Whole-Genome DNA Methylation Associated With Differentially Expressed Genes Regulated Anthocyanin Biosynthesis Within Flower Color Chimera of Ornamental Tree Prunus mume

Abstract

DNA methylation is one of the best-studied epigenetic modifications involved in many biological processes. However, little is known about the epigenetic mechanism for flower color chimera of Prunus mume (Japanese apricot, mei). Using bisulfate sequencing and RNA sequencing, we analyzed the white (FBW) and red (FBR) petals collected from an individual tree of Japanese apricot cv. ‘Fuban Tiaozhi’ mei to reveal the different changes in methylation patterns associated with gene expression leading to significant difference in anthocyanins accumulation of FBW (0.012 ± 0.005 mg/g) and FBR (0.078 ± 0.013 mg/g). It was found that gene expression levels were positively correlated with DNA methylation levels within gene-bodies of FBW and FBR genomes; however, negative correlations between gene expression and DNA methylation levels were detected within promoter domains. In general, the methylation level within methylome of FBW was higher; and in total, 4,618 differentially methylated regions (DMRs) and 1,212 differentially expressed genes (DEGs) were detected from FBW vs. FBR. We also identified 82 DMR-associated DEGs, and 13 of them, including PmBAHD, PmCYP450, and PmABC, were playing critical roles in phenylalanine metabolism pathway, glycosyltransferase activity, and ABC transporter. The evidence exhibited DNA methylation may regulate gene expression resulting in flower color chimera of Japanese apricot.

Integration of Transcriptome and Methylome Analyses Provides Insight Into the Pathway of Floral Scent Biosynthesis in Prunus mume

“…However, when limiting the analysis to certain genes, the relationship between ML and gene expression did not always follow this rule. Similar result can be found in the result of previous research ( Ma et al, 2018 ; Jiang et al, 2020 ). A more likely explanation was the complexity of the process of floral scent biosynthesis, so that methylation is not the only regulation factor.…”

“…The results are consistent with findings from the petals of P. mume cv. ‘FT’ ( Jiang et al, 2020 ), apples, and Arabidopsis .…”

“…The methylation status varies among different species, cultivars of the same species, and even tissues of the same plant ( Vaughn et al, 2007 ; Suzuki and Bird, 2008 ). Evidence has shown that DNA methylation is involved in regulating the expression of key genes during the ripening of tomato fruit ( Zhong et al, 2013 ); drought resistance ( Xu et al, 2018 ) and flowering ( Xing et al, 2019 ) of apple; peel color formation of apple ( Bai et al, 2016 ; Li et al, 2019 ), red pear ( Wang et al, 2013 ), and sweet orange ( Huang et al, 2019 ); and the flower color formation of P. mume chimera ( Jiang et al, 2020 ). However, the role it plays in the process of floral scent biosynthesis has not yet been reported.…”

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

“…DNA methylation is one of the most common epigenetic modifications in eukaryotes and is believed to play a vital role in various biological processes, including transcription regulation, embryogenesis, cellular differentiation, genomic imprinting, X-chromosome inactivation, transposon silencing and so on [ 25 – 31 ]. In plants and some vertebrates, DNA methylation is also involved in the regulation of colouration, such as flower colours [ 32 ], eggshell colours [ 33 ] and animal skin and coat colours [ 34 ]; this suggests that it is also likely involved in the regulation of shell colour. However, to date, no published studies have addressed this hypothesis.…”

Comparative Methylation and RNA-Seq Expression Analysis in CpG Context to Identify Genes Involved in Backfat vs Liver Diversification in Nanchukmacdon Pig

“…Understanding these changes requires rigorous analysis at the genome-wide level and recent studies have indicated the role of the methylated region in positively or negatively regulating the gene expression in specific tissue types [25,26]. Previous studies indicate the role of deposition of backfat is one such aspect associated with growth rate, meat quality, and reproductive performance [27].…”