Supplementary data for: Quantitative partitioning of apoplastic and symplastic Cd uptake pathways and the contribution of non-selective cation channels in two Salix genotypes"
Description
Non-selective cation channels (NSCCs) play a key role in ion membrane transport in plants. Members of NSCCs, such as CNGC, GLR, and OSCA, have been extensively characterized in herbaceous models such as Arabidopsis and rice, however, systemic analysis of NSCCs**** related genes and their roles in mediating Cd uptake in woody species remain limited. This dataset comprises five supplementary tables supporting our investigation of non-selective cation channels (NSCCs) and their role in cadmium (Cd) accumulation in two willow genotypes (Salix Jiangsuensis ‘J-799’ and S. integra ‘Yizhibi’). We performed conserved domain prediction, functional annotation, and phylogenetic analysis of NSCCs-related genes identified from transcriptomic data of both genotypes. Table_S1 presents the conserved domain prediction of NSCCs family members (GLR, OSCA, and CNGC) using Pfam and SMART databases. Table_S2 provides detailed functional annotation information for each NSCCs gene, including gene identifiers, family classification, and predicted molecular functions. Table_S3 lists the primer sequences used for qRT-PCR validation of candidate NSCCs genes. Table_S4 contains the basic sequence information for Salix NSCCs homologs used in phylogenetic relationship analysis with orthologs from Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa. Table_S5 summarizes the amino acid sequence similarities between the two Salix genotypes and Arabidopsis orthologs. Comparative analysis of these tables reveals that NSCCs-related genes in willows are predominantly annotated to GLR, OSCA, and CNGC families, with evolutionary conservation across species. Notably, GLR2.8 and CNGC20 exhibit genotype-specific sequence features and expression patterns that correlate with differential Cd accumulation capacity between the two genotypes. This dataset provides a comprehensive resource for understanding the molecular evolution and functional divergence of NSCCs in woody plants, and offers candidate gene targets for breeding Cd-accumulating willow cultivars for phytoremediation applications.
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Protein sequences of NSCC-related genes identified from RNA-seq assemblies of two willow genotypes (Salix Jiangsuensis ‘J-799’ and S. integra ‘Yizhibi’) were subjected to conserved domain prediction using NCBI CD-Search and SMART (Table S1). Functional annotation was performed using BLAST against NCBI nr, GO, KEGG, COG, Swiss-Prot, and Pfam databases; differential expression was analyzed using DESeq2 (FDR < 0.05) under Cd, La, and combined Cd+La treatments (Table S2). qRT-PCR primers were designed using Primer3 and validated by SYBR Green-based qPCR with the 2⁻ΔΔCt method (Table S3). Physicochemical properties (molecular weight, pI, GRAVY) were calculated using ProtParam, transmembrane domains predicted via TMHMM, and subcellular localization predicted using WoLF PSORT or TargetP (Table S4). BLASTP searches against the Arabidopsis thaliana proteome (TAIR10) with reciprocal BLAST confirmation were performed to identify orthologous relationships (Table S5).
Institutions
- Research Institute of Subtropical ForestyZhejiang, Hangzhou
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Funders
- National Science Foundation of ChinaGrant ID: 32572015