In silico analysis of L- and G-type lectin receptor kinases in tomato: evolution, diversity, and abiotic responses

Abstract

Solanum lycopersicum (family: Solanaceae) is a crucial crop and model organism for many phenotypic traits, and its sequenced genome provides valuable insights into plant biology and crop improvement. This study investigated lectin receptor-like kinases (LecRLKs) in tomato, focusing on L-type and G-type families. Mining the tomato genome (ITAG2.4) revealed 161 putative lectin genes across seven families, with GNA-related genes being the most abundant. Gene duplication analysis indicated that tandem and segmental duplications were the primary mechanisms driving LecRLK gene family expansion, particularly for G-type LecRLKs. These duplicated genes showed evidence of both purifying and negative selection, suggesting functional conservation and sub-functionalization. L-type and G-type LecRLKs exhibited diverse domain rearrangement architectures and subcellular localizations, with G-type LecRLKs showing greater expansion and architectural diversity. Differential expression analysis during abiotic stress (drought, heat, and cold stress) revealed key responsive genes. During drought stress, 63.2% of L-type and 18.5% of G-type LecRLK genes were expressed, with L-type Solyc09g005000.1 and G-type Solyc03g078360.1 genes showing significant 2-fold upregulation. Heat stress (42 °C) induced the upregulation of L-type Solyc04g071000.1 and G-type Solyc03g078360.1 and Solyc04g008400.1 , particularly after 12–24 h of exposure. Promoter analysis revealed numerous stress-related cis-elements. Transcription factor predictions and miRNA targeting sites suggest complex regulatory mechanisms. This comprehensive in silico characterization of tomato LecRLKs, including their expansion patterns and evolutionary pressures, provides insights into their potential roles in abiotic stress responses and lays the groundwork for enhancing crop resilience through targeted breeding or genetic engineering approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-11014-6.