Genome-wide analysis of the RING-H2 E3 ubiquitin ligase SlATL family in tomato

The Arabidopsis Toxicos en Levadura (ATL) family is a widely distributed and evolutionarily conserved group of RING-type ubiquitin ligase in plants, with crucial roles in plant growth, development, and stress response. Although ATL gene families have been identified in numerous plants, a genome-wide identification and comprehensive analysis of their characteristics and functions are still needed in tomato (Solanum lycopersicum), a key model for studying fruit development, ripening, and stress responses. By employing a bioinformatics approach, here, we identified 86 candidate members of the SlATL gene family, constructed their phylogenetic tree, and classified these into seven subfamilies based on gene structure similarity and conserved motifs. Chromosome locations and collinearity analysis further demonstrated the structural correlations and evolutionary conservation of the SlATL family. Cis-acting elements analysis indicated that the SlATL family may be closely associated with functions such as hormone responses, environmental stress, and plant growth and development. Gene ontology (GO) functional annotation of the SlATL family, along with some individual members and their interacting proteins, revealed insights into their biological roles. The findings lay a foundation for further exploration of the SlATL family in tomato growth and stress resilience.