Luo Kai-Yong, Wang Shi-Ping, Yang Ling, Luo Sen-Lin, Cheng Jia, Dong Yang, Ning Ya, Wang Wei-Bin
College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China.
Front Plant Sci. 2025 Mar 28;16:1559547. doi: 10.3389/fpls.2025.1559547. eCollection 2025.
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 . 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.
类黄酮对植物的生存和适应性进化至关重要，而查尔酮异构酶（CHI）基因是类黄酮生物合成途径中的关键限速基因。全面研究CHI基因家族的进化和多样性对植物适应性进化具有重要意义。然而，许多植物谱系中的CHI基因家族仍不清楚。本研究系统地从259种植物中鉴定了CHI基因，这些植物包括藻类、苔藓植物、蕨类植物、裸子植物和被子植物。共发现了1738个CHI基因家族成员。我们分析了植物谱系进化过程中基因重复的多样性、分布轨迹和驱动力。本研究首次在现存的苔类模式物种中鉴定出潜在的II型和IV型CHI基因。CHI基因在植物界的分布模式表明，II型CHI的起源可追溯到苔藓植物和维管植物的最后一个共同祖先，而III型CHI可能代表了CHI基因家族的祖先形式。保守基序的鉴定显示不同CHI基因类型之间的基序分布存在显著差异。研究发现，基因重复的驱动力在不同植物谱系中有所不同：分散重复（DSD）在藻类和苔藓植物中占主导地位，全基因组重复（WGD）是基部被子植物和单子叶植物的主要驱动力，而串联重复（TD）在双子叶植物中占主导地位。结构聚类分析表明，CHI折叠蛋白中的三层夹心结构在中心区域保持保守，而N端序列的反复丢失导致了结构多样性。本研究为深入了解CHI折叠蛋白的进化和多样性提供了依据，并为进一步研究其功能和鉴定新的功能性CHI基因奠定了理论基础。
