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

Hong Ma; Yongbo Liu; Detuan LiuWeibang SunXiongfang LiuYouming WanXiujiao ZhangRengang ZhangQuanzheng YunJihua WangZhenghong LiYongpeng Ma

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

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

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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 (θ = 2.58e-3; π = 1.94e-3) when compared not only to R. delavayi (θ = 11.61e-3, π = 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.

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来源
《The Plant Journal》 |2021年第5期|1533-1545|共13页
作者
Hong Ma; Yongbo Liu; Detuan LiuWeibang SunXiongfang LiuYouming WanXiujiao ZhangRengang ZhangQuanzheng YunJihua WangZhenghong LiYongpeng Ma;
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作者单位

Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650233, China;

State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China;

Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaBeijing Ori-Gene Science and Technology Co. Ltd, Beijing 102206, ChinaThe Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;

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正文语种英语
中图分类植物学;
关键词
genome sequencing; rhododendrons; deleterious mutation; population demography; conservation;

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

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