Supplementary file 1_Integrated genomic, transcriptomic, and proteomic analyses prioritize cadmium-responsive class III peroxidases in Salix variegata.docx

We identified 80 high-confidence class III PRX genes in Salix variegata and characterized their genomic organization, evolutionary relationships, protein properties, and predicted regulatory features. Root RNA-seq and data-independent acquisition proteomic datasets from plants exposed to 0 or 100 μM CdCl₂ for 10 d were then integrated to prioritize members supported across molecular layers.

Segmental and dispersed duplication were the predominant expansion modes, and most SvaPRX proteins showed sequence features compatible with extracellular localization. RNA-seq identified 42 upregulated and two downregulated SvaPRX genes. The DIA dataset comprised 22,883 peptides and 6,068 proteins, with 4,849 proteins quantified in all six samples; biological replicates showed high within-treatment correlations and separation of CK and Cd100 in principal component analysis.