Genome-Wide Identification and Analysis of Lycopene Gene Family in Tomato (Solanum lycopersicum L.)

Abstract

Tomato (Solanum lycopersicum L.) is an important vegetable crop and a major dietary source of lycopene, a naturally occurring carotenoid responsible for the characteristic red colour of ripe tomato fruits and recognized for its potent antioxidant properties. Despite the nutritional and biological importance of lycopene, there is limited information on the genomic organization and evolutionary characteristics of the lycopene-related gene family in tomato. In this study, an in-silico genome-wide analysis was conducted to identify and characterize the SlLYC gene family in S. lycopersicum. Lycopene-related genes were identified through genome-wide sequence analysis using Arabidopsis thaliana LYC gene sequences as queries, followed by verification of the identified proteins using InterPro. Chromosomal distribution, gene structure, subcellular localization, phylogenetic relationships, and conserved protein motifs were subsequently analyzed using appropriate bioinformatics tools. A total of four non-redundant SlLYC genes were identified and mapped to chromosomes 4, 6, 10, and 12 of the tomato genome. Subcellular localization analysis predicted that three SlLYC proteins were localized in the chloroplast, while one was predicted to be localized in the nucleus. Gene structure analysis revealed variation in exon-intron organization, with two of the identified genes being intronless. Phylogenetic analysis grouped the identified SlLYC proteins into three major groups in relation to LYC proteins from Arabidopsis thaliana. In addition, three conserved motifs were identified across the SlLYC protein sequences, indicating functional conservation within the gene family. These findings provide useful information on the genomic organization, evolutionary relationships, and structural characteristics of the SlLYC gene family and may support future molecular studies, genetic improvement, and breeding strategies aimed at enhancing lycopene content and nutritional quality in tomato.