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

Research output: Contribution to journalJournal articleResearchpeer-review

Documents

Marta Farré, Qiye Li, Yang Zhou, Joana Damas, Leona G. Chemnick, Jaebum Kim, Oliver A Ryder, Jian Ma, Guojie Zhang, Denis M. Larkin, Harris A. Lewin

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 BUSCO analysis. The Reference-Assisted Chromosome Assembly tool (RACA) 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.

Original languageEnglish
Article numbergiy162
JournalGigaScience
Volume8
Issue number2
Pages (from-to)1-8
ISSN2047-217X
DOIs
Publication statusPublished - 2019

Number of downloads are based on statistics from Google Scholar and www.ku.dk


No data available

ID: 212871616