Fig 1.
A graphical abstract of our study.
Table 1.
Basic information of Solanum tuberosum DCL, AGO and RDR gene families.
Fig 2.
(A–C): Phylogenetic tree for (A) DCL proteins (B) AGO proteins and (C) RDR proteins from Solanum tuberosum and Arabidopsis.
In phylogenetic tree, different groups are represented by different colors; red circles are mentioned genes of Solanum tuberosum and green circles are mentioned genes of A. thaliana.
Fig 3.
Comparative Multiple Sequence Alignment in StDCL, StAGO, StRDR Gene families.
(A) Multiple sequence alignment of RNase III domains (RIBOc I and II) from S. tuberosum and Arabidopsis DCL proteins. Red downward arrows indicate conserved EDDE (glutamate-aspartate-glutamate-aspartate) positions critical for RNase III activity, (B) Alignment of PIWI domains from S. tuberosum and Arabidopsis AGO proteins showing conserved catalytic residues. Red arrows highlight the DDH triad (H798 position indicated) essential for slicer activity, (C) RdRP domain alignment of S. tuberosum and Arabidopsis RDR proteins. The red box encloses the conserved DxDGD catalytic motif required for RDR activity.
Table 2.
Comparison of the AGO proteins in PIWI domains between Solanum tuberosum and A. thaliana.
Fig 4.
The conserved domains of the predicted DCL, AGO, and RDR proteins in Potato and Arabidopsis.
Fig 5.
The conserved motifs of the predicted DCL, AGO and RDR protein families in Potato and Arabidopsis.
Each color represents different motifs in the predicted proteins domains.
Fig 6.
Gene formation of the predicted DCL, AGO, and RDR proteins in S. tuberosum with Arabidopsis.
Fig 7.
The genomic location of the predicted StDCL, StAGO,and StRDR genes.
The scale to indicate the chromosomal length is provided on the left.
Fig 8.
Sub-cellular localization analysis for the (A) StDCL, StAGO, and StRDR proteins.
(B) The percentage of protein appeared in different cellular organelles.
Fig 9.
Estimation of gene duplications, evoluation, duplication time and Ka/Ks analysis of StAGO, StRDR, and StDCL.
The ratio of Ka to Ks is represented by Ka/Ks, with divergence time (measured in MYA) also indicated. The color bar represents the data range. Visualization of Tandem duplications (dark blue) and segmental duplications (magenta) are mapped alongside purifying (orange) and diversifying (cyan) selection pressures.
Fig 10.
Syntenic relationships between Solanum tuberosum and Arabidopsis thaliana for RNAi genes.
Fig 11.
PPI network of RNAi-related genes in potato, where red color, blue color and green color indicate StDCL, StRDR and StAGO respectively.
Fig 12.
StAGO, StDCL, and StRDR gene functions were analyzed by GO and visualized on the right of the circos plot, where gene counts per GO term, expected values, and rich factors are color-coded, and −log₁₀(p-value) is shown with three distinct colors.
Fig 13.
Collinearity relationships among StAGO, StRDR, and StDCL gene families.
Fig 14.
A heatmap represents the distribution of putative CAREs on the 2.0 kb promoter region of StDCLs, StAGOs and StRDRs.
The names of the StDCLs, StAGOs and StRDRs genes are shown on the right side of the heat map. Functions associated with CAREs of the corresponding genes, such as light responsiveness (green), phytohormone responsiveness (red), stress responsiveness (blue), and tissue-specific expression (magenta) are indicated at the bottom.
Fig 15.
The regulatory network among the TFs and the predicted RNAi genes.
The StDCL, StAGO, and StRDR genes were represented by red, green, and pink node color, respectively, and the TFs were represented by yellow node color with different shape for different families of TFs.
Fig 16.
Balloon plot represents the related number of TFs with the predicted StRNAi genes with StDCL, StAGO, and StRDR proteins on the left and TF names at the bottom.
Color intensity and size indicates number of TF presence for each proteins.
Fig 17.
A heatmap depicts TF families regulating potato RNAi-related genes, with StDCL, StAGO, and StRDR proteins on the left and TF names at the bottom.
Color intensity indicates TF presence for each protein.
Fig 18.
miRNAs interaction network of RNAi-related genes in potato, where purple color, red color, blue color and green color indicate miRNAs, StDCL, StRDR and StAGO respectively.
Table 3.
Information of highly connected potential miRNAs targeting StDCL, StAGO, and StRDR genes in Solanum tuberosum.
Fig 19.
Comprehensive gene expression pattern of StDCL, StRDR and StAGO across tissues, developmental stages, and stress conditions are represented at the bottom of the heat map.
The respective StDCL, StRDR and StAGO gene names are shown on the right side of the heat map. The color gradient from white-green-red indicates the expression levels on the right side of the heat map.