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

作者：Hong Ma, Yongbo Liu, Detuan Liu, Weibang Sun, Xiongfang Liu, Youming Wan, Xiujiao Zhang, Rengang Zhang, Quanzheng Yun, Jihua Wang, Zhenghong Li, Yongpeng Ma · 发表于：The Plant Journal · 年份：2021 · DOI：10.1111/tpj.15399 · 被引用次数：90 · 研究领域：Genetic diversity and population structure、Plant and animal studies、Genomics and Phylogenetic Studies

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) un...