Novel nomenclature and functional insights into YTH genes in the Rosaceae family

Abstract N 6-methyladenosine (m6A) is a prevalent and widespread post-transcriptional modification of eukaryotic messenger ribonucleic acid (mRNA). Historically, YT512-B homology (YTH) domain proteins have been regarded as RNA-binding proteins. Recent studies have revealed their critical roles in recognizing m6A and regulating the metabolism of m6A-modified mRNA. The identification of YTH domain proteins is essential for elucidating the regulatory mechanism of m6A. However, information concerning YTH domain proteins in the Rosaceae family remains limited. In this study, we reported the identification of a total of 185 YTH genes across 12 Rosaceae species. Cis-element analysis indicated the pivotal roles of YTH domain proteins in plant development and environmental response. Consequently, we comprehensively summarized the expression profiles of YTH genes in Fragaria vesca, Malus domestica, Prunus persica, and Rubus idaeus, revealing their tissue-specific expression patterns and involvement in plant and fruit development. Additionally, the analysis of YTH gene expression profiles in peach fruit in response to methyl jasmonate treatment suggested a potential role of YTH genes in chilling injury during low temperature storage. Moreover, through heterologous transgenesis, we confirmed that PpYTHDFE1 regulates fruit quality by promoting the accumulation of organic acids and decreasing the sugar-to-acid ratio. We devised a novel nomenclature system for YTH genes across multiple species, providing information for further research on these genes. Our findings provide a valuable reference for future investigations into the regulatory mechanisms of YTH proteins and m6A within the Rosaceae family.