Rice is one of the most important crop in the world and the genome sequences of a rice cultivar, Nipponbare has been used not only for rice research, but also as the model reference genome sequences in monocotyledon species among the crops. With the development of the next generation sequencing(NGS) techniques producing high order of coverage and with the need for epigenomic analysis, the need for resequencing of the domestic rice cultivars with the reference “Nipponbare” genome sequence at the de novo level. According the simulation of Nipponbare reference genomes with Eulerian methods, the target size of maximal contig and N50 of ones of the domestic cutivar rice were estimated to be 10M and 1M, respectively. To achieve the target size, various mate-paired libraries were constructed and sequenced. With the high order of coverage obtained from domestic rice cultivar, Ilmi, with NGS technology, the effect of trimming and error correction on reads quality profiles and size distribution of contigs were analyzed. Also the computational parameters for validation of assembled contigs were analyzed. For the analysis of epigenomic methylation modification of the genome sequences, the methyl binding microarray technology was developed. The various methyl-CG binding proteins were characterized. The binding and scanning of methyl-CG domain to promoter binding microarray and their downstream genes were analyzed. Also rice mutants related to methylation were selected to understand the effect of methylation on gene expresson and its effect on phenotypes.