Whole Genome Methylation Patterns in Mungbean

Abstract

Methylome analysis which includes DNA methylation information in whole genome level gives lots of inheritable epigenetic information. Whole genome DNA methylation analysis in plants have been conducted in Arabidopsis Thaliana, Oryza sativa (rice), Populus trichocarpa (poplar) and Glycine max (soybean). Among these, only rice and soybean are edible crops so it is needed to study various plants methylome. In this reason, we conducted DNA methylome analysis of mungbean which is an important legume crop widely cultivated in Asia. And we established the foundation of epigenetic study of mungbean. For this, we selected two mungbean cultivars- VC1973A (Seonhwanogdu), V2984 (Kyung-Ki Jaerae#5) and conducted BS-seq with Sodium Bisulfite treatment. And also, we did transcriptome analysis to see methylation information and correlation of gene expression level and methylation. In the result, The VC1973A methylome contains 107,313,781 methylated CGs (mCG- 54.1% of all CGs), 116,306,461 mCHG (44.3% of all CHGs) and 95,774,535 mCHH (5.5% of all CHHs) which represents a greater proportion of methylated cytosines compared with DNA methylome for Arabidopsis thaliana, but it is similar with soybeans Detailed methylation status of VC1973A and V2984, data over 90 percent of methylation level with supporting depth over 10, shows methylcytosines of VC1973A and V2984 were distributed by similar patterns overall but ratio of mCG, mCHG and mCHH was slightly different as 57.16%, 42.03%, 0.81% in VC1973A and 56.10%, 43.25%, 0.65% in V2984. Based this result, we made methylation map combined with each methylation level and gene density. It revealed that sites having higher density of methylcytosines show low gene density of each chromosome compared with the bulk methylcytosines regions. In comparison of two cultivars, among total 1,244,837 methylation sites, 1,226,791 sites were conserved between two cultivars. It means 98.6% of methylation between two cultivars is conserved and we considered the rest 18,046 sites (1.4%) as epiallelic sites. We did gene annotation and ontology analysis with these epialleic sites. In the results of gene ontology analysis, these epiallelic genes are involved in various organelle, DNA polymerase activity or biological processes like vitamin metabolic process etc. To see relation between duplicated genes and methylation, we compared methylation level distribution in two paralogs. 2,917 identified duplicated gene pairs show dispersed shape regardless of methylation context. In all methylation contexts, dots are distributed along the axis. We assume that this pattern results from character of mungbenan genome which has only one time of ancient duplication event and after that methylation of duplicated genes has been divided depending on its use. Keywords: Epigenetics, Epigenome, DNA methylation, Epiallele, Genome duplication Student number: 2012-21094