Objective Based on the whole-genome data of Lycium ruthenicum, this study aimed to systematically identify members of the LrMATE gene family, characterize their structural features, evolutionary relationships, and expression patterns during different fruit coloration stages, and screen candidate genes potentially involved in anthocyanin transport and accumulation. Methods Members of the LrMATE gene family were identified using hidden Markov model (HMM) searches and sequence alignment with known MATE proteins. Bioinformatics approaches were then used to analyze their physicochemical properties, chromosomal location, phylogenetic relationships, gene structures, cis-acting regulatory elements, and syntenic relationships. Combined with transcriptome data from different fruit developmental stages and changes in anthocyanin content, candidate genes related to anthocyanin accumulation were screened through correlation analysis between gene expression levels and anthocyanin content, as well as weighted gene co-expression network analysis (WGCNA). Results A total of 53 LrMATE genes were identified in the L. ruthenicum genome and were unevenly distributed across 12 chromosomes. Phylogenetic analysis classified these genes into five subfamilies, among which subfamily II contained the largest number of members, with 19 genes. Some members of this subfamily clustered closely with previously reported MATE proteins involved in the transport of plant secondary metabolites. Based on the expression patterns of LrMATE genes during different fruit developmental stages, changes in anthocyanin content, and co-expression analysis, LrMATE12, LrMATE15, LrMATE23, LrMATE26, LrMATE27, LrMATE37, and LrMATE38 were predicted to be involved in anthocyanin transport and accumulation during fruit coloration in L. ruthenicum. Conclusion This study systematically characterized the LrMATE gene family in L. ruthenicum and identified seven candidate genes potentially associated with anthocyanin transport and accumulation. These findings provide important candidate gene resources for further elucidating the molecular mechanisms through which LrMATE genes mediate anthocyanin accumulation in L. ruthenicum, and offer a theoretical basis for the development of anthocyanin-related medicinal active components, fruit quality improvement, and the breeding of high-anthocyanin germplasm resources.

Lycium ruthenicum Murr.  /  MATE gene family  /  genome-wide identification  /  anthocyanin accumulation  /  candidate genes