Genome Wide Identification and Characterization of LIM Domain Associated Gene Superfamily in Common Bean (Phaseolus...

LIM genes are essential for cytoskeletal organization and cellular stress responses in plants. This study conducted a comprehensive genome-wide investigation of LIM domain-associated genes in Phaseolus vulgaris. This study expands LIM gene classification beyond traditional domains to include LIM_bind factors, revealing that P. vulgaris has a more complex and functionally diverse regulatory toolkit than previously understood. Seventeen identified PvLIM genes are distributed across three families: LIM-LIM domain, LIM-DA1_like domain, and LIM_bind domain-containing. Following gene duplication, P. vulgaris LIM genes underwent subfunctionalization where ancestral functions were partitioned among copies, creating specialized tissue-specific and stress-responsive roles while maintaining complementary regulatory networks. PvLIM proteins form critical networks controlling cell wall metabolism, signaling pathways, actin cytoskeleton dynamics, and endocytosis. All PvLIM genes exhibit universal responsiveness to multiple stress stimuli including abscisic acid, ethylene, methyl jasmonate, wound, heat, and anaerobic stress conditions, confirming their central role in plant stress tolerance mechanisms. Gene expression analysis revealed tissue-specific functional specialization, with LIM-LIM and LIM_bind domain genes predominantly active in stem and leaf tissues, while PvLIM14 governs stem, pod, and leaf development and PvLIM16 modulates seed-related processes. PvLIM genes constitute essential molecular machinery governing plant growth, development, and stress adaptation through integrated phytohormone-mediated regulatory networks.