Zhenhui Zhong, Suhua Feng, Ben N Mansfeld, Yunqing Ke, Weihong Qi, Yi-Wen Lim, Wilhelm Gruissem, Rebecca S Bart, Steven E Jacobsen.

Plant Biotechnol J.; 2023 Feb;21(2):247-249. doi: 10.1111/pbi.13955.

Cytosine DNA methylation is involved in transposable element (TE) silencing, imprinting and X‐chromosome inactivation. Plant DNA methylation is mediated by MET1 (mammalian DNMT1), DRM2 (mammalian DNMT3) and two plant‐specific DNA methyltransferases, CMT2 and CMT3. To dissect the haplotype‐resolved DNA methylome of cassava, we conducted methylome studies in two haplotype genome‐resolved accessions of cassava (TME7 and TME204) using whole‐genome bisulfite sequencing (WGBS) and enzymatic methyl‐seq (EM‐seq), respectively. Sequencing reads were mapped to different haplotypes individually allowing zero mismatches and one best hit, which allowed the separation of reads belonging to different haplotypes. Overall, we found that although both WGBS and EM‐seq methods were used, the two haplotypes have similar whole‐genome methylation levels in TME7 and TME204. We further plotted methylation levels over transcribed regions of protein‐coding genes and TEs, and observed similar methylation levels between different haplotypes. Next, we analysed differentially methylated cytosines between haplotypes (haplotypic DMCs). We first aligned the two haplotypes and identified syntenic cytosines. We observed at least three scenarios that resulted in differential methylations between haplotypes: (i) SNP/InDel in one haplotype leads to the loss of the cytosine (47.17%), among which more than 99.25% are SNP variants; (ii) Cytosine context alterations (e.g. CG in hap1 and CHH in hap2) that lead to the methylation level changes detected in our analysis (28.98%); and (iii) Cytosines stay in the same contexts between haplotypes but exhibit different methylation levels (23.85%).  Finally, we investigated the genetic diversity of DMC sites and 400‐bp flanking sequences and found that nucleotide diversity of DMC sites is significantly higher than that of flanking sequences. Higher nucleotide diversity of DMCs demonstrated that DMC sites are under more frequent natural selection and revealed the crosstalk between sequence variations and DNA methylation mutations. Together, our analyses compared haplotype‐resolved DNA methylomes of cassava and placed genomic heterozygosity within the haplotypic epigenetic regulatory landscape.

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9884013/

Figure 1

Haplotype‐resolved DNA methylome of African cassava. (a) Whole‐genome methylation levels of hap1 and hap2 haplotypes in TME7 (n = 3) and TME204 (n = 1). (b) Metaplot of CG, CHG and CHH methylation levels over protein‐coding genes and flanking 1‐kb sequences of hap1 and hap2 haplotypes in TME7. (c) Metaplot of methylation levels over transposon elements and flanking 1 kb sequences in TME7. (d–f) Metaplot of methylation levels over structural variation regions and flanking 1 kb sequences in TME7. Regions of equal length were randomly selected in the genome (blue line). (g) Methylation levels of complete, partial and non‐ASE genes in TME7. (h) Representative screenshots of DMCs. Methylation site losses and mC context changes are indicated on top of the track (red: hap1; blue: hap2). (i) Ratio of DMCs caused by SNP/InDel and DMCs caused by different methylation levels in TME7. (j) Numbers of different types of cytosine context variations between the two haplotypes in TME7. (k) Consensus sequences of DMCs in TME7. (l) Genomic distribution enrichment of DMCs in TME7. (m–n) Nucleotide diversity of 400‐bp flanking regions of DMC in TME7 (m) and TME204 (n). Panels i, j, l and k show results for TME7.