Fig 1.
Conceptual and working flowchart for identifying HanMATE genes and their predicted roles in AST in sunflower.
The flowchart section (A) outlines the consequences of abiotic stresses on plants. The healthy and stressed plants of this section were obtained from Rani et al. 2021 [67]. Section (B) of the flowchart describes the identification techniques of HanMATE genes. In section (C), the identified HanMATE genes’ AST properties were characterized. In the final section (D), the future stress-tolerant sunflower was depicted; the image was obtained from https://www.dreamstime.com/illustration/sunflower-plant-growth-stages.html.
Fig 2.
The phylogenetic relationship of the HanMATE and AtMATE proteins in sunflower and Arabidopsis, respectively.
The colors in the figure represent different subgroups of HanMATE along with AtMATE proteins. Accordingly, we found four subgroups (I–IV) of 74 HanMATE and 46 AtMATE proteins in the figure.
Fig 3.
Domain and motif analysis of the HanMATE proteins.
The horizontal line at the bottom of each figure represents the protein’s length (0-600 aa).
Table 1.
Basic physicochemical properties of HanMATE genes.
Fig 4.
HanMATE gene structure analysis.
The horizontal line at the bottom of the figure represents the gene’s length (0-55000 bp).
Fig 5.
Mapping HanMATE genes over 17 sunflower diploid chromosomes and a contig.
In the figure, plot A displays the chromosome number on the left side and the HanMATE name on the right side for each of the chromosomes. Plot B showed HanMATE gene duplication occurrences within the genome. Duplicated gene pairs in sunflower relate to lines, and inside the chromosome numbers are stated.
Table 2.
Predicted HanMATE proteins in the subcellular organelle.
Fig 6.
Predicted likelihood of the HanMATE proteins in the subcellular localization.
Fig 7.
HanMATE gene GO enrichment analysis.
Plot A in the figure illustrates the enrichment of HanMATE genes with molecular functions, while plot B shows the enrichment of HanMATE genes with biological processes. Each of the rectangles in the plot shows the GO ID with p-value, the GO term, and the number of HanMATE genes that were enriched for that GO term.
Fig 8.
The predicted CREs in the upstream promoter regions of the HanMATE genes.
In the figure ABRE = Abscisic Acid-Responsive Element, AIE = Anaerobic Induction Element, LRE = Light Responsive Element, MeJARE = MeJA Responsive Element, ARE = Auxin Responsive Element, DIE = Drought Inducibility, GRE = Gibberellin Responsive Element, LTRE = Low Temperature Responsive Element, MEE = Meristem Expression Element, MYBHv1_BS = MYBHv1 binding site, SARE = Salicylic Acid Responsive Element, ZME = Zein Metabolism Element, X60K_PBS = 60K protein binding site, AnIE = Anoxic Inducibility Element, ATBP.1_BS = ATBP-1 Binding Site, CCRE = Cell Cycle Regulation Element, CCE = Circadian Control Element, CRE = Cis Regulatory Element, CMA3 Element = CMA3 Element, EEE = Endosperm Expression Element, FBRE = Flavonoid Biosynthesis Regulation Element, HTLE = High Transcription Level, SSRE = Seed Specific Regulation Element, and SDRE = Stress and Defense Responsive.
Fig 9.
The predicted CREs in the upstream promoter regions of the ASR MATE genes of potato, rice, wheat, maize, soybean, dragon fruit, cotton, and Arabidopsis.
Table 3.
HanMATE proteins are associated (more than 75% sequence similarity) with various ASR MATE proteins in other plants.
Fig 10.
Syntenic relationship analysis of the HanMATE proteins with ASR MATE proteins in other plants.
Fig 11.
Regulatory network analysis between miRNAs and HanMATE proteins.
In the figure, the purple- and green-colored nodes represent the HanMATE proteins and the miRNAs, respectively. The highlighted HanMATE proteins and the miRNAs with interaction scores beside the respective HanMATE proteins and the miRNAs in parentheses are the hub proteins and miRNAs.
Table 4.
Docking/binding affinity scores (kcal/mol) between the HanMATE proteins (receptors) and flavonoids.
Fig 12.
Molecular Dynamics Simulation of HanMATE protein and flavonoid complexes.
(A) Root-mean-square deviation (RMSD) of flavonoid movement. (B) Binding free energy (kJ/mol).