Idesia polycarpa is a dioecious tree; in field surveys, there are rare sex conversions in I. polycarpa individuals with bisexual flowers. To identify the molecular mechanisms underlying sex conversion in this species, an integrative analysis of the proteome and transcriptome profiles of I. polycarpa male and bisexual flowers at key developmental stages was conducted in this study using isobaric tags for relative and absolute quantification and RNA-seq technology. A total of 15,003 proteins were identified; the differentially expressed proteins (DEPs) were enriched in metabolic pathways, biosynthesis of secondary metabolites, and flavonoid metabolism pathways in all comparison groups. A total of 290,442 unigenes were obtained; these were compared with seven databases, revealing 196,366 annotated unigenes. In general, the expression of proteins and genes tended to be positively correlated, with Spearman correlation coefficients in the ranges of 0.152–0.262 (all genes and all proteins) and 0.497–0.778 (DEPs and DEGs). The integrative analysis of DEPs and DEGs between male and bisexual flowers revealed that the most significantly enriched pathways were flavonoid pathways, metabolic pathways, and the biosynthesis of secondary metabolites. Finally, four co-expressed proteins and transcripts and one gene associated with the flavonoid biosynthesis pathway were screened out. The proteins identified were p-coumaroyl shikimate 3′-hydroxylase, and shikimate/quinate hydroxycinnamoyl transferase, and the gene was caffeoyl-CoA O-methyltransferase. The analysis has revealed key potential proteins and genes involved in sex conversion at the molecular level and has provided a basis for future investigations of artificial regulation of sex differentiation in I. polycarpa.

Aroma is an appreciated fruit property, and volatile flavor plays a key role in determining the perception and acceptability of fruit products by consumers. However, metabolite composition that contributes to the aroma in fruit quality is unclear. In this study, we detected 645 volatile organic compounds of ‘Panguxiang’ pear in total, including esters, alcohols, alkanes, acids, ketones, terpenes and aldehydes. In addition, the levels of sugars, organic acids and amino acids in ‘Panguxiang’ pear were investigated using high-performance liquid chromatography. In the aroma generation, glucose was the dominant sugar, followed by sucrose and fructose. At the development transferred storage stage, organic acids may not participate in aroma biosynthesis. The amino acids that may play potential roles in aroma substance synthesis are tyrosine and glycine. Through metabolomics analysis at different stages of ‘Panguxiang’ pear, we selected 65 key metabolites that were significantly related to glucose, sucrose, fructose, tyrosine and glycine, according to the trends of metabolite concentrations. Finally, we chose eight candidate metabolites (e.g., three esters, two aldehydes, one alcohol, one acid and one ketone) as the representative aroma substances of the ‘Panguxiang’ pear compared to the metabolome of the ‘Korla’ at stage Z5. Data and results from this study can help better understand the variations in aroma quality among pear varieties and assist in developing breeding programs for pear varieties.

Idesia polycarpa is an important woody oilseed tree crucial for ensuring China’s grain and oil security. The expansion of I. polycarpa plantations has been accompanied by an increase in pests and diseases, with canker disease recently observed in two forests in Henan Province. Field surveys revealed a disease incidence of 70.12% among 328 surveyed trees, indicating a substantial threat to plantation health. The most virulent pathogen, strain SQ5, was identified as Botryosphaeria dothidea through molecular sequencing and morphological analyses. Strain SQ5 showed an optimum growth temperature of 25 °C and a mycelial lethal temperature of 60 °C. The pathogen thrives in acidic conditions and is promoted by light, with the ability to utilize various carbon and nitrogen sources. In vitro toxicity assessments identified four effective fungicides: 70% thiophanate-methyl (EC50 = 0.0169 µg/mL), 43% tebuconazole (EC50 = 0.0219 µg/mL), 20% octylamine acetate (EC50 = 0.0271 µg/mL), and 40% difenoconazole (EC50 = 0.0954 µg/mL). Field trials demonstrated that 43% tebuconazole (average efficacy = 35.29%) and 40% difenoconazole (average efficacy = 23.53%) exhibited superior control of I. polycarpa canker. This study represents the first systematic analysis of I. polycarpa canker and its control measures, laying a foundation for further research and field management strategies. Given the significance of I. polycarpa in Chinese forestry, this underscores the need for effective management strategies to sustain its productivity and mitigate risks associated with expanding plantations.

Idesia polycarpa is a woody oil tree threatened by stem canker caused by Botryosphaeria dothidea, yet the organization and infection-responsive behavior of its phenylalanine ammonia-lyase (PAL) gene family remain poorly understood. Here, we identified five IpPAL genes and characterized their phylogenetic relationships, conserved features, duplication patterns, promoter cis-elements, and infection-associated expression profiles. Segmental and tandem duplication contributed to IpPAL family evolution, and all duplicated pairs showed Ka/Ks ratios below 1, consistent with purifying selection. RNA sequencing (RNA-seq) of contrasting Chengdu and Zhangjiajie provenances revealed distinct temporal responses. In Chengdu, IpPAL2–IpPAL4 were significantly upregulated at 24 h after inoculation, whereas all five genes were upregulated at 96 h. In Zhangjiajie, all five IpPAL genes were significantly upregulated at 24 h, while IpPAL2–IpPAL5 remained upregulated at 96 h. No IpPAL gene met the differential-expression criteria between provenances under mock conditions or at 24 h; at 96 h, IpPAL1 and IpPAL3 were lower and IpPAL5 was higher in Zhangjiajie than in Chengdu. Scanning electron microscopy (SEM) provided complementary qualitative evidence of provenance-associated tissue responses. These findings demonstrate time- and gene-specific IpPAL responses to B. dothidea and identify candidate genes for further functional analysis.

The composition, richness, and diversity of rhizosphere fungal communities play significant roles in plant development in Chinese fir plantations. Understanding their structure and assembly, along with their relationship to soil physicochemical properties and root traits, is essential for maximizing the benefits of fungal symbionts for Chinese fir trees. Hence, fungal communities in two soil layers (0–20 cm and 20–40 cm) at four plantation developmental stages were analyzed using internal transcribed spacer rRNA gene sequencing. Soil physicochemical properties and root traits were examined to determine the main fungal community drivers. Our results revealed that fungal communities were significantly influenced by stand developmental stage, rhizosphere, and soil depth. Fungal biomass was highest at the young stand stage, whereas the α-diversity and evenness of the surface rhizosphere soil fungi remained stable across stages. With increasing stand age, the fungal community structure shifted from aggregated to dispersed. Co-occurrence network analysis demonstrated that stand development promoted network connectivity and modularity, with tighter local associations and distinct core functional consortia formed in the mature and over-mature stages. The proportion of positive links and positive cohesion increased along the stand developmental gradient, indicating a shift from competitive to cooperative interspecific interactions. Ascomycota and Basidiomycota consistently dominated soil fungal communities regardless of stand age, whereas Mortierellomycota and Chytridiomycota displayed sensitivity to stand development despite their low relative abundance. Soil physicochemical properties (total carbon, potassium, dissolved organic carbon, and phosphorus) were the primary drivers of rhizosphere fungal community dynamics and regulated fungal assembly by controlling soil resource availability. Additionally, the structural configuration of the fungal community was found to be intricately linked to root biomass and morphological traits.