DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.)

Abstract

The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H = A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves.

Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process

“…Previous studies have investigated histone modifications and siRNA levels in plant cell suspension cultures in vitro (Tanurdzic et al ., ). Genomewide DNA methylation analysis in leaves and leaf‐derived callus exhibited a differential methylation in tissue culture (Vining et al ., ; Zakrzewski et al ., ). In this study, we revealed the effects of the epigenome on the cotton tissue culture process in the callus, somatic embryos and several regenerated plants through DNA methylation, RNA‐Seq, sRNA‐Seq and ChIP‐Seq analyses.…”

Development of Beet necrotic yellow vein virus‐based vectors for multiple‐gene expression and guide RNA delivery in plant genome editing

“…Sugar beet (B. vulgaris) is one of the most important crops around the world for sugar production and is also an important plant resource for biomass energy and animal feed (Dohm et al, 2014;Zakrzewski et al, 2017). Thus, it is highly desirable to identify valuable genes affecting agronomically relevant traits in sugar beet plants.…”

“…Sugar beet (B. vulgaris) is an important crop for sugar production, biomass energy and animal feed (Dohm et al, 2014;Zakrzewski et al, 2017). Thus, it is highly important to carry out genomic studies in sugar beets.…”

How to Design a Whole-Genome Bisulfite Sequencing Experiment

“…In contrast to that, plant genomes have additional CHG and CHH methylation (H = adenine, thymine or cytosine). These last two correlate with the suppression of transposon activity [17], mobile genetic elements that can change their The subsequent polymerase chain reaction (PCR) translates uracil into thymine. During sequencing, this base pair shift causes cytosine/thymine-polymorphism, which can be quantified and interpreted as proportion of the original methylation at a specific site through the comparison of reads with the original strand or a reference genome ( Figure 2).…”

“…In contrast to that, plant genomes have additional CHG and CHH methylation (H = adenine, thymine or cytosine). These last two correlate with the suppression of transposon activity [17], mobile genetic elements that can change their A disadvantage of WGBS is that bisulfite sequencing cannot distinguish between 5hmC and 5mC. The 5hmC is described as the dynamic DNA modification associated with the DNA demethylation process [12] in animals.…”