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研究生:張景淞
研究生(外文):Ching-Sung Chang
論文名稱:台灣產龍膽屬的葉綠體親緣基因體學
論文名稱(外文):Plastome Phylogenomics of Taiwanese Gentiana L.
指導教授:鍾國芳鍾國芳引用關係陳志雄陳志雄引用關係
口試委員:劉世慧
口試日期:2020-01-09
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:森林環境暨資源學研究所
學門:農業科學學門
學類:林業學類
論文種類:學術論文
論文出版年:2020
畢業學年度:108
語文別:中文
論文頁數:84
中文關鍵詞:龍膽科龍膽屬小龍膽組基因體略讀葉綠體基因體
外文關鍵詞:GentianaceaeGentianaChondrophyllaeGenome skimmingChloroplast genome
DOI:10.6342/NTU202000038
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臺灣的龍膽屬(Gentiana L.)物種生長於中高海拔山區,除了台灣龍膽之外,其餘皆屬小龍膽組(sect. Chondrophyllae Bunge)。前人使用分子標記重建台灣的小龍膽組親緣關係,證實台灣的小龍膽組物種除了台東龍膽外,形成一單系群,但經歷輻射演化使得 DNA 變異累積不足,無法由短片段分子標記重建出高解析度的親緣關係。本研究採基因體略讀(genome skimming)策略,獲取台灣的 13 個龍膽物種(阿里山龍膽、竹林龍膽、台灣龍膽、黃斑龍膽、鴛鴦湖龍膽、高山龍膽、伊澤山龍膽、黑斑龍膽、玉山龍膽、塔塔加龍膽、太魯閣龍膽、台東龍膽、厚葉龍膽),與中國的華南龍膽葉綠體基因體資料,進行親緣關係樹的重建。本次取樣的小龍膽組物種,其 ndh 基因均缺失,推測與環境低溫、高照度與大幅度照度變化有關。重建出的親緣關係樹,除玉山龍膽外,其餘節點均獲得高支持度,清楚解析台灣產小龍膽組的親緣關係,並據此處理台灣產龍膽的分類,將黑斑龍膽提升為物種階層、塔塔加龍膽降為黃斑龍膽的變種,提出新組合名 G. punctulata comb. et stat. nova 與 G. flavomaculata var. tatakensis comb. et stat. nova。台灣的小龍膽組單系群物種分為二支序,可以對應到花色表徵,故本研究根據親緣關係、花色,與生育地環境特徵,提出「照度—花色假說」,可以解釋台灣產小龍膽組物種的演化驅力與花色演化。此外,亦使用葉綠體分子標記 trnL-F 區段序列重建東南亞小龍膽組物種與台灣小龍膽組物種的關係,結果顯示東南亞小龍膽組物種(G. laotica 與 Gentiana sp.)取代華南龍膽,成為台灣小龍膽組物種的最近外群。本研究結果顯示葉綠體基因體資料有助於重建快速分化物種的親緣關係。
Gentiana L. species can be found in alpine and subalpine areas in Taiwan. Most of Taiwanese Gentiana belong to section Chondrophyllae Bunge except G. davidii var. formosana. Previous phylogenetic study based on chloroplast and nucleus DNA markers revealed that Taiwanese Chondrophyllae were monophyly exclusive of G. tenuissima. The phylogenetic relations into Taiwanese Chondrophyllae were unresolved because of the rapid radiation of them. Here we employed the genome skimming strategy to obtain chloroplast genomes from 13 Taiwanese endemic species (i.e., G. arisanensis, G. bambuseti, G. davidii var. formosana, G. f. var. flavomaculata, G. f. var. yuanyanghuensis, G. horaimontana, G. itzershanensis, G. s. var. scabrida, G. s. var. punctulata, G. tatakensis, G. tarokoensis, G. tenuissima, G. tentyoensis) and G. loureirii from China. The loss of ndh genes was observed among the Chondrophyllae spp., which may be caused by the high and fluctuated light at low temperature environment. The phylogenetic tree reconstructed by plastome data highly resolved the relations between Taiwanese Chondrophyllae spp.. In accordance with the phylogeny of Taiwanese Gentiana, we treat the taxonomy status of G. s. var. punctulata as G. punctulata comb. et stat. nova and G. tatakensis as G. flavomaculata var. tatakensis comb. et stat. nova. The Taiwanese Chondrophyllae monophyly is consisted of 2 clades which correspond to the variant characters of flower colors. As the association of phylogeny, flower color, and environment characteristics of the Taiwanese Chondrophyllae spp., we propose the “illuminance—color hypothesis” to expound the evolutionary force and flower color evolution of Taiwanese Chondrophyllae. Gentiana spp. from Indochina region (G. laotica & Gentiana sp.) substitute G. loureirii for the closest outgroup of Taiwanese Chondrophyllae clade on the phylogenetic tree reconstructed with chloroplast DNA noncoding region trnL-F. The results confirmed the utility of plastome data for reconstructing phylogenetic relationships in young and rapid lineages.
摘 要 I
Abstract II
目 錄 IV
表 目 錄 VIII
圖 目 錄 IX
第一章 前言 1
1-1 台灣產龍膽屬植物介紹 1
1-1.1 台灣目前採用的龍膽屬植物分類 2
1-1.2 其他學者對於台灣產龍膽屬的分類處理 4
1-1.3 台灣產龍膽屬植物的地理分布 4
1-1.4 台灣與鄰近地區龍膽屬植物的親緣關係 7
1-2 高山植物的種化假說 8
1-3 葉綠體基因體 10
1-3.1 葉綠體基因體的結構與大小 10
1-3.2 龍膽屬的葉綠體基因體與 ndh 基因 11
1-4 次世代定序技術與基因略讀法 14
1-5 研究目標 14
第二章 材料與方法 15
2-1 以基因略讀法建構台灣產龍膽葉綠體基因體 15
2-1.1 植物材料與基因體 DNA 萃取 15
2-1.2 基因略讀法圖書庫建構與定序 15
2-1.3 定序資料處理 19
2-1.4 核苷酸位點多型性分析 21
2-2 以分子標記重建小龍膽組物種之分子親緣關係 21
2-2.1 樣本選擇與序列取得 22
2-2.2 分子親緣關係重建 23
2-3 以葉綠體基因體資料重建台灣產小龍膽組分子親緣關係 24
2-3.1 以基因編碼序列(CDS)重建「組」級分子親緣關係 24
2-3.2 分子定年 26
2-4 以全葉綠體序列重建台灣小龍膽組單系群之分子親緣關係 26
第三章 結果 27
3-1 基因略讀定序結果 27
3-2 葉綠體基因體組裝結果 27
3-3 核苷酸多型性分析結果 32
3-4 分子標記親緣關係重建結果 33
3-5 以 CDS 資料重建分子親緣關係 35
3-5.1 分子親緣關係重建結果 35
3-5.2 分子定年結果 37
3-6 以全葉綠體基因體資料重建台灣小龍膽組之分子親緣關係 38
第四章 討論 40
4-1 基因略讀法的影響因子 40
4-2 ndh 基因於各分支物種的缺失狀況與原因 40
4-3 台灣小龍膽單系群的演化機制推測 43
4-3.1 表徵與親緣關係的對應 43
4-3.2 照度可能是形塑台灣小龍膽單系群表徵與演化的因子 46
4-4 分類處理 47
4-5 台灣小龍膽組物種與其近緣物種的演化歷史 51
4-5.1 竹林龍膽於小龍膽組內的親緣關係地位 51
4-5.2 新幾內亞、東南亞小龍膽與台灣小龍膽的親緣關係 51
4-5.3 各小龍膽組單系群的演化歷史 51
4-5.4 呂宋龍膽與台灣龍膽單系群的可能關係 53
4-6 台灣龍膽屬植物的演化歷史 54
第五章 結論 56
第六章 參考資料 58
附錄 70
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