Phylogenomics in Arabidopsis based on a newly constructed genome of A. halleri ssp. gemmifera

• Main Authors: Ming-BangHuang, 黃名邦
• Other Authors: Tzen-Yuh Chiang
• Format: Others
• Language: zh-TW
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/f472y8

碩士 === 國立成功大學 === 生命科學系 === 102 === 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.