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

文献类型： 外文期刊

作者： Ma, Hong 1 ; Liu, Yongbo 2 ; Liu, Detuan 3 ; Sun, Weibang 3 ; Liu, Xiongfang 1 ; Wan, Youming 1 ; Zhang, Xiujiao 1 ; Zhan 1 ;

作者机构： 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

关键词： genome sequencing; rhododendrons; deleterious mutation; population demography; conservation

期刊名称：PLANT JOURNAL （ 影响因子：6.486； 五年影响因子：7.666 ）

ISSN： 0960-7412

年卷期： 2021 年 107 卷 5 期

页码：

收录情况： SCI

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.

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