Identification and characterization of genes related to m6A modification in kiwifruit using RNA-seq and ATAC-seq

Abstract

N-methyladenosine (mA) RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms. Despite its significance, a comprehensive analysis of mA-related genes in non-model plants, such as kiwifruit, is lacking. Here, we identified 36 mA-related genes in the kiwifruit genome according to homology and phylogenetic inference. We performed bioinformatics and evolutionary analyses of the writer, eraser, and reader families of mA modification. Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most mA-related genes were remarkably expressed under different conditions. Through construction of gene co-expression networks, we found significant correlations between several mA-related genes and transcription factors (TFs) as well as receptor-like genes during the development and ripening of kiwifruit. Furthermore, we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of mA-related genes. We identified 10 common open chromatin regions that were present in at least two tissues, and these regions might serve as potential binding sites for MADS protein, C2H2 protein, and other predicted TFs. Our study offers comprehensive insights into the gene family of mA-related components in kiwifruit, which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.