Genome-Wide Identification and Expression Analysis of TONNEAU1 Recruited Motif (TRM) Gene Family in Tomato

The TONNEAU1 Recruited Motif (TRM) gene family is integral to the growth and development of various plants, playing a particularly critical role in regulating the shape of plant organs. While the functions of the TRM gene family in other plant species have been documented, knowledge regarding the members of the tomato (<i>Solanum lycopersicum</i>). SlTRM gene family remains limited, and their specific roles are not yet well understood. In this study, we identified and analyzed 28 members of the SlTRM gene family in tomato using bioinformatics approaches based on the latest whole genome data. Our analysis included the examination of protein structures, physicochemical properties, collinearity analysis, gene structures, conserved motifs, and promoter cis-acting elements of the SlTRM gene family members. The phylogenetic analysis indicated that both tomato and <i>Arabidopsis thaliana</i> are categorized into five distinct subfamilies. Furthermore, we conducted a three-dimensional structure prediction of 28 SlTRM genes for the first time, utilizing AlphaFold3, a deep learning architecture developed by DeepMind. Subsequently, we analyzed public transcriptome data to assess the tissue specificity of these 28 genes. Additionally, we examined the expression of SlTRM genes using RNA-seq and qRT-PCR techniques. Our analysis revealed that <i>SlTRM25</i> was significantly differentially expressed, leading us to hypothesize that it may be involved in the development of lateral branches in tomatoes. Finally, we predicted the regulatory interaction network of <i>SlTRM25</i> and identified that it interacts with genes such as <i>SlFAF3/4b</i>, <i>SlCSR-like1</i>, <i>SlCSR-like2</i>, and <i>SlTRM19</i>. This study serves as a reference for the investigation of the tomato TRM gene family members and introduces a novel perspective on the role of this gene family in the formation of lateral branches in tomatoes, offering both theoretical and practical significance.