DNA methylome and transcriptome landscapes revealed differential characteristics of dioecious flowers in papaya

Abstract

Separate sexes in dioecious plants display different morphology and physiological characteristics. The differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype, which is genetically determined and epigenetically modified. In dioecious papaya (Carica papaya L.), global comparisons of epigenetic DNA methylation and gene expressions were still limited. We conducted bisulfite sequencing of early-stage flowers grown in three seasons (spring, summer and winter) and compared their methylome and transcriptome profiles to investigate the differential characteristics of male and female in papaya. Methylation variances between female and male papaya were conserved among three different seasons. However, combined genome-scale transcriptomic evidence revealed that most methylation variances did not have influence on the expression profiles of neighboring genes, and the differentially expressed genes were most overrepresented in phytohormone signal transduction pathways. Further analyses showed diverse stress-responsive methylation alteration in male and female flowers. Male flower methylation was more responsive to stress whereas female flower methylation varied less under stress. Early flowering of male papaya in spring might be associated with the variation in the transcription of CpSVP and CpAP1 coinciding with their gene-specific hypomethylation. These findings provide insights into the sex-specific DNA methylation and gene expression landscapes of dioecious papaya and a foundation to investigate the correlation between differentiated floral characteristics and their candidate genes.

DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus

“…However, we discovered that the majority of genes carrying DMRs in their gene bodies or flanking regions did not present significant changes in their expression levels. In fact, this phenomenon has also been discovered in other studies on the relationships of DNA methylation with a number of biological processes 37 – 39 . For example, one study investigated the influence of epigenetic modification on soybean domestication and evolution by comparing and analyzing the variation in DNA methylation in several soybean cultivars and related materials.…”

Transcriptome and DNA methylome dynamics reveal differential characteristics of inflorescence development between two ecotypes in Panicum hallii

“…The copyright holder for this preprint this version posted March 2, 2022. ; https://doi.org/10.1101/2022.02.28.482119 doi: bioRxiv preprint within their gene body regions. These patterns are similar to recent results reported in chickpea and papaya (Rajkumar et al, 2020;Zhou et al, 2020), suggesting the conserved antagonistic role of CG methylation in gene expression regulation at the regulatory and gene body regions.…”

A Review of Omics Technologies and Bioinformatics to Accelerate Improvement of Papaya Traits

“…Hence, transcriptome plays a role in estimating the expression of genes, as well as in deciphering the regulation of genes in tissues and organs. Unravelling the transcriptome of tissues and organs of the species that are of interest can be carried out using RNA sequencing technology (RNA-seq), which has been shown to be highly reproducible and enables the simultaneous study of expressed gene samples [73][74][75][76][77][78][79]. These RNA-seq features have made RNA-seq experiments widely used in most transcriptome studies, including the transcriptome analysis of papaya plants.…”

“…Previous studies on papaya transcriptomes have focused on the analysis of several papaya traits, such as drought effects [73], fruit quality [74,75], sex determination [76,77], and disease mechanisms [78,79] (Table 1). The molecular response of papaya plants can be observed by analysing the tissue-specific differentially expressed genes (DEGs) using a gene-enrichment analysis.…”

“…In addition, the authors found the phytohormone-biosynthesis and signal-transduction pathways in the male-to-hermaphrodite sex-reversal flowers. Similarly, Zhou et al [77] used RNA-seq technology to investigate the underlying mechanism in DNA methylation contribution to the male and female flowers. Dissecting the molecular mechanism that regulates sex expression in the papaya provides valuable resources that facilitate an understanding of sexual differentiation in the papaya.…”