應用參考序列檢測水平基因轉移現象的方法 : 以Stigmatella aurantiaca為例

Abstract

水平基因轉移的現象在原核與真核生物中都經常發生，且與相關基因的來源與功能都有重要的關係。研究水平基因轉移現象，在原核生物中可以了解其如何適應新環境、得到新的能力，如何與宿主互動等；在真核生物中則可以探究物種的起源，和基因的功能。現今由於科技的進展，大量的基因序列與基因體資料變得更容易取得，使我們更容易研究水平基因轉移現象。在此我們嚐試利用大量的基因體資料，開發廣範圍搜索水平基因轉移現象候選基因的方法；利用tBLASTn結果的bit-score與比較序列的概念，在兩基因體所做的散布圖中，找出代表特定蛋白的outlier位置點，加以排序之後建立該點的演化樹，由其分類上的不一致對比樣版演化樹來確認水平基因轉移現象的存在。本研究所使用的模式物種為黏球菌Stigmatella aurantiaca，該菌的基因體極大，或許與其內有眾多水平基因轉移現象有關。 最後結果顯示此方法可以廣泛找出Stigmatella aurantiaca內的水平基因轉移現象候選基因，但因還未有比對的其它物種，尚無法確認Stigmatella aurantiaca的基因體大小與水平基因轉移現象的直接關係。

The Horizontal Gene Transfer (HGT) events occur frequently in both prokaryotes and eukaryotes. It is important to understand the function and origination of a gene. By researching the HGT events, we may figure out how a prokaryote adaptations the environment, gains new abilities, and interactions with its’ host. Moreover, we may use HGT events to research the origination of species in eukaryotes. Nowadays, more and more full genomic sequences and annotated genes has been identified, make us easily to discover the HGT events. In this study, we try to apply mass amount of genomic data and develop the method of wide screen HGT events in species by using the results of tBLASTn (bit-score ) and reference sequences. We find the outlier dot from the dot plot which is made by two BLAST query hit genomes and analyze the protein of that dot, build phylogenetic tree, observe the incongruence of the tree topology, thus, find out the HGT events. We use Stigmatella aurantiaca as model organism in this research because the genomic size of this Myxococcales is abnormally large, therefor we suppose that it is an result of frequently HGT events . The final result show that our method could identify the HGT events in a wide range but the relationship between HGT events and Stigmatella aurantiaca’s genomic size is still not clear right now, duo to the lack of contrast genome HGT events data.