Footprints of DNA Transposable Elements in Rice Genome

• Main Authors: Yu-An Chen, 陳昱安
• Other Authors: Chih-wei Tung
• Format: Others
• Language: zh-TW
• Published: 2016
• Online Access: http://ndltd.ncl.edu.tw/handle/9664sp

碩士 === 國立臺灣大學 === 農藝學研究所 === 104 === 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.