Cytosine DNA methylation is involved in biological processes such as transposable element (TE) silencing, imprinting, and X chromosome inactivation. Plant methylation is mediated by MET1 (mammalian DNMT1), DRM2 (mammalian DNMT3), and two plant-specific DNA methyltransferases, CMT2 and CMT3 (Law and Jacobsen, 2010). De novo DNA methylation in plants is established by DRM2 via the plant specific RNA-directed DNA methylation (RdDM) pathway that depends on two DNA-dependent RNA polymerases, Pol IV and Pol V (Gallego-Bartolome et al ., 2019; Law and Jacobsen, 2010; Stroud et al ., 2013). The DNA methylome of cassava has been previously documented based on its haploid collapsed genome (Wang et al ., 2015). Since the cassava genome is highly heterozygous, DNA methylome analysis of the haplotype-collapsed genome misses many features of the methylome. With the development of long read sequencing and chromosomal conformation capture techniques, haplotype resolved genomes are available for highly heterozygous genomes (Mansfeld et al ., 2021; Qi et al ., 2022; Zhou et al ., 2020), which provides high-quality reference genomes facilitating studies of haplotype resolved DNA methylomes.

Haplotype resolved DNA methylome of African cassava genome