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

Abstract

BackgroundThe 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.FindingsUsing 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.ConclusionsOur 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.

Chromosomal‐level genome assembly of the scimitar‐horned oryx: Insights into diversity and demography of a species extinct in the wild

“…The use of Hi‐C data successfully incorporated scaffolds into 29 chromosomes, increasing the scaffold N50 to 100.4 Mb. This is more than 20 times the scaffold N50 reported for the sable antelope (~4.6 Mb, Koepfli et al, 2019) and almost double that of the N50 reported for gemsbok (47 Mb, Farré et al., 2019). In contrast, the contig N50 of the 10X‐Hi‐C assembly was >850 kb which represents a substantial improvement over both sable antelope (45.5 kb) and gemsbok assemblies (17.2 kb).…”

Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity inex Situandin SituPopulations

“…De novo prediction using Augustus 3.2.3 and human gene models resulted in a set of 21,276 candidate protein-coding genes in the sable antelope reference assembly. This quantity is comparable to the 20,892 and 21,426 protein-coding genes found in the domestic cow and Tibetan antelope genomes, respectively, but lower than the 23,125 reference gene set in the gemsbok (Zimin et al 2009; Ge et al 2013; Farré et al 2019). The candidate gene set was then filtered using eggNOG 4.5 orthology data (Huerta-Cepas et al 2016), which reduced the set to 18,828 protein-coding genes.…”

“…BUSCO evaluation of gene completeness showed that 3,890 out of 4,104 genes (94.8%) were complete, and only 113 genes (2.7%) were found missing (Table 3). The estimated genome size was 2.926 Gb based on an analysis of k -mer frequency (Marçais and Kingsford 2011), which is comparable to the genome sizes of the domestic cow (2.92 Gb) and the gemsbok (3.2 Gb), another member of the Hippotraginae (Zimin et al 2009; Farré et al 2019).…”

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

“…Alpaca genome assembly was provided by NHGRI sequencing performed at Washington University (Vicugna pacos, GCA_000164845.3, vicPac2). We included the newly sequenced genomes of gemsbok (Oryx gazella) (Farré et al 2019), giraffe (Giraffa camelopardalis), and Indian muntjac (Muntiacus muntjak) (Supplemental Table S1). Although newer assembly versions are available for outgroup human and mouse genomes, using a total of 19 genome assemblies in our work minimized the impact of possible individual misassemblies in these genomes on our reconstructions.…”