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.
Highlights
The gemsbok (Oryx gazella) is one of the largest antelopes in Africa
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
2 Gemsbok genome assembly 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
Summary
The gemsbok (Oryx gazella, NCBI:txid9958) is the largest antelope in the genus Oryx and a member of the Hippotraginae tribe of ruminants [1] (Fig. 1). The gemsbok’s biogeographical distribution includes Botswana and Namibia, traditionally inhabiting the Kalahari and Karoo deserts in southern Africa [2] The climate of these regions is highly seasonal, with cool winters (10◦C–15◦C) and hot summers (43◦C–46◦C) when most of the annual rainfall occurs (90–100 mm). High evaporation rates and low precipitation result in a semi-arid climate in both deserts [3]. Living in such extreme environments, gemsbok have evolved to be highly adapted to drought and extreme heat by minimizing water demand and loss. The cross-links were reversed, and the DNA was purified from chromatin After sequencing these libraries on the Illumina Hiseq 4000 platform, we obtained ∼382 million 150 bp read pairs
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