DNA跳躍子在水稻基因體中的足跡

Abstract

跳躍子 (transposable elements) 又稱跳躍子，是一種能在基因體中移動的DNA片段，於1940年代由Barbara McClintock發現。水稻 (Oryza sativa L.) 基因體中有1,731,500個跳躍子，其中359,321個為第二型跳躍子 (DNA transposon)。大部分第二型跳躍子進行轉位 (transposition) 時插入在靶位點 (target site)，並於轉位再次發生時形成靶位點重複 (target site duplications, TSDs) 。本研究使用生物資訊工具分析68個主要來自亞洲地區，稉、秈稻品系的次世代定序資料，從水稻基因體中搜尋中兩種形式的靶位點重複： (1) 位於第二型跳躍子兩端的側翼序列， (2) 第二型跳躍子轉位後所形成的二重複序列。以第一種形式的靶位點序列長度作為參考值，搜尋第二種形式的靶位點重複，將其視為假定的靶位點重複 (putative TSDs, pTSDs) ，並以pTSDs的染色體圖譜比較68品系間的差異。此外，也針對水稻蛋白編碼序列中由pTSDs造成的基因體變異 (genomic variation) 進行搜尋。研究結果顯示，本研究所分析的四類第二型跳躍子 (Mutator, dDart, iDart及nDart) 靶位點皆具有長度偏好性，但僅部分種類跳躍子的靶位點具有序列偏好性。pTSDs染色體圖譜在水稻品系間具有多型性，可從中觀察水稻品系間的基因漸滲 (introgression) 。68水稻品系中共有118個基因之蛋白編碼序列含有由pTSDs造成的基因體變異。未來期望將本研究結果提供給學者作為參考，增進對跳躍子的認識，並將這些知識應用於作物品種改良。

Transposable elements, also known as transposons, are mobile DNA segments in genome discovered by Barbara McClintock in 1940s. There are 1,731,500 transposable elements in rice (Oryza sativa L.) genome, of which 359,321 belong to type II transposable elements (DNA transposons). Most of the DNA transposons insert in target site during transpositions. When transpositions happen again, the target site duplications (TSDs) would be generated in most of cases. In this study, we used next generation sequencing data of 68 rice accesions that are mainly originated from Asia, including japonica and indica for bioinformatics analysis. We analyzed two types of TSDs: (1) locate at both flanking sequences of type II transposable elements, and (2) appear as two tandem repeats after transpositions of type II transposable elements. Take the length of type one TSDs as reference information to search types two TSDs in 68 rice accessions as putative target site duplications (pTSDs), and display chromosome plots of pTSDs for comparison between 68 accessions. Moreover, we also search for protein coding sequences which contain genomic variations that caused by pTSDs. The results showed that the type II transposable elements in this study (Mutator, dDart, iDart and nDart) have length preference for target site but only some of them have sequence preference for target sites. We can observe introgression event through polymorphism between accessions of pTSDs on chromosome plots. There are 118 genes in total which contain genomic variation that caused by pTSDs. We hope researchers can use the results of this study in the future for better understanding of transposable elements and also for crop improvement.