Multi-omics reveals divergent regulation of anthocyanin glycosylation and gibberellin biosynthesis underlying leaf variegation in Saxifraga stolonifera

Background Saxifraga stolonifera Curtis is a shade-tolerant, variegated-leaf herb with ornamental and medicinal value that naturally displays three stable leaf phenotypes: green, white-variegated, and purple-variegated. These phenotypes simultaneously exhibit both air space-type and pigment-type variegations. However, the key pathways and regulatory networks underlying their formation remain largely unknown. Results Here, we generated a 2.01 Gb high-quality chromosome-scale genome assembly (2n = 36). Comparative genomic analyses revealed a recent whole-genome duplication specific to S. stolonifera following the shared γ-triplication event, along with 155 expanded gene families enriched in flavonoid and phenylpropanoid biosynthesis pathways. Metabolomic profiling identified 58 anthocyanin-related compounds, among which 10 key pigments, including cyanidin-3-O-glucoside, peonidin-3-O-galactoside, and quercetin-3-O-glucoside, were responsible for the purple patches. Their accumulation corresponded with the upregulation of the anthocyanidin 3-O-glucosyltransferase gene SsBZ1 (Sst12G009310, Sst14G006050). Hormone and transcriptome analyses showed that white-variegated leaves accumulate high levels of bioactive gibberellins GA4 and GA7, driven by increased expression of gibberellin 3β-dioxygenase SsGA3ox (Sst05G017510). Weighted gene co-expression network analysis (WGCNA) further identified a GA-associated module (salmon) with SsGA3ox as the hub gene, promoting cell expansion and generating air spaces between epidermal and palisade tissues along the veins. Conclusion Collectively, our high-quality genome, metabolome, and transcriptome resources suggest that SsGA3ox-mediated gibberellin biosynthesis is potentially associated with air space-type leaf variegation, whereas the accumulation of specific anthocyanin glycosides in sub-palisade cells, mediated by SsBZ1, is associated with pigment-type variegation. These findings provide an integrative omics framework for dissecting leaf variegation mechanisms in Saxifraga and other ornamental plants. However, functional validation of the identified candidate genes is required to confirm their precise roles. We propose a model where GA-driven upstream flavonoid flux is activated in both variegated phenotypes, but the final visible pigmentation is determined by SsBZ1-mediated glycosylation specificity and spatial localization, suggesting a possible hierarchical separation between structural and pigmentation pathways during variegation formation.