Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation

doi:10.1111/tpj.15399

KIB OpenIR

	Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation
	Ma,Hong ; Liu,Yongbo ; Liu,Detuan; Sun,Weibang; Liu,Xiongfang ; Wan,Youming ; Zhang,Xiujiao ; Zhang,Rengang ; Yun,Quanzheng ; Wang,Jihua ; Li,Zhenghong ; Ma,Yongpeng
	2021
发表期刊	PLANT JOURNAL
ISSN	0960-7412
卷号	107 期号:5 页码:1533-1545
摘要	Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high-quality, chromosome-level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest-quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein-coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (theta = 2.58e-3; pi = 1.94e-3) when compared not only to R. delavayi (theta = 11.61e-3, pi = 12.97e-3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high-quality, chromosome-level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general.
关键词	genome sequencing rhododendrons deleterious mutation population demography conservation HI-C ANNOTATION YUNNAN TOOL SELECTION SEQUENCE PROGRAM SYSTEM TREE
DOI	10.1111/tpj.15399
WOS记录号	WOS:000673522700001
引用统计	被引频次：28[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73491
专题	中国科学院昆明植物研究所
作者单位	1.Chinese Acad Forestry, Res Inst Resources Insects, Kunming 650233, Yunnan, Peoples R China 2.Chinese Res Inst Environm Sci, State Key Lab Environm Criteria & Risk Assessment, Beijing 100012, Peoples R China 3.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species E, Kunming 650201, Yunnan, Peoples R China 4.Beijing Ori Gene Sci & Technol Co Ltd, Beijing 102206, Peoples R China 5.Yunnan Acad Agr Sci, Flower Res Inst, Kunming 650205, Yunnan, Peoples R China 6.Natl Engn Res Ctr Ornamental Hort, Kunming 650205, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Ma,Hong,Liu,Yongbo,Liu,Detuan,et al. Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation[J]. PLANT JOURNAL,2021,107(5):1533-1545.
APA	Ma,Hong.,Liu,Yongbo.,Liu,Detuan.,Sun,Weibang.,Liu,Xiongfang.,...&Ma,Yongpeng.(2021).Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation.PLANT JOURNAL,107(5),1533-1545.
MLA	Ma,Hong,et al."Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation".PLANT JOURNAL 107.5(2021):1533-1545.