffolder used Chicago libraries sequencing data to pinpoint potentially chimeric regions (shown in the red box) with low read coverage and a substantial reduction of link support (ii). R: reference, T: target and O: outgroup genomes.

Figure 3:

Genome assembly evaluation. The BUSCO dataset of the mammalia_odb9 including 4,104 BUSCOs was used to assess the four assemblies and compared to goat and cattle ARS-UCD1.2.

Figure 4:

Syntenic relationships between gemsbok and cattle genomes. (A) Circos plot showing syntenic relationships between cattle autosomes (labeled as BTA) and gemsbok chromosomal fragments. Chromosomes are colored based on cattle homologies. Ribbons inside the plot show syntenic relationships, while lines inside each ribbon indicate inversions. (B) Gemsbok chromosome 15 showing homologous synteny blocks (HSBs) between gemsbok, cattle, and human. SOAPdenovo + Chicago scaffolds are also displayed. The other gemsbok chromosomes can be found in Supplementary Fig. S1.

Figure 5:

Phylogenetic relationships of gemsbok. Phylogenetic tree constructed with orthologous genes. Divergence times were extracted from the TimeTree database for calibration. Numbers in brackets indicate the estimated diverge times in millions of years, and red circle indicates the calibration time.