Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Gene Family and Their Expression Analysis in Response to Anthocyanin Transportation in the Fruit Peel of Eggplant (Solanum melongena L.)

The ATP-binding cassette (ABC) gene family represents one of the most extensive and evolutionarily conserved groups of proteins, characterized by ATP-dependent transporters that mediate the movement of substrates across cellular membranes. Despite their well-documented functions in various biological processes, the specific contributions of ABC transporters in eggplant (Solanum melongena L.) remain unexplored. To address this gap, we conducted a comprehensive genome-wide identification and expression profiling of ABC transporter-encoding genes in eggplant. Our investigation identified 159 SmABC genes encoding ABC transporter that were irregularly dispersed across all 12 chromosomes. The encoded proteins exhibited considerable diversity in size, with amino acid lengths varying from 55 to 2628 residues, molecular weights ranging between 4.04 and 286.42 kDa, and isoelectric points spanning from 4.89 to 11.62. Phylogenetic analysis classified the SmABC transporters into eight distinct subfamilies, with the ABCG subfamily being the most predominant. Subcellular localization predictions revealed that most SmABC proteins were localized to the plasma membrane. Members within the same subfamily exhibited conserved motif arrangements and exon–intron structures, suggesting functional and evolutionary conservation. Promoter analysis identified both shared and unique cis-regulatory elements associated with transcriptional regulation. We identified 9 tandem duplication gene pairs and 20 segmental duplication pairs in the SmABC gene family, with segmental duplication being the major mode of expansion. Non-synonymous to synonymous substitutions (Ka/Ks) analysis revealed that paralogs of SmABC family genes underwent mainly purifying selection during the evolutionary process. Comparative genomic analysis demonstrated collinearity between eggplant, Arabidopsis thaliana, and tomato (Solanum lycopersicum), confirming homology among SmABC, AtABC, and SlABC genes. Tissue-specific expression profiling revealed differential SmABC expression patterns, with three distinct genes, SmABCA16, SmABCA17 and SmABCG15, showing preferential expression in purple-peeled fruits (A1, A3, and A5 accessions), implicating their potential involvement in anthocyanin transport. Functional validation via SmABCA16 silencing led to a significant downregulation of SmABCA16 and reduced purple coloration, indicating its regulatory role in anthocyanin transport in eggplant fruit peel. This comprehensive genomic and functional characterization of ABC transporters in eggplant establishes a critical foundation for understanding their biological roles and supports targeted breeding strategies to enhance fruit quality traits.