Study On Rice Transposon Variations Based On Large-scale Population Sequencing

Transposons are fragments of DNA that can replicate or "jump" on the genome.Translocation of activate transposons will produce rich transposon variations,which can make a difference on host's life and activities.Making use of the information of abnormally mapping reads in different individuals can indentify transposon variations.So far,the researches on rice transposons are usually amied at samll-scalerice populations or specfic functional transposons,as a result,comprehensive studies on transposons of large-scale rice populations are still scarce.With the development of next-generation sequencing technologies,more and more rice high-throughput data are generated,which provides a good opportunity for the study on rice populations.In this study,3243 high-coverage rice genome sequencing data published by the "3000 Rice Genome Project" and the rice transposon database RiTE-db were used to annotate rice transposon variations,and the main results are as follows:1 ? Using Nipponbare IRGSP 1.0 as a reference genome,the transposon variations of 3243 rice accessions were indentified,which was accurate to 1 kb.Finally,62555 transposon variations were detected,DTM and RLG are the two most variable transposons,and it was found that there are 1593 autonomous transposons and 35163 non-autonomous transposons,non-autonomous transposons are more active than autonomous transposons.The result was verified in Zhenshan 97 and Minghui 63 genomes,and the sensitivity can reach 98%.2?A preliminary analysis of transposon varitions was performed.It was found that,the enrichment regions where DNA transposons and retrotransposons are inserted are euchromatin and heterochromatin regions,respectively,however,Tos17 and the RLC family,in which it is located,are special cases in retrotransposons,as they show a preference to insert into euchromatin regions.Furthermore,the activation of transposon has hot spots,and these hot spots show the tendency of euchromatin enrichment.3?The biological significance of active transposons was excavated.Combining with 24 nt siRNA data,it was found that 24 nt siRNA is enriched in activate transposon region.By combining with ATAC-seq data,it was found that the DNA transposons are more inclined to insert into chromation open areas.In this study,we completed the annotation and analysis of transposon variation in large-scale rice populations,deepening our understanding of transposon translocation characteristics in rice populations,which may certain help for further researches on function of rice transposons and evolution of the rice genome.