干旱区生态环境知识资源中心(Arid): A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert

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DOI	10.1093/gigascience/giy162
	A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert
	Farre, Marta 1; Li, Qiye 2,3,4; Zhou, Yang 4,5; Damas, Joana 1; Chemnick, Leona G.6; Kim, Jaebum 7; Ryder, Oliver A.6; Ma, Jian 8; Zhang, Guojie 2,3,4,5; Larkin, Denis M.1; Lewin, Harris A.9,10
通讯作者	Farre, Marta ; Larkin, Denis M. ; Lewin, Harris A.
来源期刊	GIGASCIENCE
ISSN	2047-217X
出版年	2019
卷号	8 期号:2
英文摘要	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.
英文关键词	gemsbok Oryx gazella assembly annotation ruminant drought
类型	Article ; Data Paper
语种	英语
国家	England ; Peoples R China ; Denmark ; USA ; South Korea
开放获取类型	Green Accepted, Green Published, gold
收录类别	SCI-E
WOS记录号	WOS:000462551600007
WOS关键词	REVEALS INSIGHTS ; DIVERGENCE ; POPULATIONS ; PREDICTION ; EVOLUTION
WOS类目	Biology ; Multidisciplinary Sciences
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
来源机构	University of California, Davis ; University of London
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/216054
作者单位	1.Univ London, Dept Comparat Biomed Sci, Royal Vet Coll, London, England; 2.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources, Kunming 650223, Yunnan, Peoples R China; 3.Chinese Acad Sci, Kunming Inst Zool, Dept Comparat Biomed Sci Evolut, Kunming 650223, Yunnan, Peoples R China; 4.BGI Shenzhen, China Natl Genebank, Shenzhen 518120, Peoples R China; 5.Univ Copenhagen, Dept Biol, Ctr Social Evolut, Univ Pk 15, DK-2100 Copenhagen, Denmark; 6.San Diego Zoo, Inst Conservat Res, Escondido, CA USA; 7.Konkuk Univ, Dept Biomed Sci & Engn, Seoul 05029, South Korea; 8.Carnegie Mellon Univ, Sch Comp Sci, Computat Biol Dept, Pittsburgh, PA 15213 USA; 9.Univ Calif Davis, Coll Biol Sci, Dept Ecol & Evolut, UC Davis Genome Ctr, Davis, CA 95616 USA; 10.Univ Calif Davis, Sch Vet Med, Dept Reprod & Populat Hlth, Davis, CA 95616 USA
推荐引用方式 GB/T 7714	Farre, Marta,Li, Qiye,Zhou, Yang,et al. A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert[J]. University of California, Davis, University of London,2019,8(2).
APA	Farre, Marta.,Li, Qiye.,Zhou, Yang.,Damas, Joana.,Chemnick, Leona G..,...&Lewin, Harris A..(2019).A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert.GIGASCIENCE,8(2).
MLA	Farre, Marta,et al."A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert".GIGASCIENCE 8.2(2019).