Vegetos

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Research Articles | Published: 22 May, 2026

References

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Armenteros JJA, Sønderby CK, Sønderby SK, Nielsen H, Winther O (2017) DeepLoc: prediction of protein subcellular localization using deep learning. Bioinformatics 21:3387–4339


Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004) The Pfam protein families database. Nucleic Acids Res J 32(Database issue):D138–D141


Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R (2020) TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13:1194–1202


Dong M, Sun L, Wang W, Wang Y, Shan L, Liu X, Ren H (2025) B3 superfamily in cucumber (Cucumis sativus L.): identification, evolution, expression patterns, and function in glandular trichome development. Int J Mol Sci 26:4031


FAOSTAT [Internet], Canada Food and Agriculture Organization of the United Nations


Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM et al (2012) The genome of melon (Cucumis melo L). Proc Natl Acad Sci 109:11872–11877


Gasteiger E et al (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Springer protocols handbooks. Humana


Gao J, Ma G, Chen J, Gichovi B, Cao L, Liu Z et al (2023) The B3 gene family in medicago truncatula: genome-wide identification and the response to salt stress. Plant Physiol Biochem 206:108260


Guilfoyle TJ, Hagen G (2007) Auxin response factors. Curr Opin Plant Biol 10:453–460


Horton P, Park K, Obayashi T, Fujita N, Harada H, Adams-Collier CJ et al (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585–W587


Jeffares DC, Penkett CJ, Baehler J (2008) Rapidly regulated genes are intron poor. Trends Genet 24:375–378


Kagaya Y et al (1999) RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res 27:470–478


Kandeel M, Morsy M, Abd El-Lateef H, Marzok M, El-Beltagi H, Al Khodair K, Venugopala KN (2023) Genome-wide identification of B3 DNA-binding superfamily members (ABI, HIS, ARF, RVL, REM) and their involvement in stress responses and development in Camelina sativa. Agronomy 13:3: 648


Letunic I, Bork P (2018) 20 years of the SMART protein domain annotation resource. Nucleic Acids Res 46:D493–D496


Lin H, Zhu W, Silva JC, Gu X, Buell CR (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol 7:R41


Liu Z, Ge XX, Wu XM, Xu Q, Atkinson RG, Guo WW (2020) Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis. BMC Genom 21:305


Liu H, Wang X, Liu S, Huang Y, Guo YX, Xie WZ, Liu H, Tahir Ul Qamar M, Xu Q, Chen LL (2022) Citrus pan-genome to breeding database (CPBD): a comprehensive genome database for citrus breeding. Mol Plant 15:1503–1505


Luerssen H et al (1998) FUSCA3 encodes a protein with a conserved VP1/AB13-like B3 domain which is of functional importance for the regulation of seed maturation in Arabidopsis thaliana. Plant J 15:755–764


Marchler Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S et al (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:D200–D203


Matías-Hernández L, Aguilar-Jaramillo AE, Marín-González E, Suárez-López P, Pelaz S (2014) RAV genes: regulation of floral induction and beyond. Ann Bot 114:1459–1470


Mantegazza O, Gregis V, Mendes MA, Morandini P, Alves-Ferreira M, Patreze CM, Nardeli SM, Kater MM, Colombo L (2014) Analysis of the Arabidopsis REM gene family predicts functions during flower development. Ann Bot 114:1507–1515


Mohanta TK, Khan A, Hashem A et al (2019) The molecular mass and isoelectric point of plant proteomes. BMC Genom 20:631


Robert X, Gouet P (2014) Deciphering key features in protein structures with the new END script server. Nucleic Acids Res 42:W320–W324


Romanel E, Schrago C, Couñago R, Russo C, Alves-Ferreira M (2009) Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification. PLoS ONE 4(6):e5791


Ruan CC, Chen Z, Hu FC, Fan W, Wang XH, Guo LJ, Fan HY, Luo ZW, Zhang ZL (2021) Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L). BMC Genomics 22:561


Qu J, Wang B, Xu Z, Feng S, Tong Z, Chen T, Zhou L, Peng Z, Ding C (2023) Genome-Wide Analysis of the Molecular Functions of B3 Superfamily in Oil Biosynthesis in Olive (Olea europaea L). Biomed Res Int 14:20236051511


Sasnauskas G, Manakova E, Lapenas K, Kauneckaite K, Siksnys V (2018) DNA recognition by Arabidopsis transcription factors ABI3 and NGA1. FEBS. J 285:4041–4059


Shen CJ, Wang SK, Zhang SN, Xu YX, Qian Q, Qi YH et al (2013) OsARF16, a transcription factor, is required for auxin and phosphate starvation response in rice (Oryza sativa L). Plant Cell Environ 36:607–620


Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539


Sahu SS, Loaiza CD, Kaundal R (2019) Plant-mSubP: a computational framework for the prediction of single- and multi-target protein subcellular localization using integrated machine-learning approaches. AoB Plants 12:plz068


Singh V, Misra N, Gupta D, Vaish S, Singh N (2024a) Bioinformatics characterization of B3 DNA superfamily in bitter gourd (Momordica charantia) L. and its expression in different tissues development and biotic stresses. S Afr J Bot 172:488–500


Singh V, Gupta D, Singh N, Tiwari N, Sharma S (2024b) Genome-wide characterization of the DNA-binding B3 superfamily Lagenaria siceraria and profiling its expression in biotic stresses. Res J Bio 19(10):31–45


Stone SL et al (2008) Arabidopsis LEAFY COTYLEDON 2 induces maturation traits and auxin activity: implications for somatic embryogenesis. Proc Natl Acad Sci 105:3151–3156


Swaminathan K, Peterson K, Jack T (2008) The plant B3 superfamily. Trends Plant Sci 13:64755


Ulmasov T et al (1997) ARF1, a transcription factor that binds to auxin response elements. Science 276:1865–1868


Vaish S, Parveen R, Gupta D, Basantani MK (2022) Genome-wide identification and characterization of glutathione S-transferase gene family in Musa acuminata L. AAA group and gaining an insight to their role in banana fruit development. J Appl Genet 63:609–631


Wang WB, Ao T, Zhang YY, Wu D, Xu W, Han B, Liu AZ (2021) Genome-wide analysis of the B3 transcription factors reveals that RcABI3/VP1 subfamily plays important roles in seed development and oil storage in castor bean (Ricinus communis). Plant Divers 44:201–212


Wang WB, Ao T, Zhang Y, Wu D, Xu W, Han B et al (2022) Genome-wide analysis of the B3 transcription factors reveals that RcABI3/VP1 subfamily plays important roles in seed development and oil storage in castor bean (Ricinus communis). Plant Divers 44:201–212


Wang T, Long C, Chang M et al (2024a) Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening. Sci Rep 14:2226


Wang Y, Zhao B, Wang W, Zhou Z, Zhang X, Du J, Song J, Huang X, Ouyang K, Zhong T, Liao F (2024b) Comprehensive analysis of B3 family genes in pearl millet (Pennisetum glaucum) and the negative regulator role of PgRAV-04 in drought tolerance. Front Plant Sci 15:1400301


Xia F, Sun T, Yang S, Wang X, Chao J, Li X, Hu J, Cui M, Liu G, Wang D, Sun Y (2019) Insight into the B3 transcription factor superfamily and expression profiling of B3 genes in axillary buds after topping in tobacco (Nicotiana tabacum L). Genes (Basel) 10:164F


Hu W, de Meaux J, Rohde A (2015) Transcriptome-wide analysis of the winter-to-spring transition in Arabidopsis. Plant Biol 17(1):156–165 https://doi.org/10.1111/plb.12180


Kumar R, Tyagi AK, Sharma AK (2011) Genome-wide analysis of abundance and organization of microsatellites in grape (Vitis vinifera), papaya (Carica papaya) and poplar (Populus trichocarpa), and their use in genetic linkage mapping in grape. Trop Plant Biol 4(3–4):203–219 https://doi.org/10.1007/s12042-011-9077-6


Peng, C., Wang, S., Lei, J., & Jun, W. (2015). Transcriptome profiling of Capsicum annuum leaves in response to heat stress. Horticultural Plant Journal, 1(1), 15–22 https://doi.org/10.1016/j.hpj.2015.04.004


Qu J, Ye J, Geng G, et al (2006) Dissecting functions of KATANIN1 in maintaining cell-wall structural integrity and polarity in Arabidopsis. J Integr Plant Biol 48(11):1320–1329 https://doi.org/10.1111/j.1744-7909.2006.00366.x


Suzuki M, Ketterling MG, Li QB, McCarty DR (2007) Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling in maize. Plant Physiol 144(3):1316–1333 https://doi.org/10.1104/pp.107.101030


Swarbreck D, Wilks C, Lamesch P, et al (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36(Database issue):D1009–D1014 https://doi.org/10.1093/nar/gkm865


Tsukagoshi H, Morikami A, Nakamura K (2007) Reactive oxygen species are involved in an abscisic acid-signaling pathway in Arabidopsis root. Plant J 50(1):61–71 https://doi.org/10.1111/j.1365-313X.2007.03035.x

 

Author Information

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Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, India