References
-
Shen, N. et al. Plant flavonoids: Classification, distribution, biosynthesis, and antioxidant activity. Food Chem. 383, 132531 (2022).
-
Li, P., Ruan, Z., Fei, Z., Yan, J. & Tang, G. Integrated transcriptome and metabolome analysis revealed that flavonoid biosynthesis may dominate the resistance of Zanthoxylum bungeanum against stem canker. J. Agric. Food Chem. 69, 6360–6378 (2021).
-
Deshmukh, A. B. et al. De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway. Phytochemistry 156, 201–213 (2018).
-
Ni, J. et al. Ethylene mediates the branching of the jasmonate-induced flavonoid biosynthesis pathway by suppressing anthocyanin biosynthesis in red Chinese pear fruits. Plant Biotechnol. J. 18, 1223–1240 (2020).
-
Liu, W. et al. The flavonoid biosynthesis network in plants. Int. J. Mol. Sci. 22, 1–18 (2021).
-
Wang, J., Zhang, C. & Li, Y. Genome-wide identification and expression profiles of 13 key structural gene families involved in the biosynthesis of rice flavonoid scaffolds. Genes https://doi.org/10.3390/genes13030410 (2022).
-
Liu, S. et al. Identification and characterization of thirteen gene families involved in flavonoid biosynthesis in Ginkgo biloba. Ind. Crops Prod. 188, 115576 (2022).
-
Kubra, G. et al. Expression characterization of flavonoid biosynthetic pathway genes and transcription factors in peanut under water deficit conditions. Front. Plant Sci. 12, 680368 (2021).
-
Yu, C. et al. Genomic and transcriptomic studies on flavonoid biosynthesis in Lagerstroemia indica. BMC Plant Biol. 24, 171 (2024).
-
Wang, Y. et al. Metabolomic and transcriptomic analysis of flavonoid biosynthesis in two main cultivars of Actinidia arguta Sieb.Zucc. grown in Northern China. Front. Plant Sci. 13, 1–15 (2022).
-
Yin, Q. et al. Genome-wide identification and functional characterization of UDP-glucosyltransferase genes involved in flavonoid biosynthesis in glycine max. Plant Cell Physiol. 58, 1558–1572 (2017).
-
Kuo, Y.-T., Chao, Y.-T., Chen, W.-C., Shih, M.-C. & Chang, S.-B. Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids. Ann. Bot. 123, 69–77 (2019).
-
Wu, X. et al. Chalcone synthase (CHS) family members analysis from eggplant (Solanum melongena L.) in the flavonoid biosynthetic pathway and expression patterns in response to heat stress. PLoS One 15, e0226537 (2020).
-
Emelianova, K., Martínez Martínez, A., Campos-Dominguez, L. & Kidner, C. Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family. Sci. Rep. 11, 17773 (2021).
-
Chao, N. et al. Functional characterization of two chalcone isomerase (CHI) revealing their responsibility for anthocyanins accumulation in mulberry. Plant Physiol. Biochem. 161, 65–73 (2021).
-
Schulz, E., Tohge, T., Zuther, E., Fernie, A. R. & Hincha, D. K. Natural variation in flavonol and anthocyanin metabolism during cold acclimation in A rabidopsis thaliana accessions. Plant Cell Environ. 38, 1658–1672 (2015).
-
Li, P. et al. The Arabidopsis UDP-glycosyltransferases UGT79B2 and UGT79B3, contribute to cold, salt and drought stress tolerance via modulating anthocyanin accumulation. Plant J. 89, 85–103 (2017).
-
Hasan, M. & Rima, R. Genetic engineering to improve essential and conditionally essential amino acids in maize : transporter engineering as a reference genetic engineering to improve essential and conditionally essential amino acids in maize : transporter engineering as a ref. Transgenic Res. 30, 207–220 (2022).
-
Zhu, L., Ding, Y., Wang, S., Wang, Z. & Dai, L. Genome-wide identification, characterization, and expression analysis of CHS gene family members in Chrysanthemum nankingense. Genes https://doi.org/10.3390/genes13112145 (2022).
-
Cheng, Y., Zhang, M., Cao, X., Mao, J. & Chen, B. Identification and expression analysis of CHS gene family in grape. Journal of fruit science 40 (2023).
-
Zhang, Y. et al. Identification of flavanone 3-hydroxylase gene family in strawberry and expression analysis of fruit at different coloring stages. Int. J. Mol. Sci. https://doi.org/10.3390/ijms242316807 (2023).
-
Han, Y. et al. Functional analysis of two flavanone-3-hydroxylase genes from camellia sinensis: a critical role in flavonoid accumulation. Genes 8, 300 (2017).
-
Falcone Ferreyra, M. L. et al. The identification of maize and Arabidopsis type I flavone synthases links flavones with hormones and biotic interactions. Plant Physiol. 169, 1090–1107 (2015).
-
Liu, S., Ju, J. & Xia, G. Identification of the flavonoid 3′-hydroxylase and flavonoid 3′,5′-hydroxylase genes from Antarctic moss and their regulation during abiotic stress. Gene 543, 145–152 (2014).
-
Yue, L. et al. Genome-wide identification and characterization of flavonol synthase (FLS) gene family in Brassica vegetables and their roles in response to biotic and abiotic stresses. Sci. Hortic. 331, 113168 (2024).
-
Qian, X. et al. Identification and expression analysis of DFR gene family in brassica napus L. Plants 12, 2583 (2023).
-
Han, Y., Ding, T., Su, B. & Jiang, H. Genome-wide identification, characterization and expression analysis of the chalcone synthase family in maize. Int. J. Mol. Sci. https://doi.org/10.3390/ijms17020161 (2016).
-
Isa, A., Garba, A. A., Sabo, M. U. & Fagam, A. S. Evaluation of morphological traits of barley (hordeum vulgare L.) varieties in different inter-row spacings and nitrogen rates under irrigation. Niger. J. Agric. Agric. Technol. 5, 166–175 (2025).
-
Ancuța, B. E., Muntean, L. & Russu, F. Barley (Hordeum vulgare L.): Medicinal and therapeutic uses – review. Hop Med. Plants 27, 87–95 (2019).
-
Blake, T., Blake, V. C., Bowman, J. G. P. & Abdel-Haleem, H. Barley feed uses and quality improvement. Barley: production, improvement, and uses 522, (2011).
-
Munns, R. & Tester, M. Mechanisms of salinity tolerance. Annu. Rev. Plant Biol. 59, 651–681 (2008).
-
Wiegmann, M. et al. Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues. Sci. Rep. 9, 6397 (2019).
-
Korn, M., Peterek, S., Mock, H., Heyer, A. G. & Hincha, D. K. Heterosis in the freezing tolerance, and sugar and flavonoid contents of crosses between Arabidopsis thaliana accessions of widely varying freezing tolerance. Plant Cell Environ. 31, 813–827 (2008).
-
Pennisi, E. The blue revolution, drop by drop, gene by gene. Science 320, 171–173 (2008).
-
Kowalczewski, P. Ł et al. Influence of abiotic stress factors on the antioxidant properties and polyphenols profile composition of green barley (Hordeum vulgare L.). Int. J. Mol. Sci. 21, 397 (2020).
-
Chen, C. et al. Tbtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 13, 1194–1202 (2020).
-
Rabby, M. et al. Comprehensive analysis of the oligopeptide transporter gene family in maize: Genome-wide identification, structural characterization, and stress- responsive expression. S. Afr. J. Bot. https://doi.org/10.1016/j.sajb.2024.10.004 (2024).
-
Mia, S. et al. In silico evolutionary origin , structural properties , molecular docking , following expression analysis of the nitrate transporters in maize to explore their roles in abiotic stress tolerance. Physiol. Mol. Biol. Plants https://doi.org/10.1007/s12298-025-01669-0 (2025).
-
Tamura, K., Stecher, G. & Kumar, S. MEGA11 : Molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 1–6 (2021).
-
Lin, Z. & Chen, F. Comprehensive genome-wide identification and expression profiling of eceriferum ( CER ) gene family in passion fruit ( Passiflora edulis ) under fusarium kyushuense and drought stress conditions. Front. Plant Sci. 13, 584 (2022).
-
Song, S. et al. Genome-wide identification and expression analyses of the aquaporin gene family in Passion fruit (Passiflora edulis), revealing PeTIP3-2 to be involved in drought stress. Int. J. Mol. Sci. 23, 1–23 (2022).
-
Islam, M. N., Rabby, M. G., Hossen, M. M., Bonny, M. & Hasan, M. M. Genome-wide identification following functional analysis of amino acid permease and cationic amino acid transporter gene families in maize and their role in drought stress. S. Afr. J. Bot. 168, 360–371 (2024).
-
Mia, S. et al. Molecular characterization following expression analysis of sugar transporters in passion fruit to explore their roles in fruit development and abiotic stress tolerance. 3 Biotech 1–28, (2026).
-
Huang, D. et al. Genome-wide association and expression analysis of the lipoxygenase gene family in Passiflora edulis revealing PeLOX4 might be involved in fruit ripeness and ester formation. Int. J. Mol. Sci. https://doi.org/10.3390/ijms232012496 (2022).
-
Kesawat, M. S. et al. Genome-wide identification and characterization of the brassinazole-resistant (BZR) gene family and its expression in the various developmental stage and stress conditions in wheat (triticum aestivum L). Int. J. Mol. Sci. 22, 8743 (2021).
-
Kumar, A. et al. Genome-wide identification and in silico analysis of NPF, NRT2, CLC and SLAC1/SLAH nitrate transporters in hexaploid wheat (Triticum aestivum). Sci. Rep. 12, 1–20 (2022).
-
Jeyasri, R. et al. The role of OsWRKY genes in rice when faced with single and multiple abiotic stresses. Agronomy https://doi.org/10.3390/agronomy11071301 (2021).
-
Ge, S. X., Jung, D., Jung, D. & Yao, R. ShinyGO: A graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628–2629 (2020).
-
Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. & Ishiguro-Watanabe, M. KEGG: biological systems database as a model of the real world. Nucleic Acids Res. 53, D672–D677 (2025).
-
Hasan, M., Mia, S. & Yang, J. Molecular mechanisms of how black barley accumulates higher anthocyanins than blue barley following transcriptomic evaluation and expression analysis of key genes in anthocyanins biosynthesis pathway. Front. Plant Sci. https://doi.org/10.3389/fpls.2025.1650803 (2025).
-
Islam, N., Rabby, G., Hossen, M. & Kamal, M. In silico functional and pathway analysis of risk genes and SNPs for type 2 diabetes in Asian population. PLoS One https://doi.org/10.1371/journal.pone.0268826 (2022).
-
Shadhin, M. S. T. et al. In silico functional, structural, and pathogenicity assessment of single nucleotide polymorphisms in the human SOX9 gene. Sci. Rep. https://doi.org/10.1038/s41598-025-30462-y (2025).
-
Ismail, N. A. & Jusoh, S. A. Molecular docking and molecular dynamics simulation studies to predict flavonoid binding on the surface of DENV2 E protein. Interdiscip. Sci. Comput. Life Sci. 9, 499–511 (2017).
-
Grasso, G. et al. Fragmented blind docking : a novel protein – ligand binding prediction protocol. J. Biomol. Structure and. Dyn. 40, 13472–13481 (2022).
-
Morris, G. M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009).
-
Eberhardt, J., Santos-Martins, D., Tillack, A. F. & Forli, S. AutoDock Vina 1.2. 0: new docking methods, expanded force field, and python bindings. J. Chem. Inf. Model. 61, 3891–3898 (2021).
-
Shaweta, S., Akhil, S. & Utsav, G. Molecular docking studies on the anti-fungal activity of Allium sativum (Garlic) against Mucormycosis (black fungus) by BIOVIA discovery studio visualizer 21.1.0.0. Ann. Antivirals Antiretrovir. 5, 028–032 (2021).
-
Ahammad, F. et al. Pharmacoinformatics and molecular dynamics simulation-based phytochemical screening of neem plant (Azadiractha indica) against human cancer by targeting MCM7 protein. Brief. Bioinform. 22, bbab098 (2021).
-
Mia, M. S. et al. Genome-wide exploration: Evolution, structural characterization, molecular docking, molecular dynamics simulation and expression analysis of sugar transporter (ST) gene family in potato (Solanum tuberosum). Comput. Biol. Chem. 117, 108402 (2025).
-
Mark, P. & Nilsson, L. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J. Phys. Chem. A 105, 9954–9960 (2001).
-
Roos, K. et al. OPLS3e: extending force field coverage for drug-like small molecules. J. Chem. Theor. Comput. 15, 1863–1874 (2019).
-
Kamal, M. M. et al. In silico functional, structural and pathogenicity analysis of missense single nucleotide polymorphisms in human MCM6 gene. Sci. Rep. 14, 1–18 (2024).
-
Song, Z. et al. Identification and characterization of yellow stripe-like genes in maize suggest their roles in the uptake and transport of zinc and iron. BMC Plant Biol. 24, 1–17 (2024).
-
Mazhar, H. S. U. D. et al. Genome-wide identification, and in-silico expression analysis of YABBY gene family in response to biotic and abiotic stresses in potato (Solanum tuberosum). Genes https://doi.org/10.3390/genes14040824 (2023).
-
He, A. et al. Genome-wide identification and expression analysis of the SPL gene family and its response to abiotic stress in barley (Hordeum vulgare L.). BMC Genom. 25, 846 (2024).
-
Schmittgen, T. D. & Livak, K. J. Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3, 1101–1108 (2008).
-
Zhu, J. et al. Functional analysis on the role of HvHKT1.4 in barley (Hordeum vulgare. L) salinity tolerance. Plant Physiol. Biochem. 215, 061 (2024).
-
Tohge, T., de Perez Souza, L. & Fernie, A. R. On the natural diversity of phenylacylated-flavonoid and their in planta function under conditions of stress. Phytochem. Rev. 17, 279–290 (2018).
-
Chatterjee, T. K. & Fisher, R. A. Cytoplasmic, nuclear, and Golgi localization of RGS proteins: Evidence for n-terminal and rgs domain sequences as intracellular targeting motifs*. J. Biol. Chem. 275, 24013–24021 (2000).
-
Rogozin, I. B., Carmel, L., Csuros, M. & Koonin, E. V. Origin and evolution of spliceosomal introns. Biol. Direct 7, 11 (2012).
-
Li, H., Liu, G. & Xia, X. Correlations between recombination rate and intron distributions along chromosomes of C. elegans. Prog. Nat. Sci. 19, 517–522 (2009).
-
Wong, A., Gehring, C. & Irving, H. R. Conserved functional motifs and homology modeling to predict hidden moonlighting functional sites. Front. Bioeng. Biotechnol. 3, 82 (2015).
-
Matassi, G., Sharp, P. M. & Gautier, C. Chromosomal location effects on gene sequence evolution in mammals. Curr. Biol. 9, 786–791 (1999).
-
Prieto, P. Chromosome manipulation for plant breeding purposes. Agronomy 10, 1965 (2020).
-
Walden, N. & Schranz, M. E. Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae. Genome Biol. Evol. 15, evad034 (2023).
-
Ridout, K. E., Dixon, C. J. & Filatov, D. A. Positive selection differs between protein secondary structure elements in drosophila. Genome Biol. Evol. 2, 166–179 (2010).
-
Ren, Z., Ren, P. X., Balusu, R. & Yang, X. Transmembrane helices tilt, bend, slide, torque, and unwind between functional states of rhodopsin. Sci. Rep. 6, 34129 (2016).
-
Attwood, M. M. & Schiöth, H. B. Characterization of five transmembrane proteins: With focus on the Tweety, Sideroflexin, and YIP1 domain families. Front. Cell Dev. Biol. 9, 708754 (2021).
-
Ibraheem, O., Botha, C. E. J. & Bradley, G. In silico analysis of cis-acting regulatory elements in 5′ regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. Comput. Biol. Chem. 34, 268–283 (2010).
-
Xiong, J. et al. Characterization of PtAOS1 promoter and three novel interacting proteins responding to drought in Poncirus trifoliata. Int. J. Mol. Sci. 21, 4705 (2020).
-
Lv, Y. et al. Identification of putative drought-responsive genes in rice using gene co-expression analysis. Bioinformation 15, 480 (2019).
-
Zhang, Y., Gao, P. & Yuan, J. S. Plant protein-protein interaction network and interactome. Curr. Genomics 11, 40–46 (2010).
-
Liu, H. et al. The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings. PeerJ 9, e11371 (2021).
-
Hao, S. et al. McWRI1, a transcription factor of the AP2/SHEN family, regulates the biosynthesis of the cuticular waxes on the apple fruit surface under low temperature. PLoS One 12, e0186996 (2017).
-
Theune, M. L., Bloss, U., Brand, L. H., Ladwig, F. & Wanke, D. Phylogenetic analyses and GAGA-motif binding studies of BBR/BPC proteins lend to clues in GAGA-motif recognition and a regulatory role in brassinosteroid signaling. Front. Plant Sci. 10, 466 (2019).
-
Challapa-Mamani, M. R. et al. Molecular docking and molecular dynamics simulations in related to leishmania donovani: an update and literature review. Trop. Med. Infect. Dis. 8, 1–13 (2023).
-
Bitencourt-Ferreira, G., Veit-Acosta, M. & de Azevedo, W. F. Hydrogen bonds in protein-ligand complexes. In Docking Screens for Drug Discovery 93–107 (2019).
-
Prabantu, V. M., Naveenkumar, N. & Srinivasan, N. Influence of disease-causing mutations on protein structural networks. Front. Mol. Biosci. 7, 1–11 (2021).
-
Alam, R. et al. GC-MS analysis of phytoconstituents from Ruellia prostrata and Senna tora and identification of potential anti-viral activity against SARS-CoV-2. RSC Adv. 11, 40120–40135 (2021).
-
Imon, R. R. et al. Natural defense against multi-drug resistant pseudomonas aeruginosa: cassia occidentalis L in vitro and in silico antibacterial activity. RSC Adv. 13, 28773–28784 (2023).
-
Hansson, T., Oostenbrink, C. & van Gunsteren, W. Molecular dynamics simulations. Curr. Opin. Struct. Biol. 12, 190–196 (2002).
-
Ouyang, L. et al. Genome-wide analysis of UDP-glycosyltransferase gene family and identification of a flavonoid 7-O-UGT (AhUGT75A) enhancing abiotic stress in peanut (Arachis hypogaea L.). BMC Plant Biol. 23, 626 (2023).
-
Ma, D., Sun, D., Wang, C., Li, Y. & Guo, T. Expression of flavonoid biosynthesis genes and accumulation of flavonoid in wheat leaves in response to drought stress. Plant Physiol. Biochem. 80, 60–66 (2014).
