How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera. A series of genes putatively associated with alpine adaptation (e.g. CBFs, ERF-VIIs, and RAD51C) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNLs, prRLPs, and XII RLKs), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1, DMC1, and MSH3) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.

中文翻译：

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应对高山栖息地：三叶草（忍冬科）适应策略的基因组见解


植物如何找到在高山栖息地茁壮成长的方式仍然很大程度上未知。在这里，我们展示了高山药草 Triplostegia mudulifera（忍冬科）的染色体水平基因组组装，以及来自其他 Dipsacales 物种的 13 个转录组。我们在 T. tubercules 中检测到全基因组重复事件，该事件发生在 Dipsacales 多样化之前。研究发现，全基因组复制后基因的优先保留有助于增加 T. mudulifera 中与寒冷相关的基因。一系列被认为与高山适应相关的基因（例如 CBF、ERF-VII 和 RAD51C）在腺金银花中表现出比其低海拔近亲忍冬更高的表达水平。对五对高海拔和低海拔物种的比较基因组分析（包括 T. mudulifera 和 L. japonica 的比较）表明，与低地近缘植物相比，高山植物中与抗病性相关的基因家族经历了显着的趋同性收缩。基因库大小的减少主要集中在用于病原体识别的基因进化枝（例如CNL、prRLP和XII RLK），而用于信号转导和发育的基因进化枝几乎保持不变。这一发现反映了在恶劣的高山地区生存的节能策略，在该地区，需要权衡较少的病原体挑战和有限的生长资源。我们还鉴定了适应高山的候选基因（例如RAD1、DMC1和MSH3），这些基因处于收敛正向选择下或在所研究的高山植物中表现出进化速率的收敛加速。总的来说，我们的研究为这种植物和其他高山植物的高海拔适应策略提供了新的见解。