De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China | |
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; Sun, Weibang1,2,7 | |
2019-07-01 | |
Source Publication | GIGASCIENCE |
ISSN | 2047-217X |
Volume | 8Issue:7Pages:10 |
Abstract | 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. |
Keyword | Acer Yangbiense Psesp Pacbio Sequencing Genome Assembly Genome Annotation |
DOI | 10.1093/gigascience/giz085 |
Indexed By | SCI |
WOS ID | WOS:000482312700009 |
Citation statistics | |
Document Type | 期刊论文 |
Identifier | http://ir.kib.ac.cn/handle/151853/68656 |
Collection | 中国科学院东亚植物多样性与生物地理学重点实验室 |
Corresponding Author | Ma, Yongpeng; Sun, Weibang |
Affiliation | 1.Chinese Acad Sci, Yunnan Key Lab Integrat Conservat Plant Species W, Kunming Inst Bot, Kunming 650201, Yunnan, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, 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 |
Recommended Citation 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. |
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