Search Results (41)

This study performed a phylogenomic analysis of the C2H2 gene family across 30 Basidiomycota species, identifying 1032 genes distributed across six evolutionary clades (Groups I–VI). Functional diversification and lineage-specific expansions were observed: Group II (37.1%) formed a conserved core, while wood decayers (e.g., Schizophyllum commune) and edible fungi (e.g., Pleurotus ostreatus) exhibited clade-specific expansions in Groups III and V, respectively. Physicochemical profiling revealed an acidic bias in Agaricomycotina proteins (pI 4.3–5.8) compared to alkaline trends in pathogens (Ustilaginomycotina/Pucciniomycotina; pI 8.3–8.6). Comparative genomics indicated that saprotrophs retained long genes (12.4 kb) with abundant introns (mean = 6.2/gene), whereas pathogens exhibited genomic streamlining (introns ≤ 2). Synteny network analysis revealed high ancestral conservation in core clusters (Cluster_1–2: 58% homologs) under strong purifying selection (Ka/Ks = 0.18–0.22), while peripheral clusters (Cluster_Mini) approached neutral evolution (Ka/Ks = 0.73). This study reveals stage-specific expression dynamics of 17 C2H2 zinc finger genes in Sarcomyxa edulis, highlighting their roles in coordinating developmental transitions (e.g., SeC2H2_1 in low-temperature adaptation, SeC2H2_7/12 in primordia initiation, and SeC2H2_8/9/13 in fruiting body maturation) through temporally partitioned regulatory programs, providing insights into fungal morphogenesis and stress-responsive adaptation. These findings underscore the dual role of C2H2 genes in sustaining conserved regulatory networks and facilitating ecological adaptation, providing new insights into fungal genome evolution. Full article

The application of an environmentally friendly plant growth regulator to regulate plant growth and development represents a promising strategy for sustainable agriculture. Thymol is a kind of plant-derived natural compound. We have found that thymol is a potential biostimulant with the capability to trigger plant defense against abiotic stresses. Little is known about whether and how thymol modulates plant root system architecture. In this study, physiological, histochemical, and molecular approaches were applied to identify the role of thymol in promoting lateral root development in watermelon seedlings. Thymol significantly promoted LRP (lateral root primordia) initiation and lateral root formation. Rboh (respiratory burst oxidase homolog)-dependent reactive oxygen species (ROS) generation was involved in thymol-promoted lateral root development from LRP. Then, the Rboh gene family with nine members (ClRboh1–ClRboh9) was identified from watermelon genome. Thymol significantly induced the expression of a set of ClRbohs in roots. These results suggested that thymol was able to stimulate lateral root formation by triggering Rboh-dependent ROS production. These findings may help understand the biological function of thymol as an elicitor of lateral root in both applied and fundamental study. Full article

The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon and multi-omics data (transcriptome and metabolome) analyses of the mycelia, primordia, and fruiting bodies were conducted in the present study. Genome sequencing based on PacBio HiFi and Hi-C resulted in a 36.3 Mb genome sequence that mapped to 12 chromosomes, comprising 11,886 protein-coding genes. A total of 25 cold-responsive (COR) genes and 520 cold-adapted enzymes were identified in the genome. Multi-omics analyses showed that the pathways related to carbohydrate metabolism in the mycelia under low temperature (10 °C) were significantly enriched. Further examination of the expression profiles of carbohydrate-active enzymes (CAZymes) involved in carbohydrate metabolism revealed that out of 515 CAZyme genes in F. filiformis, 58 were specifically upregulated in mycelia under low-temperature conditions. By contrast, the expression levels of these genes in primordia and fruiting bodies reverted to those prior to low-temperature exposure. These indicate that CAZyme genes are important for the low-temperature adaptation of F. filiformis. This research contributes to the targeted breeding of F. filiformis. Full article

Mei (Prunus mume Sieb. et Zucc.) is a rare woody species that flowers in winter, yet its large-scale propagation is limited by the variable ability of cuttings to form adventitious roots (ARs). In this study, two cultivars were compared: P. mume ‘Xiangxue Gongfen’ (GF), which roots readily, and P. mume ‘Zhusha Wanzhaoshui’ (ZS), which is more recalcitrant. Detailed anatomical observations revealed that following cutting, the basal region expanded within 7 days, callus tissues had appeared by 14 days, and AR primordia emerged between 28 and 35 days. Notably, compared to the recalcitrant cultivar ZS, the experimental cultivar GF exhibited significantly enhanced callus tissue formation and AR primordia differentiation. Physiological analyses showed that the initial IAA concentration was highest at day 0, whereas cytokinin (tZR) and gibberellin (GA1) levels peaked at 14 days, with ABA gradually decreasing over time, resulting in increased IAA/tZR and IAA/GA1 ratios during the rooting process. Transcriptomic profiling across these time points identified significant upregulation of key genes (e.g., PmPIN3, PmLOG2, PmCKX5, PmIAA13, PmLAX2, and PmGA2OX1) and transcription factors (PmWOX4, PmSHR, and PmNAC071) in GF compared to ZS. Moreover, correlation analyses revealed that PmSHR expression is closely associated with IAA and tZR levels. Overexpression of PmSHR in tobacco further validated its role in enhancing lateral root formation. Together, these findings provide comprehensive insights into the temporal, hormonal, and genetic regulation of AR formation in P. mume, offering valuable strategies for improving its propagation. Full article

The eye primordium of vertebrates initially forms exactly at the side of the head. Later, the eyeball architecture is tuned to see ahead with better visual acuity, but its molecular basis is unknown. The position of both eyes in the face alters in patients with holoprosencephaly due to Sonic hedgehog (Shh) mutations that disturb the development of the ventral midline of the neural tube. However, patient phenotypes vary extensively, and microforms without a brain anomaly relate instead to alternation of gene expression of the Shh signaling center in the facial primordia. We identified novel missense mutations of the Shh gene in two patients with a dislocated fovea, where the photoreceptor cells are condensed. Functional assays showed that Shh upregulates Patched and Gli and downregulates Pax6, and that Shh mutations alter these activities. Gain of function of Shh in a chick embryo retards retinal development and eyeball growth depending on the location of Shh expression, while loss of function of Shh promotes these features. We postulate that a signaling molecule like Shh that emanates from the face controls the extent of differentiation of the neural retina in a position-specific manner and that this may result in the formation of the fovea at the correct location. Full article

Euryodendron excelsum H. T. Chang, a monotypic plant endemic to China, exhibits significant variations in adventitious root formation in cuttings across different age groups through unclear molecular mechanisms. In this study, we performed RNA-sequencing (RNA-seq) and data analysis at three stages—initial excision (S0), root primordia (S1), and emergence of adventitious roots (S2)—for lateral buds from transplanted triennial tissue culture seedlings and decennial E. excelsum plants. We identified 13,424 differentially expressed genes (DEGs) between different rooting stages and age groups, including 8216 upregulated and 5208 downregulated genes. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the S1 and S2 DEGs identified were mainly involved in phenylpropanoid biosynthesis, plant hormone signal transduction, plant–pathogen interactions, biosynthesizing various secondary plant metabolites, and starch and sucrose metabolism. Key auxin-pathway genes were expressed at significantly higher levels in culture seedlings than in adult plants, as were WUSCHEL-related homeobox and LATERAL ORGAN BOUNDARIES DOMAIN genes (related to adventitial root growth and development), which together promote the formation, growth, and development of adventitial root primordia. The dysregulated expression of 15 DEGs identified by RNA-seq were verified via real-time quantitative polymerase chain reaction analysis. This study investigates the morphological processes of adventitious root formation in cuttings of E. excelsum of different ages, and the potential molecular mechanisms involved. Our finding provides a basis for research on cutting propagation, conservation applications, and optimization of tissue culture for E. excelsum, and may help improve the rooting rate of E. excelsum cuttings. Full article

To develop and utilize the wild fungi resources in Tibet, a wild fungal specimen collected from Qiangna Town, Milin County, Tibet was isolated, purified, and characterized. Through morphological examination and ITS sequence analysis, the strain—designated as X21266—was identified as Tyromyces kmetii. The effects of different carbon sources, nitrogen sources, pH, and temperature on the mycelial growth of T. kmetii under solid-state culture conditions were investigated. In addition, research on domestication cultivation was conducted. The results showed that the optimal carbon source for T. kmetii was fructose, the preferred nitrogen source was beef powder, and the optimal pH and temperature were pH 5.0 and 25 °C, respectively. Domestication cultivation results showed a mycelial initiation time of 34 days; primordia formation occurred after 17 days in an environment with appropriate light and low-temperature stimulation; and during the fruiting stage, a temperature of 25–28 °C and humidity above 90% were maintained, with mature fructification forming after 16 days. This study provides fundamental experimental data for the subsequent development and utilization of T. kmetii. Full article

The lateral root (LR) is an essential component of the plant root system, performing important functions for nutrient and water uptake in plants and playing a pivotal role in cereal crop productivity. Nitrate (NO₃⁻) is an essential nutrient for plants. In this study, wheat plants were grown in 1/2 strength Hoagland’s solution containing 5 mM NO₃⁻ (check; CK), 0.1 mM NO₃⁻ (low NO₃⁻; LN), or 0.1 mM NO₃⁻ plus 60 mg/L 2,3,5-triiodobenzoic acid (TIBA) (LNT). The results showed that LN increased the LR number significantly at 48 h after treatment compared with CK, while not increasing the root biomass, and LNT significantly decreased the LR number and root biomass. The transcriptomic analysis showed that LN induced the expression of genes related to root IAA synthesis and transport and cell wall remodeling, and it was suppressed in the LNT conditions. A physiological assay revealed that the LN conditions increased the activity of IAA biosynthesis-related enzymes, the concentrations of tryptophan and IAA, and the activity of cell wall remodeling enzymes in the roots, whereas the content of polysaccharides in the LRP cell wall was significantly decreased compared with the control. Fourier-transform infrared spectroscopy and atomic microscopy revealed that the content of cell wall polysaccharides decreased and the cell wall elasticity of LR primordia (LRP) increased under the LN conditions. The effects of LN on IAA synthesis and polar transport, cell wall remodeling, and LR development were abolished when TIBA was applied. Our findings indicate that NO₃⁻ starvation may improve auxin homeostasis and the biological properties of the LRP cell wall and thus promote LR initiation, while TIBA addition dampens the effects of LN on auxin signaling, gene expression, physiological processes, and the root architecture. Full article

Lateral roots (LRs) receive signals from the inter-root environment and absorb water and nutrients from the soil. Auxin regulates LR formation, but the mechanism in tomato remains largely unknown. In this study, ‘Ailsa Craig‘ tomato LRs appeared on the third day and were unevenly distributed in primary roots. According to the location of LR occurrence, roots were divided into three equal parts: the shootward part of the root (RB), the middle part of the root (RM), and the tip part of the root (RT). Transverse sections of roots from days 1 to 6 revealed that the number of RB cells and the root diameter were significantly increased compared with RM and RT. Using roots from days 1 to 3, we carried out transcriptome sequencing analysis. Identified genes were classified into 16 co-expression clusters based on K-means, and genes in four associated clusters were highly expressed in RB. These four clusters (3, 5, 8, and 16) were enriched in cellulose metabolism, microtubule, and peptide metabolism pathways, all closely related to LR development. The four clusters contain numerous transcription factors linked to LR development including transcription factors of LATERAL ORGAN BOUNDRIES (LOB) and MADS-box families. Additionally, auxin-related genes GATA23, ARF7, LBD16, EXP, IAA4, IAA7, PIN1, PIN2, YUC3, and YUC4 were highly expressed in RB tissue. Free IAA content in 3 d RB was notably higher, reaching 3.3–5.5 ng/g, relative to RB in 1 d and 2 d. The LR number was promoted by 0.1 μM of exogenous IAA and inhibited by exogenous NPA. We analyzed the root cell state and auxin signaling module during LR formation. At a certain stage of pericycle cell development, LR initiation is regulated by auxin signaling modules IAA14-ARF7/ARF19-LBD16-CDKA1 and IAA14-ARF7/ARF19-MUS/MUL-XTR6/EXP. Furthermore, as a key regulatory factor, auxin regulates the process of LR initiation and LR primordia (LRP) through different auxin signaling pathway modules. Full article

Rice leaf morphology is a pivotal component of the ideal plant architecture, significantly impacting rice yield. The process of leaf development unfolds through three distinct stages: the initiation of leaf primordia, the establishment and maintenance of polarity, and leaf expansion. Genes regulating leaf morphology encompass transcription factors, hormones, and miRNAs. An in-depth synthesis and categorization of genes associated with leaf development, particularly those successfully cloned, hold paramount importance in unraveling the complexity of rice leaf development. Furthermore, it provides valuable insights into the potential for molecular-level manipulation of rice leaf types. This comprehensive review consolidates the stages of rice leaf development, the genes involved, molecular regulatory pathways, and the influence of plant hormones. Its objective is to establish a foundational understanding of the creation of ideal rice leaf forms and their practical application in molecular breeding. Full article

The architecture of the root system is fundamental to plant productivity. The rate of root growth, the density of lateral roots, and the spatial structure of lateral and adventitious roots determine the developmental plasticity of the root system in response to changes in environmental conditions. One of the genes involved in the regulation of the slope angle of lateral roots is DEEPER ROOTING 1 (DRO1). Its orthologs and paralogs have been identified in rice, Arabidopsis, and several other species. However, nothing is known about the formation of the slope angle of lateral roots in species with the initiation of lateral root primordia within the parental root meristem. To address this knowledge gap, we identified orthologs and paralogs of the DRO1 gene in cucumber (Cucumis sativus) using a phylogenetic analysis of IGT protein family members. Differences in the transcriptional response of CsDRO1, CsDRO1-LIKE1 (CsDRO1L1), and CsDRO1-LIKE2 (CsDRO1L2) to exogenous auxin were analyzed. The results showed that only CsDRO1L1 is auxin-responsive. An analysis of promoter–reporter fusions demonstrated that the CsDRO1, CsDRO1L1, and CsDRO1L2 genes were expressed in the meristem in cell files of the central cylinder, endodermis, and cortex; the three genes displayed different expression patterns in cucumber roots with only partial overlap. A knockout of individual CsDRO1, CsDRO1L1, and CsDRO1L2 genes was performed via CRISPR/Cas9 gene editing. Our study suggests that the knockout of individual genes does not affect the slope angle formation during lateral root primordia development in the cucumber parental root. Full article

Lepista sordida is a type of high-quality rare edible and medicinal mushroom, and its research boom is just beginning. More than 80 million tons of grain crop residues are produced each year in Heilongjiang Province. To realize the exploration and utilization of wild L. sordida mushrooms and also provide a theoretical support for the high-value utilization of these resources in Heilongjiang Province, we evaluated the cultivation of L. sordida mushrooms using rice straw, corncob, and soybean straw as substrates. L. sordida grew on all three substrates, and the biological efficiency and yield of the mushrooms grown on soybean straw and corncob were 32.33 ± 1.78% and 4.20 ± 0.23 kg m⁻², and 30.15 ± 0.93% and 3.92 ± 0.12 kg m⁻², respectively, which increased by 9.38% and 2.08% compared with that on the rice straw substrate with 3.84 ± 0.12 kg m⁻² and 29.56 ± 0.89%. The time it took for the mycelia to colonize and initiate primordia on the soybean straw substrate was 22.33 ± 0.58 d and 19.67 ± 0.58 d, respectively, which was delayed by 2 d and 3 d compared with that on the rice straw substrate with 20.67 ± 2.08 d and 16.33 ± 0.58 d, respectively. The fruiting bodies grown on corncob and soybean straw substrates were relatively larger than those on the rice straw substrate. The highest amount of crude protein was 57.38 ± 0.08 g 100 g⁻¹, and the lowest amount of crude polysaccharide was 6.03 ± 0.01 g 100 g⁻¹. They were observed on mushrooms collected from the corncob substrate. The contents of the heavy metal mercury, lead, arsenic, and cadmium in the fruiting bodies grown on each substrate were within the national safety range. Full article

Exogenous ethylene is commonly utilized to initiate flower induction in pineapple (Ananas comosus (L.) Merr.). However, the molecular mechanisms and metabolic changes involved are not well understood. In this study, we explored the genetic network and metabolic shifts in the ‘Comte de Paris’ pineapple variety during ethylene-induced flowering. This was achieved through an integrative analysis of metabolome and transcriptome profiles at vegetative shoot apexes (0 d after ethephon treatment named BL_0d), the stage of bract primordia (8 d after ethephon treatment named BL_8d), stage of flower primordia (18 d after ethephon treatment named BL_18d), and the stage of stopped floret differentiation (34 d after ethephon treatment named BL_34d). We isolated and identified 804 metabolites in the pineapple shoot apex and inflorescence, categorized into 24 classes. Notably, 29, 31, and 46 metabolites showed significant changes from BL_0d to BL_8d, BL_8d to BL_18d, and BL_18d to BL_34d, respectively. A marked decrease in indole was observed, suggesting its role as a characteristic metabolite during flower induction. Transcriptomic analysis revealed 956, 1768, and 4483 differentially expressed genes (DEGs) for BL_0d vs. BL_8d, BL_8d vs. BL_18d, and BL_18d vs. BL_34d, respectively. These DEGs were significantly enriched in carbohydrate metabolism and hormone signaling pathways, indicating their potential involvement in flower induction. Integrating metabolomic and transcriptomic data, we identified several candidate genes, such as Agamous-Like9 (AGL9), Ethylene Insensitive 3-like (ETIL3), Apetala2 (AP2), AP2-like ethylene-responsive transcription factor ANT (ANT), and Sucrose synthase 2 (SS2), that play potentially crucial roles in ethylene-induced flower induction in pineapple. We also established a regulatory network for pineapple flower induction, correlating metabolites and DEGs, based on the Arabidopsis thaliana pathway as a reference. Overall, our findings offer a deeper understanding of the metabolomic and molecular mechanisms driving pineapple flowering. Full article

Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants. Full article

Mudanjiang is a major producer of black wood ear (Auricularia heimuer) mushrooms in China. It has been estimated that more than 1.5 million tons of spent substrates of A. heimuer (SSA) are produced each year. Most of these are discarded or burned and have become an important source of pollution, which urgently merits research to find appropriate uses for them. To explore the feasibility of SSA as a substrate for cultivating Lepista sordida mushrooms, experiments were conducted to assess the effects of the addition of 0, 40%, 73%, and 98% SSA on the days required for the mycelia to fully colonize the substrate and initiate primordia, biological efficiency (BE), yield, and composition of the chemical biomass of the L. sordida fruiting bodies. The yield of fruiting bodies with 0, 40%, 73%, and 98% SSA supplementation for three flushes was 3.90 ± 0.74 kg m⁻², 4.06 ± 0.77 kg m⁻², 4.03 ± 0.62 kg m⁻², and 4.51 ± 0.65 kg m⁻², respectively. The addition of 98% SSA significantly delayed the number of days for the mycelia to fully colonize and form primordia by 6 and 3 d, respectively. This treatment also significantly increased the yield and BE by 15.64% compared with that of the control group. The crude polysaccharide content of 25.64 ± 0.38 g 100 g⁻¹ was higher in the samples grown on the 98% SSA substrate, which was shown to increase by 78.93% compared with that of the control substrate with 73% corn straw (14.33 ± 0.03 g 100 g⁻¹). The content of crude protein of 51.10 ± 0.08 g 100 g⁻¹ was higher in the samples grown on the 40% SSA substrate, which increased by 11.14% compared with the protein content of the control group. This study reveals that SSA would be a good substrate for the cultivation of L. sordida and is an efficient, promising, and cost-effective substrate additive that can improve the quality and yield of these mushrooms, while substantially reducing the problems of disposing of SSA. Full article