Tomato Sulfotransferase Genes Traced Across 61 Accessions Reveal Evolution and Functional Divergence

Sulfotransferases, enzymes that regulate sulfur metabolism and secondary metabolism in plants, have been mapped across the genomes of 61 tomato accessions in a new pan-genomic study published in BMC Plant Biology. Because single-reference analyses cannot fully capture population-level evolutionary patterns, the researchers identified sulfotransferase genes from pan-genomic data spanning the full tomato domestication gradient, then dissected their expansion and functional differentiation across phylogeny, structural variation, selection pressure, transcriptome and metabolome dimensions.

The analysis showed that the tomato sulfotransferase family falls into three subfamilies: TPST, NFST and SULT. Of these, the SULT subfamily underwent the most prominent expansion and accumulated abundant transposable element insertions, suggesting that mobile genetic elements contributed materially to the family’s diversification.

Three mechanisms collectively drove the expansion of the gene family: whole-genome duplication, tandem duplication and dispersed duplication. Gene clusters harboring extensive structural variation were dominated by tandem-duplicated genes, indicating that local duplication played a particularly important role in generating the structural diversity observed across tomato populations.

A key distinction emerged between core and dispensable genes. Dispensable genes—those absent from some accessions—harbored significantly higher transposable element abundance than core genes, linking gene presence-absence variation to transposable element activity within the family.

Selection analyses indicated that the entire sulfotransferase family evolved under purifying selection, consistent with the functional importance of these enzymes. However, dispensable genes and high-copy clusters experienced relaxed selective constraints, implying that recently expanded or variable members may be freer to diverge in function.

One cluster stood out for its evolutionary signal. The C2-1 cluster, enriched in wild tomatoes, carried positively selected sites that the authors suggest may facilitate stress adaptation in wild tomato populations, offering a candidate link between sequence change and ecological tolerance.

Functional divergence was also evident at the level of gene activity. The SULT subfamily exhibited the greatest transcriptional divergence among the subfamilies, and distinct presence-absence variation and copy-number variation clusters played differentiated roles in metabolic regulation, tying structural genomic differences to variation in tomato metabolism.

To make the results usable, the team constructed a dedicated web platform hosting all multi-omics data and analytical results, supporting data browsing, visualization and batch download. The authors conclude that duplication events, transposable element insertions, structural variation and differential selection jointly shaped the evolutionary landscape of the tomato sulfotransferase family, providing theoretical support for sulfur metabolism research and tomato germplasm improvement while the platform enables open data sharing and research reproducibility.

Subject of Research: Pan-genomic evolution and metabolic functional divergence of sulfotransferase genes in tomato

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

Article References: Han, S., Liu, M., Wang, J., Zou, J., Ding, Y., Liu, Y., Cui, L., Zhang, L., Wang, R., & Yuan, M. (2026). Pan-genomic characterization of tomato sulfotransferases: evolution, structural variation and metabolic functional divergence. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10237-x

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10237-x

Keywords: tomato, sulfotransferases, pan-genomics, gene duplication, transposable elements, structural variation, presence-absence variation, copy-number variation, purifying selection, sulfur metabolism, germplasm improvement, Pan-genomic