Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation
Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation
复制标题
极度濒危杜鹃花的染色体水平基因组组装和群体遗传分析为其保护提供了见解
DOI：
10.1111/tpj.15399
复制
发表时间：
2021-07-17
期刊：
影响因子：
7.2
通讯作者：
Ma, Yongpeng
中科院分区：
文献类型：
--
作者：
Ma, Hong;Liu, Yongbo;Ma, Yongpeng
杜鹃花是木本植物，具有很高的园艺价值，闻名世界。然而，许多野生物种目前面临灭绝的威胁。在这里，我们报告的第一次高品质，染色体水平的基因组杜鹃griersonianum，这有助于约10%的所有园艺杜鹃品种，但在其野生形式已被评估为极度濒危。最终的基因组组装，其重叠群N50大小约为34 M，总长度为677 M，是迄今为止在该属内测序的最高质量的基因组，部分原因是其杂合性低（0.18%）。已鉴定的重复序列约占基因组的57%，预测了38280个蛋白质编码基因，支持率较高。我们进一步对31个R. griersonianum及其广布近缘种R. delavayi，并进行了额外的保护基因组分析。结果表明，R. griersonianum的遗传多样性较低（theta = 2.58e-3; pi = 1.94e-3），不仅与R. delavayi（theta = 11.61e-3，pi = 12.97e-3），但对大多数其它木本植物也有较好的抗性。此外，三个严重的遗传瓶颈检测使用的阶梯图和fastsimcoal 2分析，这被认为是发生在中更新世晚期和末次盛冰期（LGM）期间。在这些瓶颈之后，R. griersonianum恢复并保持稳定的有效种群大小（> 25000）至今。有趣的是，R。griersonianum在纯合状态下比R. Delavayi，以及几种有害突变（例如，在基因中参与对热胁迫的反应）可能会损害这种植物对周围环境的适应。该高质量的染色体水平的基因组和种群基因组分析的极度濒危的R。griersonianum将提供一个宝贵的资源，以及对该物种的未来研究，以促进保护和杜鹃属一般的见解。
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.