冰期後不同拓殖路線的兩種臺灣特有楓屬植物對海拔適應的遺傳機制

Abstract

物種是如何應對快速變化的環境以達到區域性適應一直是演化生物學重要的議題，而不同物種在面對環境變化時是否呈現相同的適應性反應也鮮少被探討。本研究使用兩種在末次冰河期後在海拔上有著不同拓殖路線的臺灣楓屬植物-尖葉楓（Acer caudatifolium）以及紅榨楓（A. rubescens）作為研究材料，探討海拔梯度如何影響此二物種在基因組層級上的適應，並比較兩物種對於海拔的適應機制是否相同。我首先使用轉錄組定序（RNA-seq）量化高低海拔族群的基因表現量，並使用表現差異分析篩選出族群之間具有顯著差異的候選基因。接著我使用PAML估算編碼區的同義置換及非同義置換的比值來判斷各個基因在不同的海拔族群是否受到正向天擇。再來我還使用Multiplexed shotgun genotyping（MSG）獲取大量的單位點變異（SNPs）,利用族群基因體的方式檢測與海拔有關的環境因子是否與兩物種的族群遺傳變異有關聯。此外，我也藉由遺傳-環境關聯性分析來檢測單一SNPs與各個環境因子的關聯性，以觀察兩物種在面對相同類型的環境變化時主要是哪些基因座起關鍵作用。最後我將具有表現差異、受到天擇且跟環境因子有關聯的基因座進行資料庫的比對，以了解這些基因座的功能及其代謝途徑。結果顯示大部分海拔之間具有差異表現以及在PAML檢測中有偵測到正向天擇的基因在兩物種之間都不相同；然而遺傳-環境關聯性分析結果發現大部分與海拔環境因子具有顯著關聯性的基因座在兩物種之間具有高度的重疊，說明此二物種對於海拔環境的選汰壓力有著在不同層級的相似以及相異之處。另外，基因功能註解的結果也顯示大部分的候選基因都與環境變化有關，如節律調節、氣孔開關調節、以及開花時間等。本研究結果有助於詮釋不同海拔植物族群的適應機制，以及植物面對不同環境時適應能力的改變有進一步的了解。How species respond to heterogeneous environments is critical to understanding adaptation. Whether the adaptive response to environmental changes is conserved or diverged among species in genome-wide sequence and expression level is still remained unclear. Here, I combined transcriptomic (RNA-seq) and population genomic approaches, to infer the genomic architecture of altitudinal adaptation of two Taiwanese maple species, Acer caudatifolium and Acer rubescens. After comparing the gene expression profiles of low- and high-altitude populations of each species, I found the majority of differential expressed genes were different between species. Besides, an obvious divergent pattern in the population-specific adaptive evolution of protein-coding sequences was also identified. Furthermore, I acquired genome-wide SNPs data from multiplexed shotgun genotyping (MSG) and quantify the relative contributions of altitudinal-related environmental variables to genetic variation and detect the candidate loci underlying altitudinal adaptation. The result shows that the temperature seasonality might play an important role in genetic variation in both species, and I surprisingly found that most of the genomic regions associated with altitudinal-related environmental variables are identical between species, suggesting that genomic regions involved in environmental selection in these two species are in extensive parallelism. I also figure out the functions of the differential expressed genes, positive selected genes as well as the environmental associated genes, and I found most of them were related to abiotic stress responses, ex. circadian rhythm, stomatal movement, flowering times and etc. This study provided a better understanding of how altitudinal gradient shapes the gene expression profiles and genomic-wide sequence variations of plant species in very different ways.