Table 1.
List of 16 GmNCEDs and their basic physiochemical characterizations.
Fig 1.
Phylogenetic relationship between GmNCED and RcNCED, PpNCED, VvNCED, AtNCED, and OsNCED.
GmNCED was classified into 6 groups (A, B, C, D, E, and F), each marked by different colors and shapes. The red color star labeled the GmNCED. Whereas, RcNCED was labeled as triangular green, PpNCED was labeled as the light carmine pink triangle, VvNCED was labeled dark blue triangular, AtNCED was labeled as black triangular, and OsNCED was labeled as the magenta color triangle.
Fig 2.
The gene structure of GmNCED genes.
The grouping and colors of the GmNCED gene family members are based on the phylogenetic relationship. For the color bar, red represents exons, deep blue lines represent upstream/downstream and 0, 1, 2 represents intron phase.
Fig 3.
Feature domains of GmNCED proteins.
The positions of the RPE65 conserved domain are demonstrated in sky blue color whereas the entire protein sequence of respective GmNCED is magenta colored.
Fig 4.
The distribution of conserved motifs in GmNCED proteins.
Each motif is illustrated by a specific-colored box aligned on the right side of the figure. Different colors indicate individual motifs identified within each protein domain.
Fig 5.
The estimation of divergence time and Ka/Ks ratio of GmNCED genes.
The ratio of nonsynonymous (Ka) and synonymous (Ks) is represented by Ka/Ks. The time of divergence (measured in million years ago, MYA) is also represented. The different color bar represents the data range.
Fig 6.
The collinearity analysis of the GmNCED gene family.
Green color rectangles represent chromosomes of GmNCED. The purple red-colored lines linked between chromosomes represent collinear relations between the chromosomes.
Fig 7.
The synteny analysis between GmNCED, AtNCED, OsNCED, VvNCED genes chromosome.
Red color rectangles represent the GmNCED chromosomes. Meanwhile, green rectangles represent AtNCED chromosomes. Furthermore, magenta color rectangles represent OsNCED chromosomes while blue color rectangles represent VvNCED chromosomes. The same color format is used to represent the syntenic relationship linkage between different species.
Fig 8.
The chromosomal mapping and duplications of GmNCED genes.
The number of distinct chromosomes is at the top of each chromosome bar. The chromosome scale is in millions of bases (Mb), indicating the length of each chromosome on the left. The chromosome is colored yellow, while sky blue lines indicate segmental duplications.
Fig 9.
Sub-cellular localization analysis of GmNCED genes.
A. The heatmap represents the sub-cellular localization analysis of GmNCED genes. The names of each GmNCED gene are shown on the left side of the heatmap, while the names of the respective cellular organelles are shown at the bottom of the heatmap. The intensity of color on the right side of the heatmap indicates the presence of protein signals corresponding to the genes. B. The percentage distribution of GmNCED gene signal across various cellular organelles is represented by a bar diagram. The percentages of protein signals appearing in different cellular organelles are shown on the left side of the diagram.
Fig 10.
The distribution of putative cis-acting regulatory elements on the 2.0 kb promoter region of GmNCED is represented by a heatmap.
The names of each GmNCED are shown on the left side of the heatmap. The number of putative cis-acting elements for each GmNCED gene is displayed on the right side of the heatmap and is represented by distinct colors. Functions associated with cis-acting elements 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 as red, yellow, green, and dark blue respectively.
Fig 11.
GmNCED gene’s function analysis through gene ontology.
Classification of the GmNCED genes function are shown in circos plot. The number of genes involved under a certain GO ID, expected value, and rich factor are shown in a distinctive color. The scaling of the -log10 p-value is shown in three distinctive colors (red, yellow, and green).
Fig 12.
A heatmap represents transcription factors (TFs) in GmNCED genes.
The color intensity of the heatmap indicates the presence of TFs corresponding to the proteins. The TFs are distributed into 7 TF families recognized by distinctive color. The 7 TFs family are ERF, MYB, bZIP, LBD, C2H2, GATA, and TALE which are colored red, light green, light red, orange, yellow, lime, light green, and dark green respectively.
Fig 13.
The regulatory network between TFs and GmNCED genes.
The GmNCED is shown in round red. Whereas, the TFs are shown in green colors and different shapes. The 7 TF families ERF, MYB, C2H2, GATA, bZIP, LBD, and TALE have represented the shapes as diamond, parallelogram, rectangular, octagonal, triangle, hexagonal, and V respectively.
Fig 14.
Prediction of potential micro-RNAs targeting GmNCED genes.
A. Network illustration of predicted miRNA targets GmNCED genes. The red rectangle represents GmNCED genes while microRNA is labeled as sky blue ellipse. B. The schematic diagram indicates the GmNCED genes targeted by miRNAs. The green round rectangular is shown as exons of the respective gene, the blue round rectangular represents UTR, the straight black line represents intron and the red color small round rectangular represents miRNA.
Table 2.
Information about abundant miRNA ID, functions, and their targeted GmNCED genes.
Fig 15.
Protein-protein interaction of GmNCED proteins based on known Arabidopsis proteins.
The proteins were displayed at network nodes with the proteins in nodes, and the line colors indicate different data sources.
Fig 16.
Transcriptomic profiling of GmNCED in dehydration, salt, and drought stress.
A. The name of the respective GmNCED genes are shown on the left side of the heatmap. The bottom of the heatmap contains the control, dehydration, and sodium salt treatment at different hours. B. The name of the respective GmNCED genes are shown on the left side of the heatmap. The bottom of the heatmap contains the control and drought stress treatment at different hours. The FPKM value are transformed into the log2 format and are shown in the color gradient from low to high expression (green to red color) on the right side of both the heatmaps.
Fig 17.
Transcriptomic profiling of GmNCED genes in seed developmental stages in the south and delta region.
The name of the respective GmNCED genes are shown on the left side of the figure. The bottom of the heatmap contains different stages of high yielding and heat tolerant seed; 6hr imbibed seed, germinated seed, and mature seed produced in south and delta region. The color gradient (white to red color), on the right side of the heatmap, shows low to high expression.