CG gene body DNA methylation changes and evolution of duplicated genes in cassava

Abstract

DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.

Genomic DNA methylation analyses reveal the distinct profiles in castor bean seeds with persistent endosperms

“…While inspecting the distribution of CG, CHG, and CHH methylations in gene and TE regions, we observed that the CG methylation occurred preferentially in the gene body regions relative to the flanking regions, similar to previous reports in other plants (Hsieh et al, 2009;Zemach et al, 2010a;Song et al, 2013;Lu et al, 2015;Wang et al, 2015), whereas the extents of CHG and CHH methylation were low in gene body regions and relatively higher in flanking regions (Fig. 4A), consistent with their global DNA methylation patterns (Fig.…”

“…The higher proportion of CHH methylation arose in both embryo and endosperm of castor bean, consistent, in a way, with the high proportion of CHH methylation identified from the leaves of cassava (about 58%; Wang et al, 2015). In spite of the global CG and CHG DNA hypomethylation that arose in endosperm relative to embryo, CHH methylation did not exhibit a significant reduction in endosperm.…”

ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development

“…In particular, we found that ATX3/4/5-targeted genic loci have fairly lower level of the gene-body CG methylation and higher level of H3K27me3 than SDG2 targets, raising the questions of why and how such characteristics are conferred. It has been known that, in general, the activity of gene transcription is positively correlated with the gene-body methylation and negatively correlated with H3K27me3 mark (Zhang et al, 2006;Kouzarides, 2007;Wang et al, 2015;Yang et al, 2016). Indeed, we found that the expression of genes for the ATX3/4/5-targeted loci is significantly lower than SDG2 targets.…”

Evolution of Gene Duplication in Plants

“…The degree of regulatory interaction divergence is dependent on the duplication mechanism: most WGD-derived duplicates share some regulatory interactions, while non-WGD duplicates tend not to have overlapping regulators (Arsovski et al, 2015). Gene body methylation is found to impact transcription (Lister et al, 2008;Takuno and Gaut, 2012), and divergence in methylation pattern between duplicates is significantly, although rather weakly, correlated with expression divergence in Arabidopsis (Wang et al, 2014a), rice (Wang et al, 2013b), and cassava (Manihot esculenta; Wang et al, 2015a). Beyond transcriptional regulation, duplicates with divergent microRNA-binding sites tend to have more divergent expression profiles , and duplicates also can differ significantly in alternative splicing.…”