Pan-genomic characterization of tomato sulfotransferases: evolution, structural variation and metabolic functional divergence

Sulfotransferases (SOTs) regulate plant sulfur metabolism and secondary metabolism, yet single-reference-based analysis cannot fully reveal the population evolutionary characteristics of the tomato SOT family. In this study, SOT genes were identified from pan-genomic data of 61 tomato accessions spanning the full domestication gradient, and their expansion mechanisms and functional differentiation were systematically dissected across phylogeny, structural variation, selection pressure, transcriptome and metabolome dimensions. The tomato SOT family fell into three subfamilies, TPST, NFST and SULT. The SULT subfamily underwent the most prominent expansion and accumulated abundant TE insertions. Whole-genome duplication, tandem duplication and dispersed duplication collectively drove family expansion, with gene clusters harboring extensive structural variation being dominated by tandem-duplicated genes. Dispensable genes harbored significantly higher TE abundance than core genes. The entire family evolved under purifying selection, while dispensable genes and high-copy clusters experienced relaxed selective constraints. The wild-enriched C2-1 cluster carried positively selected sites that may facilitate stress adaptation in wild tomatoes. The SULT subfamily exhibited the greatest transcriptional divergence, and distinct PAV and CNV clusters played differentiated roles in metabolic regulation. Finally, a dedicated web platform was constructed to host all multi-omics data and analytical results, supporting data browsing, visualization and batch download. Collectively, duplication events, TE insertions, structural variation and differential selection jointly shaped the evolutionary landscape of the tomato SOT family, providing theoretical support for sulfur metabolism research and tomato germplasm improvement. The accompanying web platform further enables open data sharing and research reproducibility.