Table 1.
List of 26 StFH proteins and their basic physio-chemical characterization.
Fig 1.
Phylogenetic relationship between StFH, AtFH, ZmFH, MtFH, LjFH, and OsFH.
StFHs were classified into seven groups (A, B, C, D, E, F, and G). Different colors and shapes mark each gene family, with StFH labeled with red stars, AtFH with rectangular blue rectangles, ZmFH with dark yellow triangles, MtFH with green ellipses, OsFH with red-violet circles, and LjFH with purple rectangles.
Fig 2.
The grouping and colors of the StFH members were based on the phylogenetic tree. Black lines represent introns, deep blue represents exons, numbers 0, 1, and 2 represent intron phases, and deep yellow lines represent upstream/downstream.
Fig 3.
Positions of the FH2 conserved domain and other domains are demonstrated in light blue color, whereas the entire protein sequence of the respective StFH is shown in purple.
Fig 4.
The distribution of conserved motifs in StFH.
Each motif was illustrated by a color box aligned on the right side of the figure. Different colors indicate individual motifs within each StFH protein.
Fig 5.
Estimation of gene duplication time and Ka/Ks analysis of StFH.
The ratio of Ka to Ks is represented by Ka/Ks, with divergence time (measured in million years ago, MYA) also indicated. The color bar represents the data range.
Fig 6.
The collinearity analysis of the StFH gene family.
Different color rectangles represent chromosomes 1 to 12 in StFH. The dark blue lines linking chromosomes represent collinear relationships between them.
Fig 7.
The synteny analysis of S. tuberosum with A. thaliana, O. sativa, and Z. mays.
The green, red, blue, and magenta-colored chromosome rectangles represent S. tuberosum, A. thaliana, O. sativa, and Z. mays. The dark blue color indicates a syntenic relationship between the species.
Fig 8.
The chromosomal locations and duplications of StFH.
The chromosome-scale is in millions of bases (Mb), showing the length of each chromosome on the left. The chromosomes are colored yellow. The blue lines indicate segmental duplications and the red stars represent tandem duplications.
Fig 9.
The distribution of StFH genes on multiple sub-genomes of S. tuberosum.
The Otava, Phureja DM 1–3516 R44, and Tuberosum RH89-039-16 chromosomes are purple, green, and red, respectively. The chromosome-scale is in millions of bases (Mb).
Fig 10.
Sub-cellular localization analysis of StFH.
(A) The heat map represents the sub-cellular localization analysis of StFH proteins. The names of each StFH protein are shown on the left side of the heat map, while the names of the respective cellular organelles are shown at the bottom. The intensity of the color indicates the presence of protein signals corresponding to the genes. The cellular organelles include nuclear, mitochondrial, cytoplasmic, chloroplast, cytoskeletal, peroxisomal, Golgi, vacuole, endoplasmic reticulum (ER), plasma membrane (PM), and extracellular locations. (B) The percentage distribution of StFH protein signals across various cellular organelles is represented by a bar diagram. The percentages of protein signals in different cellular organelles are shown on the left side of the diagram.
Fig 11.
A heatmap represents the distribution of putative CAREs on the 2.0 kb promoter region of StFH.
The names of the CAREs of each StFH gene are shown on the left side of the heat map. The number of putative CAREs for each StFH gene is displayed on the right side of the heat map and represented by different colors (black = 0, green = 1–5, yellow = 6–10). Functions associated with CAREs of the corresponding genes, such as light responsiveness, tissue-specific expression, phytohormone responsiveness, and stress responsiveness, are shown at the bottom of the heatmap and labeled green, red, blue, and magenta, respectively.
Fig 12.
StFH gene function analysis through gene ontology.
The classification of the StFH gene function is shown on the right side of the circos plot. The number of genes involved under a specific GO ID, expected value, and rich factor are shown in distinctive colors. The scaling of the -log10 p-value is shown in three distinctive colors (red, yellow, and green).
Fig 13.
A heatmap illustrates the TFs regulating StFH.
The StFH proteins are on the left, and TF names are at the bottom of the heat map. The color intensity on the right side of the heat map indicates the presence of TFs corresponding to the proteins. Distinctive colors represent the seven TF families: ERF (red), bZIP (orange), LBD (blueberry), NAC (magenta), C2H2 (light green), GATA (sky blue), and HSF (dark green).
Fig 14.
The regulatory network between TF and StFH.
Different colors and shapes represent TFs and their interactions with StFH genes. The StFH genes are shown in magenta rectangles, and the TF families are represented by various shapes and colors: ERF (purple diamond), NAC (dark yellow hexagon), GATA (light yellow round rectangle), LBD (lime green hexagon), bZIP (bright aqua ellipse), C2H2 (red parallelogram), and HSF (pastel orange triangle).
Fig 15.
Prediction of potential miRNAs targeting StFH.
(A) The network illustration of predicted miRNA targets shows StFH genes in blue-green and miRNAs in light pink ellipses. (B) The schematic diagram indicates the StFH genes targeted by miRNAs, with exons (purple), UTR (light green), introns (black lines), and miRNAs (red rectangles).
Fig 16.
Protein-protein interaction of StFH based on known Arabidopsis proteins.
The network nodes represent proteins, and the line colors indicate different data sources.
Fig 17.
Tissue-specific expression pattern of StFH.
The respective StFH gene names are shown on the right side of the heat map. Various tissues are represented at the bottom of the heat map. The color gradient from green to red indicates the expression levels on the right side of the heat map.
Fig 18.
Expression pattern of StFH under drought stress.
The respective StFH gene names are shown on the right side of the heatmap. The stages of the plant in two varieties (Atlantic and Qingshu No. 9) are represented at the bottom of the heat map. The color gradient from white to red indicates the expression levels on the right side of the heat map.
Table 2.
Information about abundant miRNA ID, functions, and their targeted StFH genes.