Dictyophora indusiata(Vent. Ex Pers.) Fisch. (DI) is an edible and medicinal fungus widely used in East Asian countries. However, during DI cultivation, the formation of fruiting bodies cannot be regulated, which leads to yield and quality losses. The present study performed a combined genome, transcriptome, and metabolome analysis of DI. Using Nanopore and Illumina sequencing approaches, we created the DI reference genome, which was 67.32 Mb long with 323 contigs. We identified 19,909 coding genes on this genome, of which 46 gene clusters were related to terpenoid synthesis. Subsequent transcriptome sequencing using five DI tissues (cap, indusia, mycelia, stipe, and volva) showed high expression levels of genes in the cap, indicating the tissue’s importance in regulating the fruiting body formation. Meanwhile, the metabolome analysis identified 728 metabolites from the five tissues. Mycelium was rich in choline, while volva was rich in dendronobilin; stipe had monosaccharides as the primary component, and the cap was the main source of indole acetic acid (IAA) synthesis. We confirmed the importance of tryptophan metabolism for DI fruiting body differentiation based on KEGG pathway analysis. Finally, the combined multiomics analysis identified three new genes related to IAA synthesis of the tryptophan metabolic pathway in the cap, which may regulate DI fruiting body synthesis and improve DI quality. Thus, the study’s findings expand our understanding of resource development and the molecular mechanisms underlying DI development and differentiation. However, the current genome is still a rough draft that needs to be strengthened.

Introduction: Endophytes play a significant role in regulating plant root development and facilitating nutrient solubilization and transportation. This association could improve plant growth. The present study has uncovered a distinct phenotype, which we refer to as "white root", arising from the intricate interactions between endophytic fungi and bacteria with the roots in a sugarcane and bamboo fungus (Dictyophora indusiata) intercropping system.Methods: We investigated the mechanisms underlying the formation of this “white root” phenotype and its impact on sugarcane yield and metabolism by metabarcoding and metabolome analysis.Results and Discussion: Initial analysis revealed that intercropping with D. indusiata increased sugarcane yield by enhancing the number of viable tillers compared with bagasse and no input control. Metabarcoding based on second-generation and third-generation sequencing indicated that D. indusiate and Bacillus aryabhattai dominates the fungal and bacterial composition in the “white root” phenotype of sugarcane root. The coexistence of D. indusiata and B. aryabhattai as endophytes induced plant growth-promoting metabolites in the sugarcane root system, such as lysoPC 18:1 and dihydrobenzofuran, probably contributing to increased sugarcane yield. Furthermore, the association also enhanced the metabolism of compounds, such as naringenin-7-O-glucoside (Prunin), naringenin-7-O-neohesperidoside (Naringin)*, hesperetin-7-O-neohesperidoside (Neohesperidin), epicatechin, and aromadendrin (Dihydrokaempferol), involved in flavonoid metabolism during the formation of the endophytic phenotype in the sugarcane root system. These observations suggest that the “white root” phenotype promotes sugarcane growth by activating flavonoid metabolism. This study reports an interesting phenomenon where D. indusiata, coordinate with the specific bacteria invade, forms a “white root” phenotype with sugarcane root. The study also provides new insights into using D. indusiata as a soil inoculant for promoting sugarcane growth and proposes a new approach for improve sugarcane cultivation.

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a key vegetable crop in Asia, but its commercial value is often reduced by premature flowering triggered by vernalization. The molecular mechanisms behind this process are not fully understood. MADS-box genes, as crucial transcriptional regulators, play vital roles in plant development, including flowering. In this study, 102 MADS-box genes were identified in Chinese cabbage through bioinformatics analyses, covering phylogeny, chromosomal localization, and gene structure. Real-time quantitative PCR and RNA-seq data analysis revealed that the expression level of AGL27 declined as vernalization time increased. To determine BrAGL27′s functions, we obtained BrAGL27-overexpressed (OE) Arabidopsis thaliana lines that showed significantly later flowering compared with the wild type (WT). The expression levels of flowering suppressor genes AtFLC and AtTEM1 were significantly high-regulated in the BrAGL27-OE lines compared to WT plants, while the expression levels of the floral genes AtSPL15, AtSOC1, AtFT, and AtAP3 were significantly lower in the BrAGL27-overexpressed lines than in the wild type. These findings enhance understanding of MADS-box genes in vernalization and flowering regulation, offering a basis for further research on bolting resistance and flowering control in Chinese cabbage.

Sugarcane tillering is a key determinant of crop productivity, yet the integrated roles of rhizosphere microbiome dynamics, nutrient status, and hormone signaling in regulating tiller development remain poorly understood. Here, we compared rhizosphere microbial communities, endogenous hormone profiles, and nutrient element concentrations in sugarcane cultivars with contrasting tillering capacities. High-tillering varieties exhibited significantly greater microbial diversity and more complex co-occurrence network structures in the rhizosphere, characterized by enrichment of Acidobacteriota, Chloroflexi, and Planctomycetes and functional pathways related to nitrogen fixation, phosphorus solubilization, and auxin biosynthesis. In contrast, low-tillering varieties harbored simplified, stress-adapted microbial consortia and prioritized pathways linked to oxidative stress response and heavy metal detoxification. Hormonal analysis revealed that high-tillering cultivars maintained higher levels of growth-promoting hormones—particularly auxin (IAA) and active cytokinins—in tiller buds while low-tillering cultivars accumulated elevated abscisic acid (ABA) and inactive cytokinin conjugates. Nutrient analysis indicated that high-tillering genotypes possessed higher nitrogen and phosphorus contents, supporting vigorous axillary bud activation and shoot proliferation, whereas low-tillering varieties accumulated more zinc and manganese, potentially reflecting stress adaptation. Network-level integration of microbial, hormonal, and nutrient profiles underscored genotype-specific feedback between rhizosphere microbiota and plant physiological states, highlighting modular associations that link microbial hubs with tissue-specific nutrient and hormone signatures. Our findings reveal a systems-level mechanism by which rhizosphere microbial community structure and function interact with plant-nutrient–hormonal status to regulate tillering in sugarcane. These insights provide a basis for microbiome-informed strategies to enhance sugarcane productivity through integrated nutrient–hormonal–microbe management.

Sugarcane productivity varies widely among genotypes, but the biochemical traits underlying these differences remain poorly characterized. In this study, six contrasting sugarcane cultivars were profiled to investigate how ionomic, hormonal, flavonoid, and photosynthetic pigment signatures are associated with yield and sucrose accumulation. Morphological traits and field performance revealed marked genotypic variation, with ZZ14 and GL1215 achieving the highest yields and sugar content, while GT59 and GT60 performed less favorably. Multivariate analyses of ionomic data showed that potassium, magnesium, and calcium were consistently enriched in high-yield cultivars, whereas sodium, boron, and manganese were negatively associated with growth traits. Hormone profiling revealed that high-yielding genotypes utilize diverse strategies: while the high-yielding GL1215 achieved superior sugar content with the lowest levels of growth-promoting hormones, the LT1790 genotype, despite having the highest levels of these hormones, showed suboptimal yield due to a costly trade-off with its hyperactive defense system. Flavonoid analysis indicated that LT1790 contained the highest levels of Quercetin, rutin, and caffeic acid, suggesting enhanced antioxidant capacity, whereas GT59 preferentially accumulated chlorogenic acid. Canonical correlation analysis confirmed that nutrient balance and metabolite composition strongly correlated with plant height, stem diameter, and sugar concentration. Together, these results suggest that high-yield sugarcane genotypes achieve a superior metabolic balance, combining efficient nutrient uptake and robust antioxidant capacity with a favorable hormone profile that promotes strong growth without triggering a costly constitutive defense system.

Introduction: Phenotypic evaluation and whole-genome resequencing (WGR) techniques play critical roles in the identification and utilization of crop germplasm resources. This study integrated 28 phenotypic traits and WGR data to assessphenotypic variation and genetic diversity among 209 angled luffa (Luffa acutangula) accessions. Methods: A total of 209 angled luffa accessions were evaluated using 28 phenotypic traits and whole-genome resequencing. Phenotypic variation was assessed by coefficients of variation and Shannon-Wiener diversity indices. Principal component analysis (PCA), population structure analysis, phylogenetic tree construction, and hierarchical clustering were performed to analyze phenotypic and genetic diversity. Results: Extensive phenotypic variation was observed, with coefficients of variation for 20 quantitative traits ranging from 8.41% to 54.09%, and Shannon-Wiener diversity indices (H') from 1.79 to 2.51. For 8 quality-related traits, coefficients of variation ranged from 4.93% to 45.11%, with H' values between 0.13 and 1.97. Principal component analysis revealed 9 principal components, with fruit length and skin color exhibiting the highest loadings, enabling the identification of 12 superior germplasm accessions. Genetic diversity indices indicated limited overall genetic variation (Ne = 1.390, I = 0.528, Ho = 0.125, He = 0.236) with a high inbreeding coefficient (FIS = 0.470), indicating significant inbreeding within this population. Population structure, phylogenetic tree, and hierarchical clustering analyses consistently partitioned the accessions into six subgroups, with each subgroup displaying similar phenotypic and genetic characteristics. Discussion: Together, these findings provide an integrated phenotypic and genomic landscape of ridged loofah diversity and have laid a solid foundation for the innovative utilization, molecular genetic improvement, and new variety selection of angled luffa germplasm resources in the future.