Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China.
School of Life Sciences, Yunnan Normal University, Kunming 650500 Yunnan, China.
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae052.
Rhododendron nivale subsp. boreale Philipson et M. N. Philipson is an alpine woody species with ornamental qualities that serve as the predominant species in mountainous scrub habitats found at an altitude of ∼4,200 m. As a high-altitude woody polyploid, this species may serve as a model to understand how plants adapt to alpine environments. Despite its ecological significance, the lack of genomic resources has hindered a comprehensive understanding of its evolutionary and adaptive characteristics in high-altitude mountainous environments.
We sequenced and assembled the genome of R. nivale subsp. boreale, an assembly of the first subgenus Rhododendron and the first high-altitude woody flowering tetraploid, contributing an important genomic resource for alpine woody flora. The assembly included 52 pseudochromosomes (scaffold N50 = 42.93 Mb; BUSCO = 98.8%; QV = 45.51; S-AQI = 98.69), which belonged to 4 haplotypes, harboring 127,810 predicted protein-coding genes. Conjoint k-mer analysis, collinearity assessment, and phylogenetic investigation corroborated autotetraploid identity. Comparative genomic analysis revealed that R. nivale subsp. boreale originated as a neopolyploid of R. nivale and underwent 2 rounds of ancient polyploidy events. Transcriptional expression analysis showed that differences in expression between alleles were common and randomly distributed in the genome. We identified extended gene families and signatures of positive selection that are involved not only in adaptation to the mountaintop ecosystem (response to stress and developmental regulation) but also in autotetraploid reproduction (meiotic stabilization). Additionally, the expression levels of the (group VII ethylene response factor transcription factors) ERF VIIs were significantly higher than the mean global gene expression. We suspect that these changes have enabled the success of this species at high altitudes.
We assembled the first high-altitude autopolyploid genome and achieved chromosome-level assembly within the subgenus Rhododendron. In addition, a high-altitude adaptation strategy of R. nivale subsp. boreale was reasonably speculated. This study provides valuable data for the exploration of alpine mountaintop adaptations and the correlation between extreme environments and species polyploidization.
Rhododendron nivale subsp. boreale Philipson et M. N. Philipson 是一种高山木本植物，具有观赏品质，是海拔约 4200 米的山地灌丛栖息地的主要物种。作为一种高海拔木本多倍体，该物种可以作为研究植物如何适应高山环境的模型。尽管它具有生态意义，但缺乏基因组资源阻碍了对其在高山山地环境中的进化和适应特征的全面了解。
我们对 R. nivale subsp. boreale 进行了测序和组装，这是第一个 Rhododendron 亚属的组装，也是第一个高山木本四倍体，为高山木本植物提供了重要的基因组资源。组装结果包括 52 条假染色体（scaffold N50 = 42.93 Mb；BUSCO = 98.8%；QV = 45.51；S-AQI = 98.69），它们属于 4 个单倍型，包含 127810 个预测的蛋白质编码基因。联合 k-mer 分析、共线性评估和系统发育研究证实了同源四倍体的身份。比较基因组分析表明，R. nivale subsp. boreale 起源于 R. nivale 的新多倍体，并经历了 2 轮古老的多倍体事件。转录表达分析表明，等位基因之间的表达差异在基因组中普遍存在且随机分布。我们鉴定了扩展的基因家族和正选择的特征，这些特征不仅涉及到对山顶生态系统的适应（对压力的反应和发育调节），还涉及到同源四倍体的繁殖（减数分裂稳定）。此外，（VII 类乙烯响应因子转录因子）ERF VIIs 的表达水平明显高于全球平均基因表达水平。我们推测这些变化使该物种能够在高海拔地区成功生存。
我们组装了第一个高山同源四倍体基因组，并在 Rhododendron 亚属内实现了染色体水平的组装。此外，还合理推测了 R. nivale subsp. boreale 的高山适应策略。这项研究为探索高山山顶适应和极端环境与物种多倍化之间的关系提供了有价值的数据。
