Genome-wide identification and characterization of YTH domain-containing genes, encoding the m6A readers, and their expression in tomato.

KEY MESSAGE: 9 YTH genes in tomato were identified and cloned, and their expression patterns were comprehensively analyzed, which reveal potential multiple roles in development and fruit ripening. N6-methyladenosine (m6A) is an abundant and pervasive post-transcriptional modification in eukaryotic mRNAs. The YTH domain-containing proteins act as m6A readers to read m6A marks and transduce their downstream regulatory effects by altering m6A-mRNA metabolism processes. Identification of YTH proteins is essential for understanding the regulatory mechanisms of m6A in physiological processes, but little is known about YTH proteins in tomato, a model system for fruit development. Here, we report that tomato genomes contain a total of 9 SlYTH genes. While YTH proteins of both tomato and Arabidopsis can be classified into two subfamilies, the member distributions in subfamilies are very different between the two species. Homology modeling exhibited the similar three-dimensional structures of SlYTH proteins to human YTHDF1 or YTHDC1. Multiple hormone-response elements locating on the promoters of SlYTH genes indicate that they are involved in the physiological processes related to phytohormone. SlYTH genes are ubiquitous and spatiotemporal dynamic expression in tomato. Eight SlTYH genes have the strongest expression in stamens among the parts of flowers. Throughout fruit ontogeny, most of the SlYTH genes display obvious high mRNA levels during the developmental phases (4 dpa to mature green); moreover, SlYTH1 and SlYTH2 have absolute predominant expressions demonstrated by RNA-seq. The results lay a foundation for future characterizations on the functions of YTH proteins and m6A regulatory mechanism in tomato.