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De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China

文献类型：期刊论文

作者Yang, Jing1,2; Wariss, Hafiz Muhammad1,2,3; Tao, Lidan1,2; Zhang, Rengang4; Yun, Quanzheng4; Hollingsworth, Peter5; Dao, Zhiling1,2; Luo, Guifen1,2; Guo, Huijun6; Ma, Yongpeng1,2
刊名GIGASCIENCE
出版日期2019-07-01
卷号8期号:7页码:10
ISSN号2047-217X
关键词Acer yangbiense PSESP PacBio sequencing genome assembly genome annotation
DOI10.1093/gigascience/giz085
通讯作者Ma, Yongpeng(mayongpeng@mail.kib.ac.cn) ; Sun, Weibang(wbsun@mail.kib.ac.cn)
英文摘要Background: Acer yangbiense is a newly described critically endangered endemic maple tree confined to Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on "plant species with extremely small populations (PSESP)". Findings: We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is similar to 666 Mb, with 13 chromosomes covering similar to 97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization. Conclusion: Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide fundamental conservation genomics resources, as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.
WOS研究方向Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
语种英语
WOS记录号WOS:000482312700009
源URL[http://ir.kib.ac.cn/handle/151853/68655]  
专题昆明植物研究所_中国科学院东亚植物多样性与生物地理学重点实验室
通讯作者Ma, Yongpeng; Sun, Weibang
作者单位1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China
2.Chinese Acad Sci, Yunnan Key Lab Integrat Conservat Plant Species W, Kunming Inst Bot, Kunming 650201, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Beijing Origene Sci & Technol Co Ltd, Beijing 102206, Peoples R China
5.Royal Bot Garden Edinburgh, 20a Inverleith Row, Edinburgh, Midlothian, Scotland
6.Southwest Forestry Univ, Kunming 650224, Yunnan, Peoples R China
7.Chinese Acad Sci, Kunming Inst Bot, Kunming Bot Garden, Kunming 650201, Yunnan, Peoples R China
推荐引用方式
GB/T 7714		 Yang, Jing,Wariss, Hafiz Muhammad,Tao, Lidan,et al. De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China[J]. GIGASCIENCE,2019,8(7):10.
APA Yang, Jing.,Wariss, Hafiz Muhammad.,Tao, Lidan.,Zhang, Rengang.,Yun, Quanzheng.,...&Sun, Weibang.(2019).De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China.GIGASCIENCE,8(7),10.
MLA Yang, Jing,et al."De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China".GIGASCIENCE 8.7(2019):10.

入库方式： OAI收割

来源：昆明植物研究所

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