Genome assembly and DNA methylation variation in an epimutant population of hybrid poplar clone NL895

Epimutant populations represent important genetic resources for plant breeding and selection. However, the variation and dynamics of epigenomic modifications among epimutants are still elusive. In this study, we analyzed DNA methylation patterns at both whole-genome and allelic levels in an epimutant population of a model hybrid poplar NL895 (Populus deltoides × P. euramericana cv. ‘Nanlin895’). Epimutants were generated through the application of 5-Azacytidine (5-Aza) during tissue culture. A haplotype-resolved assembly of NL895 was constructed to serve as a reference for epigenomic analysis. Compared to control plants, averaged DNA methylation levels across the entire genome were reduced in epimutants. The methylation patterns of epimutants exhibited high diversity in several aspects, including the number of differentially methylated regions (DMRs), distribution of DMRs in sequence contexts, and genomic features. The observed epigenomic diversity suggests stochastic effects resulting from 5-Aza treatment. At the gene level, non-expressed genes consistently displayed higher rates of methylation across all examined epimutants. Among allele-specific expressed genes (ASEGs), fold changes between parental alleles were more pronounced in allele pairs exhibiting greater disparities in DNA methylation rates. For allele-specific methylation regions (ASMRs), the differences in methylation levels were notably elevated in ASMRs overlapped with genomic structural variations (SVs). Our results provide valuable germplasm resources characterized by phenotypic variations for poplar breeding, and the dynamics of DNA methylation in hybrid poplar epimutants highlights potential clues for application of hybrid vigor.