Osmanthus fragransis a well-known ornamental plant that has been domesticated in China for 2500 years. More than 160 cultivars have been found during this long period of domestication, and they have subsequently been divided into four cultivar groups, including the Yingui, Jingui, Dangui, and Sijigui groups. These groups provide a set of materials to study genetic evolution and variability. Here, we constructed a reference genome ofO. fragrans‘Liuyejingui’ in the Jingui group and investigated its floral color traits and domestication history by resequencing a total of 122 samples, including 119O. fragransaccessions and three otherOsmanthusspecies, at an average sequencing depth of 15×. The population structure analysis showed that these 119 accessions formed an apparent regional cluster. The results of linkage disequilibrium (LD) decay analysis suggested that varieties with orange/red flower color in the Dangui group had undergone more artificial directional selection; these varieties had the highest LD values among the four groups, followed by the Sijigui, Jingui, and Yingui groups. Through a genome-wide association study, we further identified significant quantitative trait loci and genomic regions containing several genes, such as ethylene-responsive transcription factor 2 and Arabidopsis pseudoresponse regulator 2, that are positively associated with petal color. Moreover, we found a frameshift mutation with a 34-bp deletion in the first coding region of the carotenoid cleavage dioxygenase 4 gene. This frameshift mutation existed in at least one site on both alleles in all varieties of the Dangui group. The results from this study shed light on the genetic basis of domestication in woody plants, such asO. fragrans.

Histone acetylation and methylation, governed by various histone modification (HM) gene families, are vital for plant biological processes. However, there are limited studies that have explored HMs in ornamental horticultural trees, including sweet osmanthus (Osmanthus fragrans). We performed genome-wide search and identified 208 OfHMs, encompassing 81 histone methyltransferases (OfHMTs), 51 histone demethylases (OfHDMs), 49 histone acetyltransferases (OfHATs) and 27 histone deacetylases (HDACs). Our comprehensive analysis covered chromosome locations, gene structures, conserved domains, cis-acting elements, phylogenetic comparisons, protein interaction networks and functional enrichment pathways for these gene families. Additionally, tandem and fragment replications were unveiled as contributors to the expansion of OfHMs, with some genes exhibiting positive selection. Furthermore, we examined OfHM expression profiles across various tissues and flowering stages, and under 5′-azacytidine (Aza) and ethylene treatments. Most OfHMs displayed heightened expression in leaves, and were downregulated during the flower opening and senescence stages, including OfPRMTs, OfHDTs, OfHDAs, OfSRTs, OfJMJs and OfHAGs; 75.86% and 80.77% of the differentially expressed OfHMs were upregulated after Aza and ethylene treatments, including OfHAGs, OfHDAs and OfSDGs. This study offers a comprehensive analysis of the OfHM gene family, which indicated their potential involvement in ethylene and Aza responses, and in the flowering process. These findings provide valuable insights into the role of OfHMs in flowering and stress responses.

Intoduction: Osmanthus fragrans, a well-regarded traditional flower in China, holds extensive applications in gardening, food, cosmetics, and traditional Chinese medicine. Despite its importance, research on long non-coding RNAs (lncRNAs) in O. fragrans has been constrained by the absence of reliable reference genes (RGs).Methods: We employed five distinct algorithms, i.e., delta-Ct, NormFinder, geNorm, BestKeeper, and RefFinder, to evaluate the expression stability of 17 candidate RGs across various experimental conditions.Results and discussion: The results indicated the most stable RG combinations under different conditions as follows: cold stress: lnc00249739 and lnc00042194; drought stress: lnc00042194 and lnc00174850; salt stress: lnc00239991 and lnc00042194; abiotic stress: lnc00239991, lnc00042194, lnc00067193, and lnc00265419; ABA treatment: lnc00239991 and 18S; MeJA treatment: lnc00265419 and lnc00249739; ethephon treatment: lnc00229717 and lnc00044331; hormone treatments: lnc00265419 and lnc00239991; Al³⁺ treatment: lnc00087780 and lnc00265419; Cu²⁺ treatment: lnc00067193 and 18S; Fe²⁺ treatment: lnc00229717 and ACT7; metal ion treatment: lnc00239991 and lnc00067193; flowering stage: lnc00229717 and RAN1; different tissues: lnc00239991, lnc00042194, lnc00067193, TUA5, UBQ4, and RAN1; and across all samples: lnc00239991, lnc00042194, lnc00265419 and UBQ4. The reliability of these selected RGs was further validated by analyzing the expression patterns of lnc00003036, lnc00126603, and lnc00250780. This study represents the first comprehensive evaluation of lncRNA RG stability in O. fragrans, significantly enhancing the accuracy and depth of lncRNA expression analyses in this species, contributing to advancements in plant stress resistance breeding and improving environmental adaptability.

Ethylene-insensitive 3/ethylene-insensitive 3-like (EIN3/EIL) transcription factors are central regulators of ethylene signaling and stress adaptation in plants. However, their roles in Osmanthus fragrans, a globally cherished ornamental and aromatic plant with significant economic value, remain poorly characterized. Here, we identified nine OfEIL genes across eight chromosomes in the O. fragrans “Liuye Jingui” genome. Conserved motif analysis revealed core domains (Motif1/2/4/7), and promoter cis-elements highlighting hormone-related, stress-related, and growth-related regulatory potential. During late flowering stages, six OfEILs (3/4/5/6/7/9) were significantly upregulated. Under 5-azacytidine (AZA, a DNA demethylation agent), OfEIL2 and OfEIL7 were downregulated, whereas the ETH treatment activated OfEIL3/7/8/9. Strikingly, OfEIL7 exhibited dual regulatory roles, correlating strongly with natural flowering progression, AZA-induced demethylation, and ETH responses. Functional divergence was observed in petal senescence, with OfEIL2–5 and OfEIL7–9 showing stage-specific and tissue-specific expression patterns. These results position OfEIL7 as a key hub integrating epigenetic and hormonal signals to modulate floral longevity and stress adaptation. Our study provides the first genome-wide characterization of the EIL family in O. fragrans, offering critical insights for molecular breeding aimed at enhancing ornamental traits and environmental resilience in this economically significant species.