Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening

Abstract

Tomato fruit cells are characterized by a strong increase in nuclear ploidy during fruit development. Average ploidy levels increased to similar levels (above 50C) in two distinct fruit tissues, pericarp and locular tissue. However, ploidy profiles differed significantly between these two tissues suggesting a tissue-specific control of endoreduplication in tomato fruit. To determine possible relationships between endoreduplication and epigenetic mechanisms, the methylation status of genomic DNA from pericarp and locular tissue of tomato fruit was analysed. Pericarp genomic DNA was characterized by an increase of CG and/or CNG methylation at the 5S and 18S rDNA loci and at gyspsy-like retrotransposon sequences during fruit growth. A sharp decrease of the global DNA methylation level together with a reduction of methylation at the rDNA loci was also observed in pericarp during fruit ripening. Inversely, no major variation of DNA methylation either global or locus-specific, was observed in locular tissue. Thus, tissue-specific variations of DNA methylation are unlikely to be triggered by the induction of endoreduplication in fruit tissues, but may reflect tissue-specific ploidy profiles. Expression analysis of eight putative tomato DNA methyltransferases encoding genes showed that one chromomethylase (CMT) and two rearranged methyltransferases (DRMs) are preferentially expressed in the pericarp during fruit growth and could be involved in the locus-specific increase of methylation observed at this developmental phase in the pericarp.

A DEMETER-like DNA demethylase governs tomato fruit ripening

“…In support of this idea, recent work describing the methylome dynamics in tomato fruit pericarp revealed substantial changes in the distribution of DNA methylation over the tomato genome during fruit development, and demethylation during ripening at specific promoters such as the NON RIPENING (NOR) and COLORLESS NON RIPENING (CNR) promoters (20,21). This observation is consistent with previous studies indicating that genome cytosine methylation levels decrease by 30% in pericarp of fruits during ripening, although DNA replication is very limited at this stage (22).…”

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

“…SAM-MTases are ubiquitous enzymes that catalyze the transfer of methyl groups from S-adenosyl methionine (SAM) to a myriad of compounds (e.g., DNA, RNA, proteins, sterols, pectin, lignin, flavonoids, phenylpropanoids, and alkaloids) and also act in the biosynthesis pathway of ethylene and polyamines. Many of those compounds have an important role in fruit ripening (Moffatt and Weretilnyk, 2001;Roje, 2006;Teyssier et al, 2008;Singh et al, 2010;MacLean and NeSmith, 2011;Paul et al, 2012;Van de Poel et al, 2013;Zhang et al, 2015).…”

A comparative analysis of DNA methylation in diploid and tetraploid apple (Malus × domestica Borkh.)

“…The transcription of genes encoding DNA methyltransferases varies during plant development (Yamauchi et al 2008). MET1 gene is expressed in vegetative organs or in reproductive organs, but decreases with the maturity of the organ (Fujimoto et al 2006;Teyssier et al 2008). DRM gene can be expressed in roots, leaves, stems, flowers, and its expression intensity has no direct relationship with the maturity of tissues and organs (Wada et al 2003).…”

“…DRM gene can be expressed in roots, leaves, stems, flowers, and its expression intensity has no direct relationship with the maturity of tissues and organs (Wada et al 2003). CMT3 genes are unique to plants, isolated from maize, oil palm, tomatoes and so on (Papa et al 2001;Rival et al 2008;Teyssier et al 2008). The present qRT-PCR analysis was able to show that MET1 was most strongly transcribed in the leaf, while CTM3 transcript abundance was highest in the fruit.…”