背景:杜鹃花亚种。borealePhilipsonetM.N.Philipson是一种具有观赏品质的高山木本植物,在海拔4,200m的山区灌木丛栖息地中作为主要物种。作为高海拔的木质多倍体,该物种可以作为了解植物如何适应高山环境的模型。尽管具有生态意义,基因组资源的缺乏阻碍了对其在高海拔山区环境中的进化和适应特征的全面理解。
结果:我们测序并组装了R.nivale亚种的基因组。无聊,第一个杜鹃花亚属和第一个高海拔木质开花四倍体的组合,为高山木本植物群提供了重要的基因组资源。组装包括52个假染色体(支架N50=42.93Mb;BUSCO=98.8%;QV=45.51;S-AQI=98.69),属于4个单倍型,拥有127,810个预测的蛋白质编码基因。联合k-mer分析,共线性评估,系统发育研究证实了同源四倍体的身份。比较基因组分析显示,Nivale亚种。boreale起源于R.nivale的新多倍体,经历了2轮古代多倍体事件。转录表达分析表明,等位基因之间的表达差异在基因组中是常见且随机分布的。我们确定了扩展的基因家族和正选择的特征,它们不仅涉及对山顶生态系统的适应(对压力和发育调节的响应),而且还涉及自四倍体繁殖(减数分裂稳定)。此外,(第VII组乙烯反应因子转录因子)ERFVIs的表达水平显着高于平均全局基因表达。我们怀疑这些变化使这个物种在高海拔地区取得成功。
结论:我们组装了第一个高海拔的自体多倍体基因组,并在杜鹃花亚属内实现了染色体水平的组装。此外,R.nivale亚科的高空适应策略。无聊是合理推测的。这项研究为探索高山山顶适应以及极端环境与物种多倍体化之间的相关性提供了有价值的数据。
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.