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系統識別號 U0026-2408201418021200
論文名稱(中文) 葉芽阿拉伯芥基因體和阿拉伯芥屬的親緣基因體學
論文名稱(英文) Phylogenomics in Arabidopsis based on a newly constructed genome of A. halleri ssp. gemmifera
校院名稱 成功大學
系所名稱(中) 生命科學系
系所名稱(英) Department of Life Sciences
學年度 102
學期 2
出版年 103
研究生(中文) 黃名邦
研究生(英文) Ming-Bang Huang
學號 l56011075
學位類別 碩士
語文別 中文
論文頁數 56頁
口試委員 口試委員-黃浩仁
指導教授-蔣鎮宇
口試委員-江友中
中文關鍵字 葉芽阿拉伯芥  比較基因體學  種化  outlier分析 
英文關鍵字 A. halleri ssp. gemmifera  comparative genomics  speciation  Outlier 
學科別分類
中文摘要 阿拉伯芥 (Arabidopsis thaliana) 是一年生的自交草本植物,也是擁有最詳盡基因體資料的模式植物。阿拉伯芥最近緣的物種為Arabidopsis lyrata和Arabidopsis halleri,均為多年生異交且須仰賴昆蟲授粉,顯示阿拉伯芥屬在交配系統和世代交替速度都有明顯差異。分布於北美五大湖區A. lyrata的亞種lyrata為二個完成解序的阿拉伯芥屬物種;而 A. halleri ssp. gemmifera是A. halleri的五個亞種中唯一分布於東亞的物種。因此本文藉由比較 A. halleri ssp. gemmifera與A. thaliana 、 A. lyrata和日本的A. halleri ssp. gemmifera的基因體來分析阿拉伯芥屬間的演化和種內的遺傳多樣性。BLAST 分析結果顯示阿拉伯芥屬的同源基因 (orthologs) 有10532個。本文使用outlier分析將大於Ks值分布的95.00 %外的基因群設定為Ks的outliers,並假定這些outliers是種化初期分歧的基因。PAML 結果顯示,outliers中有39.00 %的基因有發生過正向天擇,而同源基因中只有17.00 %;PhiPack的結果顯示outliers和同源基因的重組率有顯著差異。相較於A. thaliana,A. lyrata 與 A. halleri ssp. gemmifera兩者的同義置換速率較慢,顯示世代交替的速率會影響演化速率。親緣樹的結果顯示0.40 % 的基因親緣樹不符合物種親緣樹,再由兩者的地理分布推斷親緣樹不符合的原因可能為譜系不完全分離 (incomplete lineage sorting)。比較兩個 A. halleri ssp. gemmifera同源基因體後發現 25.01 % 的同源基因有發生變異,其中只有1.40 % 受到天擇的影響,顯示多數的變異是不受天擇影響。綜合以上所述,本文推測 A. thaliana分化的原因可能跟較快的演化速率和正向天擇有關;兩個姊妹種的分歧則主要是正向天擇催化的結果。而日本和台灣的A. halleri ssp. gemmifera可能受到不同的天擇壓力。
英文摘要 Arabidopsis thaliana, an annual self - compatible grass, is the most popular model plant.
A. thaliana has two sister species, Arabidopsis lyrata and Arabidopsis halleri.
A. lyrata is distributed in America and northern Europe. A. halleri is distributed in Europe and east Asia, but only A. halleri ssp. gemmifera is distributed in Taiwan. Both of them are perennial and outcrossing which reveal the difference in Arabidopsis. In this paper, we used comparative genomics to analysis three Arabidopsis genomes in order to figure out the evolution of Arabidopsis . Moreover, this paper also compared the A. halleri ssp. gemmifera genome of Taiwan and Japan’s to analysis the variation between the individuals. Using BLAST analysis, we discovered 10532 orthologs in Arabidopsis. In Ks outlier analysis , there were 705 Ks outlier found in the orthologs .By using PAML and PhiPack, we identified outlier genes had significant higher positive selection and reconbination rate than background genes . The Ks mutation rate in A. thaliana is significantly higher than the other two sister species. In the phylogenetic tree result, 0.40 % of genes displayed A. lyrata clustered with A. halleri ssp. gemmifera. Within species, only 25.01% genes had variation and 1.40 % had positive selection . Besides only a little overlap between Taiwan and Japan. Positive selection is an activators of three species ,but the higher evolution rate is also an activators for A. thaliana diverge. Also Taiwan and Japan’s A. halleri ssp. gemmifera are faceing different selection power.
論文目次 中文摘要 I
Extended Abstract II
誌謝 V
圖目錄 VIII
壹、 前言 1
一、 Arabidopsis thaliana和其近源物種 1
二、 次世代定序的發展和非模式物種基因體組裝 3
三、 比較基因體學 5
四、 物種形成 6
五、 物種適應和正向天擇 7
貳、 研究目的 9
參、 材料與方法 10
一、 研究材料 10
二、 基因體的基本分析 10
三、 基因體演化分析 14
肆、 結果 17
一、 基因體與同源基因 17
二、 演化事件分析 21
伍、 討論 26
陸、 結論 33
柒、 引用文獻 34
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