Background: Dihydroflavonol 4-reductase (DFR) is a key enzyme in the flavonoid biosynthetic pathway that regulates anthocyanin and proanthocyanidin accumulation in plants. Although DFR genes have been studied in various species, their origin of the DFR gene family, its distribution across the plant kingdom, and the reasons behind the emergence of different DFR subtypes Methods: This study performed a whole-genome analysis of DFR genes in 237 plant species, including algae, mosses, ferns, gymnosperms, and angiosperms, integrating phylogeny, conserved motifs, duplication mechanisms, positive selection, and expression pattern analyses. Results: These results indicate that the DFR gene family originated from the common ancestor of extant ferns and seed plants, and the emergence of asparagine (Asn)-type and aspartic (Asp)-type DFRs is associated with gymnosperms. Notably, we report for the first time the presence of Asn-type, Asp-type, and arginine (Arg)-type DFRs in some species, which breaks the previous notion that Arg-type DFRs are exclusive to ferns. Tandem duplication is considered the primary driving force behind the expansion of the DFR family and is associated with the formation of different DFR subtypes. Furthermore, Asn-type DFRs were highly expressed during the early stages of seed development, suggesting their important role in seed development. Conclusions: Overall, this study revealed the dynamic evolutionary trajectory of the DFR gene family in plants, providing a theoretical foundation for future research on DFR genes.

Flavonoids are crucial for plant survival and adaptive evolution, and chalcone isomerase (CHI) genes serve as key rate-limiting gene in the flavonoid biosynthesis pathway. It is important for plant adaptive evolution to comprehensively study the evolution and diversity of the CHI gene families. However, the CHI gene families in many plant lineages remain elusive. This study systematically identified CHI genes from 259 species including algae, bryophytes, ferns, gymnosperms, and angiosperms. A total of 1,738 CHI gene family members were discovered. We analyzed the diversity, distribution trajectory, and the driving forces of gene duplication during the evolution of the plant lineages. The present study is the first to identify potential type II and type IV CHI genes in the extant liverwort model species Marchantia polymorpha. The distribution pattern of CHI genes across the plant kingdom reveals that the origin of type II CHI can be traced back to the last common ancestor of bryophytes and vascular plants, and type III CHI may represent the ancestral form of the CHI gene family. The identification of conserved motifs showed significant differences in motif distribution among different CHI gene types. It was found that the drivers of gene duplication varied across plant lineages: dispersed duplications (DSD) were predominant in algae and bryophytes, whole-genome duplication (WGD) was the main driver in basal angiosperms and monocots, while tandem duplications (TD) predominating in eudicots. Structural clustering analysis demonstrated the 3-layer sandwich structure in the CHI-fold proteins remained conserved in the central region, while repeated loss of N-terminal sequences contributed to structural diversity. This study provides a deeper understanding of the evolution and diversity of the CHI-fold proteins and lays a theoretical foundation for further studies of their function and the identification of new functional CHI genes.

An important area of interest for therapeutic development is the IL-1 superfamily, a critical group of immune regulators with profound implications in a variety of disorders. This study clarifies the evolutionary patterns of IL-1 family members by thoroughly analyzing more than 400 animal species, demonstrating their ancient roots that extend back to the earliest vertebrates. Important results show that, although IL-1 ligands expanded significantly over the evolution of mammals, their corresponding receptors remained remarkably structurally conserved. Identifying both lineage-specific adaptations and evolutionarily conserved residues provides vital information for treatment design. These findings point to the possibility of two different therapeutic strategies: addressing species-specific variants may allow for more targeted interventions, whereas focusing on conserved motifs may result in broad-acting treatments. The study also identified less well-known species as useful models for comprehending early immune systems. In addition to advancing our knowledge of the function of the IL-1 family in autoimmune, inflammatory, and carcinogenic illnesses, this research lays the groundwork for the development of more potent targeted therapeutics by creating an evolutionary framework for the IL-1 family.

The Interleukin-12 (IL-12) family ligand subunits (IL-12s) and receptor subunits (IL-12Rs) constitute pivotal regulators of immune homeostasis, with direct implications in autoimmune pathologies and oncogenesis. Through phylogenetic reconstruction, synteny analysis, and sequence alignment across 400+ animal species, we delineated the evolutionary trajectories and functional diversification of these immune mediators. Phylogenetic analysis revealed IL-12Rs originated prior to the mollusk era (514-686.2 million years ago, Mya), while ligand subunits p19/p28 emerged during the mammalian and avian epoch (180-225 Mya). Structural characterization identified three evolutionarily invariant signature motifs within the fibronectin type III (fn3) domain essential for receptor-ligand interface stability. Furthermore, phylogenetically ultra-conserved residue and motif configurations were mapped, revealing candidate therapeutic epitopes. These findings establish an evolutionary framework explaining functional conservation/divergence in IL-12 signaling components. The identified ancient receptor architectures coupled with derived ligand innovations provide a blueprint for cross-species immunotherapy design targeting conserved interaction interfaces. The conserved molecular signatures offer dual utility in developing precision therapies and interspecies disease management strategies, particularly for translational applications across human medicine, agriculture, and aquaculture.

Background: The RSPO gene family encodes secreted glycoproteins that are rich in cysteine, which generally serve as activators of the Wnt signaling pathway in animals. Four types of this family have been identified in a few model species. However, the evolution of the family remains unclear. Methods: In this study, we identified a total of 1496 RSPO homologs through an extensive survey of the RSPO genes in 430 animals. Gene family clustering and phylogenetic analysis identified four major subtypes of the family (RSPO1–RSPO4) and clarified their distribution of copy number in different species. Results and Conclusions: Members of the RSPO4 subfamily that were closest to ancestral forms existed in both Deuterostomes and Protostomates, and we speculate that representatives of this subfamily already existed in Urbilatera, the last common ancestor of Deuterostomes. Particularly, in some RSPO3 subtypes of Actinopterygii (ray-finned fishes), an FU repeated motif with three conserved cysteines was identified. Further conservative analysis of amino acids and alignment of tertiary protein structure revealed the potential functional sites for each subgroup. The results provide insight into the phylogenetic relationships and evolutionary patterns of conserved motifs of RSPO family genes in animal kingdoms, which will guide further studies on the biological functions of RSPO in other non-model species.