A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari Desert
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella) : an iconic antelope of the Kalahari Desert. / Farré, Marta; Li, Qiye; Zhou, Yang; Damas, Joana; Chemnick, Leona G.; Kim, Jaebum; Ryder, Oliver A; Ma, Jian; Zhang, Guojie; Larkin, Denis M.; Lewin, Harris A.
In: GigaScience, Vol. 8, No. 2, giy162, 2019, p. 1-8.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella)
T2 - an iconic antelope of the Kalahari Desert
AU - Farré, Marta
AU - Li, Qiye
AU - Zhou, Yang
AU - Damas, Joana
AU - Chemnick, Leona G.
AU - Kim, Jaebum
AU - Ryder, Oliver A
AU - Ma, Jian
AU - Zhang, Guojie
AU - Larkin, Denis M.
AU - Lewin, Harris A.
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
U2 - 10.1093/gigascience/giy162
DO - 10.1093/gigascience/giy162
M3 - Journal article
C2 - 30649288
VL - 8
SP - 1
EP - 8
JO - GigaScience
JF - GigaScience
SN - 2047-217X
IS - 2
M1 - giy162
ER -
ID: 212871616