ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
This article is part of the Research TopicEvolutionary Adaptations of Plant Genes: A Comprehensive Study of Phylogenomics, Epigenetic Changes, and Protein DynamicsView all 16 articles
Genomic Analyses of 238 Seed Plants Reveal the Evolutionary Mechanisms Driving Specialization of F3H, ANS, and FLS in Flavonoid Biosynthesis
Provisionally accepted
- 1Yunnan Agricultural University State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, China
- 2Yunnan Agricultural University, Kunming, China
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The innovation in flavonoid metabolism is vital for the adaptation of seed plants to terrestrial habitats. This study conducted a comprehensive evolutionary analysis of three key 2-oxoglutarate-dependent dioxygenase (2ODD) families, flavanone 3-hydroxylase (F3H), anthocyanidin synthase (ANS), and flavonol synthase (FLS), across 238 seed plant genomes. Phylogenetic and collinearity analyses indicate that these families descend from a single ancestral gene (ancestor X) and subsequently diversified through repeated gene-duplication events. The evolutionary trajectory of F3H, ANS, and FLS is consistent with the Escape from Adaptive Conflict (EAC) model, wherein gene duplication facilitated the resolution of ancestral multifunctionality through subfunctionalization. Conserved motif analysis demonstrated that the three families exhibit significant structural conservation, and variations in lineage-specific motifs corroborate functional differentiation. According to duplication-type analyses, transposed duplication (TRD) and whole-genome duplication (WGD) were the primary factors driving family expansion, whereas selection pressure analyses revealed predominant purifying selection. The regulatory diversity and functional specialization of these genes have been demonstrated through promoter cis-element profiling and expression analysis in Brassica napus. Collectively, our findings elucidate the molecular evolutionary mechanisms underlying flavonoid pathway diversification and provide new insights into the origin of flavonol and anthocyanin biosynthesis in seed plants.
Keywords: 2-oxoglutarate-dependent dioxygenase (2ODD), Flavonoid biosynthesis, functional divergence, Gene Duplication, seed plant evolution
Received: 11 Sep 2025; Accepted: 12 Dec 2025.
Copyright: © 2025 Liu, Zhou, Wang, Jia, Li, Hao and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Tingting Hao
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