Genome-Wide Identification of the Chalcone Synthase Gene Family in Phoebe zhennan and Its Association with Golden-Thread Wood Color Formation and Drought Response
Aug 2026· Genes· Vol 17, pp. 1027· 0 citations· 63 references
Abstract
Chalcone synthase (CHS) is a key enzyme in flavonoid biosynthesis, and its activity strongly influences the efficiency of flavonoid production in plants. By controlling the biosynthesis of secondary metabolites, CHS contributes to plant adaptation to diverse environmental stresses. Here, we identified CHS members across the Phoebe zhennan genome and systematically examined their gene structures, phylogenetic relationships, and potential roles in golden-thread wood color formation and drought response. Genome-wide screening resolved 11 putatively functional PzCHSs, which were unevenly distributed across six chromosomes. Physicochemical analyses indicated that most PzCHS proteins were hydrophilic. Phylogenetic reconstruction divided the PzCHS family into three groups, whose members generally shared similar gene structures. One tandem duplication event and five segmental duplication events were detected. Synteny analysis revealed extensive collinearity between the CHS families of P. zhennan, Phoebe bournei and Cinnamomum camphora, consistent with their close evolutionary relationships. Promoter regions of PzCHS genes were enriched for phytohormone-responsive and growth-related cis-elements, suggesting roles in development and hormonal regulation. Transcriptome profiling showed that PzCHS6 was upregulated in the transition zone of wood and under drought stress, suggesting that this gene may be associated with both golden-thread wood color formation and drought response. These results provide a framework for functional dissection of the CHS members and offer candidate genes for golden-thread wood color improvement and drought response breeding.
Chalcone synthase (CHS) is a pivotal enzyme in flavonoid biosynthesis involved in plant development, defense, and secondary metabolism. Xanthoceras sorbifolium (yellowhorn) is a medicinal and ornamental species with high resistance to environmental stresses, but its CHS gene family remains uncharacterized. We performed a pangenome-wide identification of CHS genes across five yellowhorn genomes (Xzs4, Xwf8, Xjg, Xg11, and Xzg2). Across the five yellowhorn genomes, 27 CHS genes were identified and classified into four core pangenes, present in all five genomes, and two dispensable genes, present only in a subset of genomes. Phylogenetic analysis grouped these genes into three major clades, and chromosomal mapping and duplication analyses identified four tandemly duplicated gene pairs under purifying selection. The analyses of conserved structural features, including protein motifs and exon-intron organization, together with promoter cis-regulatory elements and gene ontology annotation, further indicated the potential involvement of CHS genes in flavonoid biosynthesis and stress-responsive mechanisms. Gene expression profiling identified significant upregulation of Xg11_CHS1 and Xg11_CHS3 under cold and drought stress, with tissue-specific expression patterns. These findings provide valuable insights into the evolution, functional diversification, and stress-responsive roles of the CHS gene family, identifying candidate genes for future studies targeting stress tolerance and flavonoid biosynthesis in yellowhorn.
Xiang-Yu Zuo, Pei Liu, Pei-Wen Lei et al.· Functional Plant Biology· 0 citations
Geranylgeranyl diphosphate synthase (GGPS) is a key enzyme in terpenoid biosynthesis, but its role in Phoebe zhennan remains largely unknown. Here, 14 PzGGPS genes were identified and classified into three groups with conserved gene structures and motifs. Among them, PzGGPS12 was identified as a key gene for terpenoid biosynthesis, wood fragrance formation, and drought tolerance. Functional analyses showed that PzGGPS12 catalyzes the production of terpene precursors and promotes the accumulation of mono-, sesqui-, di-, and triterpenoids, thereby enhancing drought resistance through metabolic flux regulation. Furthermore, PzNAC6, PzWRKY12, and PzC3H8 were identified as major upstream transcription factors controlling the PzGGPS12 expression. These results reveal the regulatory network of PzGGPS12 and highlight its dual roles in wood fragrance formation and drought adaptation, providing new insights into terpenoid metabolism and molecular breeding of P. zhennan.
Jiang-Hong Qian, Xin Huang, Yun-Jie Gu et al.· Journal of Agricultural and...· 0 citations
Carotenoid cleavage dioxygenases (CCDs) play critical roles in plant growth, development, and abiotic stress responses, yet their genome-wide identification and drought response mechanisms remain unexplored in wheat. In this study, 34 TaCCD genes were identified in wheat, distributed across 15 chromosomes and phylogenetically classified into five subfamilies. Gene structure analysis indicated that members within each subfamily shared conserved motifs and similar intron-exon arrangements. Cis-regulatory element analysis suggested the potential roles of these genes in stress adaptation, developmental processes, and hormone signaling. Moreover, prediction of tertiary structures and protein-protein interactions revealed unique structural features and potential interacting partners of the TaCCD proteins. In addition, TaNCED9a, a member of the TaCCD family, showed the highest transcript level in wheat roots among all detected TaCCD genes and was significantly induced by drought stress. Subcellular localization assay indicated that TaNCED9a was located in chloroplasts. Downregulation of TaNCED9a expression led to reduced drought resistance in wheat, accompanied by an accumulation of reactive oxygen species and a decrease in endogenous abscisic acid levels. Using yeast one-hybrid, dual-luciferase, and tobacco transient co-expression assays, the upstream regulatory factor TaDREB-7A was identified, which can regulate the expression of TaNCED9a. Additionally, a KASP molecular marker was developed to identify the superior haplotype TaNCED9a-HapI, which exhibited a significantly higher germination rate compared to TaNCED9a-HapII under drought conditions, and was predominant in wheat. These results offer valuable insights into the TaCCD gene family's response mechanisms to drought stress in wheat, simultaneously identifying promising genetic resources for enhancing drought tolerance through molecular breeding.
Ya-Ning Bu, Zi-Han Liu, Jian-Fei Zhou et al.· Plant physiology and biochem...· 0 citations
: The basic leucine zipper (bZIP) transcription factors constitute one of the largest and most functionally diverse gene families in plants, playing central roles in growth, development, and stress adaptation. However, systematic information on this family remains limited in Lilium davidii var. unicolor , an economically important ornamental and edible bulb crop with a remarkably large and complex genome. In this study, we conducted a genome-wide survey and identified 64 LdbZIP genes. Phylogenetic analysis with Arabidopsis and rice assigned the LdbZIPs to 11 of the 13 recognized subfamilies, with no member of subfamily IV or VIII detected. The encoded proteins exhibited obvious heterogeneity in physicochemical properties. Most LdbZIP proteins were predicted to be hydrophilic and structurally flexible, yet all were predicted to have nuclear localization, whereas several members also showed possible endoplasmic reticulum or cytoplasmic localization. Fifty-four segmentally duplicated pairs and one tandemly duplicated pair were identified, and all duplicated pairs had Ka/Ks ratios below 1. Promoter regions of LdbZIPs were contained a wide variety of cis -regulatory elements associated with light, phytohormone, and stress responses, suggesting broad involvement in environmental adaptation. Expression profiling uncovered significant spatial variations across plant tissues. Crucially, transcriptomic and relative expression analyses demonstrated a dynamic reprogramming of LdbZIP genes during dormancy release and regeneration. Together, these results provide a systematic overview of the structural features, evolutionary divergence, and expression characteristics of the LdbZIP gene family in L. davidii var. unicolor , thereby establishing a foundation for future functional characterization of candidate genes involved in dormancy release and asexual regeneration.
expression analysis indicated tissue-specific expression patterns, with higher expression levels observed in roots and qRT-PCR profiling detected increased expression of multiple candidate PtrCOMT genes upon high-salt treatment, hinting that members of this family may be implicated in plant salt stress regulatory processes.
This work sets a starting point for furthur investigation into cotton GolS genes and provides novel resources for breeding programmes aimed at enhancing abiotic stress tolerance in cotton.
Umm e Abaida Noor, Muhammad Shaban, M. Azmat et al.· Biologia· 0 citations
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