Genome-Wide Identification and Characterization of LIM Gene Family in Grapevine (Vitis vinifera L.) and Their Expression Analysis at Early Bud Developmental Stages

The LIM gene (an acronym for Lin-11, Isl-1, and Mec-3 domain) is a transcription factor family widely distributed in plants. LIM proteins in plants regulate various biological processes, including cytoskeletal organization, secondary cell wall development, and cellular differentiation. They have been identified and characterized in many plant species. However, a comprehensive genome-wide study of the LIM gene family and their associated transcription factors in various important fruit species, such as grapevine (Vitis vinifera), has not been investigated. In this study, we conducted an extensive in silico genome-wide identification and characterization of LIM genes in grapevine using integrated bioinformatics tools. We analyzed the expression of identified LIM genes during early bud development in grapevines using RNA-seq samples. The analysis predicted six VvLIM genes in V. vinifera, corresponding to the LIM genes in the model plant Arabidopsis. Phylogenetic tree analysis revealed that the LIM genes in grapevine could be classified into four subfamilies: alpha LIM, beta LIM, delta LIM, and gamma LIM. A study of conserved motifs, domains, and gene structures (exon length and intron numbers) of VvLIM genes showed a higher similarity within the same gene family. Gene ontology analysis demonstrated that the predicted VvLIM genes are associated with various biological and molecular functions. Network analysis between transcription factors (TFs) and identified VvLIM genes revealed several important TF families, including MYB, NAC, ERF, bZIP, bHLH, C2H2, MIKC_MADS, and TCP. Furthermore, cis-acting regulatory elements related to light-responsive (LR), hormone-responsive (HR), stress-responsive (SR), and other (OT) functions were detected in the predicted VvLIM genes. In addition, we examined the expression changes of the six candidate VvLIM genes during early bud development in grapevines using RNA-seq samples. Differential expression patterns were observed for VvLIM genes involved in bud development, with specific timing coinciding with key developmental stages. Moreover, the expression of VvLIM genes associated with inflorescence primordia and endodormancy provided insights into the molecular mechanisms underlying bud development in grapevines, thus enhancing our understanding at the molecular level. This study will provide valuable information on grapevine LIM genes, laying a solid foundation for subsequent wet-lab characterization of the functional mechanisms of the identified VvLIM genes and their regulatory elements.