Genome-Wide Identification and Expression Analysis of Cytosine DNA Methyltransferase Genes Related to Somaclonal Variation in Pineapple (Ananas comosus L.)

Abstract

DNA methylation plays an important role in somaclonal variation. Cytosine-5 DNA methyltransferases (C5-MTases) are crucial enzymes for maintaining the de novo genome DNA methylation status, and the gene family has been identified and characterized in several species. However, limited information is available about the role of C5-MTases in the somaclonal variation of pineapple. Herein, the characteristic of DNA methylation in the leaf variants of pineapple showed that the methylation rate of variants decreased and the demethylation was mainly. Six AcC5-MTases were identified from pineapple genome. Phylogenetic analysis indicated that the six members could be classified into four subgroups, namely, AcMET, AcCMT, AcDRM, and AcDNMT, demonstrating evolutionary conservation in the C5-MTases across pineapple and other plant species. Cis-elements were presented in AcC5-MTase promoters, including light-responsive, phytohormone-responsive, and plant growth and development elements. Furthermore, we investigated the expression profiles of AcC5-MTases in different tissues and their transcript abundance in the leaves of somaclonal variation. Interestingly, most AcC5-MTase genes were highly expressed in leaf and carpopodium. AcMET, AcCMT2, and AcDRM2 were upregulated in pineapple somaclonal variants, indicating that AcC5-MTases might play an important role in the somaclonal variation of pineapple. Our results will aid in understanding the complex roles of methylation in plants and provide a basis for analyzing the role of methylation modification in the somaclonal variation of pineapple.

Molecular characterization and expression analysis of DNA methyltransferase genes during kiwifruit ripening

“…Subcellular localization prediction results presented that thirteen kiwifruit DNMTs were localized in nucleus, two in the chloroplast and one in plasma membrane (Table 1). Similarly, most DNMTs were also located in the nucleus in other plant species, such as wheat (Gahlaut et al, 2020), pineapple (Lin et al, 2022), and amaranth (Lancíková et al, 2023). Due to the importance of protein subcellular localization in determining its function, these predictions offered a clue for possible functions of these DNMTs.…”

“…In strawberry, Fv-methylase4 and Fv-methylase5 were increased with the continuous fruit ripening (Gu et al, 2016). In pineapple, the expression levels of AcMET, AcDNMT, AcDRM1 and AcDRM2 in maturate sarcocarp were higher than those in immaturate sarcocarp (Lin et al, 2022). On the contrary, AcDMT1, AcDMT9, AcDMT10, AcDMT12 and AcDMT13 showed a downward trend during kiwifruit ripening, indicating they negatively regulate fruit ripening and softening (Fig.…”

“…In strawberry, Fv-methylase2, Fv-methylase6 and Fv-methylase9 were decreased in fruit ripening (Gu et al, 2016). The expression levels of pineapple AcCMT1 and AcCMT2 in maturate sarcocarp were lower than those in immaturate sarcocarp (Lin et al, 2022). The different expression pattern of DNMTs during fruit ripening provided evidence for diverse roles in fruit ripening and softening.…”

“…In plants, DNA methylation appears in CG, CHG and CHH (H represents A, T or C) contexts in the genome (Chen et al, 2021). As an important DNA methylation related gene, DNA methyltransferase (DNMT) genes have been isolated and identi ed from Arabidopsis (Genger et al, 1999), rice (Ahmad et al, 2014), legumes (Garg et al, 2014), strawberry (Gu et al, 2016), wheat (Gahlaut et al, 2020), tomato (Guo et al, 2020), pineapple (Lin et al, 2022).…”

“…al., 2014), strawberry(Gu et al, 2016), wheat(Gahlaut et al, 2020), tomato(Guo et al, 2020), pineapple(Lin et al, 2022), amaranth(Lancíková et al, 2023). However, there has not been reported for DNMTs in kiwifruit.…”