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Toona ciliata var. pubescens, known as “Chinese mahogany”, has high commercial value and is classified as a level II priority protected wild plant in China. However, due to overexploitation and its poor natural regeneration capacity, natural T. ciliata var. pubescens forests show varying degrees of decline in habitat adaptability. Arbuscular mycorrhizal fungi (AMF) symbiosis presents a potential strategy to enhance its regeneration. In this study, T. ciliata var. pubescens seedlings were inoculated with Septoglomus viscosum, followed by RNA-Seq analysis to compare gene expression differences between AMF-inoculated (AMI) and non-mycorrhizal (NM) treatments three months post-inoculation. A total of 16,163 differentially expressed genes (DEGs) were upregulated by AMF colonization, constituting 96.46% of the total DEGs. Specifically, 14,420 DEGs were exclusively expressed in the AMI treatment, while 35 DEGs were completely silenced. Most of the upregulated DEGs were located on the cell membrane, nucleus, and cytoskeleton and functioned in protein binding, S-adenosylmethionine-dependent methyltransferase activity, and lipid binding during cellular/macromolecule/protein localization, intracellular/protein transport, the cell cycle, and signal transduction. Additionally, lots of key genes related to oxidative stress responses, nutrient transport, and small GTPase-mediated signal transduction were found to be upregulated. These results suggest that AMF inoculation may enhance root cell growth by activating genes involved in nutrient uptake, stress responses, signal transduction, and substance transportation. This study elucidates the molecular mechanisms underlying the growth promotion of T. ciliata var. pubescens through AMF symbiosis, laying a foundation for the future application of AMF in its natural forest regeneration.

Toona ciliata var. pubescens ( Toona in Meliaceae) ( Tc ) is listed as an endangered species, and there are natural regeneration obstacles due to its long-term excessive exploitation and utilization. Arbuscular mycorrhizal fungi (AMF) can produce beneficial effects for plant growth and natural regeneration. However, the characteristics of the AMF community in natural Tc forests are poorly understood. The Illumina PE250 high-throughput sequencing method was used to study the characteristics of the AMF community in the rhizosphere soil and roots associated with three dominant tree species ( Tc ; Padus buergeriana , Pb ; and Maesa japonica , Mj ) in a natural Tc forest in Guanshan National Natural Reserve, South Central China. The results found that Glomeraceae was the most abundant AMF family in the rhizosphere soil and roots. Moreover, the relative abundance of Archaeosporaceae in rhizosphere soil was significantly larger than that in the roots; in contrast, the relative abundance of Glomeraceae in rhizosphere soil was significantly lower than that in the roots ( p < 0.05). Regarding different tree species, the relative abundances of Acaulosporaceae and Geosiphonaceae were larger in Mj and Tc than in Pb . AMF operational taxonomic units (OTUs) were 1.30-, 1.43-, and 1.71-fold higher in the Tc , Pb , and Mj rhizosphere soil, respectively, than in the corresponding roots. Nevertheless, higher AMF community richness was found in the roots compared to that in the rhizosphere soil based on the Chao index. This finding indicated that AMF of a relatively high aggregation degree were in roots, and more AMF groups with relatively low abundance occurred in the rhizosphere soil, which correspondingly lowered the calculated richness index of the AMF community. A redundancy analysis showed that different soil chemical properties impacted variations in the AMF community characteristics differently. This study has great significance for the interpretation of AMF diversity survey and the application design of AMF in vegetation restoration.

The aspect can affect plant communities and soil physical and chemical properties through different microclimates. However, little is known about the effect of aspect on arbuscular mycorrhizal (AM) fungal diversity and community composition, although AM fungi are beneficial for plant nutrient absorption and natural restoration. In this study, AM fungal community and diversity distribution patterns in the rhizosphere soil and roots of seven widespread plants in a natural Toona ciliata var. pubescens (Tc) forest on the north-facing (NF) aspect and south-facing (SF) aspect were investigated using Illumina PE250 high-throughput sequencing in the Guanshan National Nature Reserve, Jiangxi Province, China. Our results exhibited that aspect did not affect AM fungal diversity but significantly affected AM fungal community structure and composition. Glomeraceae was the most common and abundant family in the Tc natural forest. The Glomeromycota sequence proportion of root AM fungal community was significantly larger on NF than on SF (p < 0.05). The relative abundance of Acaulosporaceae of root AM fungal community differed significantly with aspect, being greater on NF than on SF (p < 0.05). In addition, the number of Glomeromycota sequences was significantly larger on SF than on NF, while the number of OTUs and the relative abundance of unclassified fungi in rhizosphere soil in Tc showed the opposite trend (p < 0.05). The soil properties (organic matter, nitrogen, potassium, phosphorus, and pH) were significantly correlated with these changes. These findings indicate that the habitat of NF with low insolation, high soil moisture, and high nutrient content might promote the functional realization of AM fungi; the habitat of SF with high insolation, low soil moisture, and low soil nutrient content might be beneficial for the proliferation and preservation of AM fungal groups. This study provides important information on the ecological processes of AM fungal community construction and microbiological mechanisms in natural Tc forests.

Sequence-related amplified polymorphism (SRAP) markers were used to investigate the genetic diversity among 30 populations of Toona ciliata Roem. sampled from the species’ distribution area in China. To analyze the polymorphism in the SRAP profiles, 1505 primer pairs were screened and 24 selected. A total of 656 SRAP bands ranging from 100 to 1500 bp were acquired, of these 505 bands (77%) were polymorphic. The polymorphism information content (PIC) values ranged from 0.32 to 0.45, with an average of 0.41. An analysis of molecular variance (AMOVA) indicated that the most significant variation was attributable to differences among the populations and that variation within the populations was small. STRUCTURE analysis divided the 30 populations into two parts. The unweighted pair group method of arithmetic averages (UPGMA) clustering and principal coordinates analysis (PCoA) showed that the 30 populations could be classified into four types. The results demonstrate a clear geographical trend for T. ciliata in China and provide a theoretical basis for future breeding and conservation strategy of T. ciliata.

The study of plant species abundance distribution (SAD) in natural communities is of considerable importance to understand the processes and ecological rules of community assembly. With the distribution of tree, shrub and herb layers of eight natural communities of Toona ciliata as research targets, three different ecological niche models were used: broken stick model, overlapping niche model and niche preemption model, as well as three statistical models: log-series distribution model, log-normal distribution model and Weibull distribution model, to fit SAD of the different vegetation layers based on data collected. Goodness-of-fit was compared with Chi square test, Kolmogorov–Smirnov (K–S) test and Akaike Information Criterion (AIC). The results show: (1) based on the criteria of the lowest AIC value, Chi square value and K–S value with no significant difference ( p  > 0.05) between theoretic and observed SADs. The suitability and goodness-of-fit of the broken stick model was the best of three ecological niche models. The log-series distribution model did not accept the fitted results of most vegetation layers and had the lowest goodness-of-fit. The Weibull distribution model had the best goodness-of-fit for SADs. Overall, the statistical SADs performed better than the ecological ones. (2) T . ciliata was the dominant species in all the communities; species richness and diversity of herbs were the highest of the vegetation layers, while the diversities of the tree layers were slightly higher than the shrub layers; there were fewer common species and more rare species in the eight communities. The herb layers had the highest community evenness, followed by the shrub and the tree layers. Due to the complexity and habitat diversity of the different T . ciliata communities, comprehensive analyses of a variety of SADs and tests for optimal models together with management, are practical steps to enhance understanding of ecological processes and mechanisms of T . ciliata communities, to detect disturbances, and to facilitate biodiversity and species conservation.

Background Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata . To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata , the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives. Results (1)  T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other. Conclusions This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.

Background Before studying gene expression of different organisms, it is important to determine the best reference gene. At present, the most accurate method of detecting gene expression is quantitative real-time PCR (RT-qPCR). With this method, reference genes that are stable in different biological systems and under different conditions can be obtained. Toona ciliata Roem ( T. ciliata ). is a valuable and fast-growing timber specie. In this study, 20 reference genes were identified using RT-qPCR, as a primary prerequisite for future gene expression analysis. Four different methods, geNorm, NormFinder, BestKeeper, and RankAggreg were used to evaluate the expression stability of the 20 candidate reference genes in various tissues under different conditions. Results The experimental results showed that TUB-α was the most stably expressed reference gene across all samples and UBC17 was the most stable in leaves and young stems under Hypsipyla robusta ( H. robusta ) and methyl jasmonate (MeJA) treatments. In addition, PP2C59 and UBC5B were the best-performing genes in leaves under H. robusta treatment, while HIS1 and ACT7 were the best reference genes in young stems. The two best reference genes were 60S-18 and TUB-α after treatment at 4 °C. The expression of HIS6 and MUB1 was the most stable under PEG6000 treatment. The accuracy of the selected reference genes was verified using the transcription factor MYB3 ( TcMYB3) gene. Conclusions This is the first report to verify the best reference genes for normalizing gene expression in T. ciliata under different conditions, which will facilitate future elucidation of gene regulations in this species.

Toona ciliata and Toona sinensis, two economically important timber species in China, exhibit interspecific variation in floral traits that are related to mating systems. The MADS‐box genes play a crucial role in floral patterning of angiosperms. Here we identified 97 and 75 MADS‐box genes at the genome scale in T. ciliata and T. sinensis, respectively, which were classified into Type I and Type II groups. Genes within the same subfamily exhibited high homology and conserved motifs. Promoter analysis revealed cis‐acting elements related to growth, light response, hormone signaling, and stress response. Gene duplication was prevalent, with several genes undergoing multiple duplications. Most MADS‐box genes were under purifying selection between T. ciliata and T. sinensis, while eight orthologous genes in the AGL32, Mβ, MIKC*, AG/STK, and AP1/FUL subfamilies were under weakly positive selection. Transcriptomic analysis showed high gene expression in SEP, AP1/FUL, AG/STK, PI, and AP3 subfamilies, highlighting their roles in floral development. A significantly negative correlation occurred between the evolutionary rate (Ka/Ks $$ {K}_a/{K}_s $$ ) and gene expression level of MADS‐box genes, suggesting evolutionary constraints on highly expressed genes. TWAS (transcription‐wide association study) indicated that some MADS‐box genes were significantly associated with floral traits in T. sinensis. The overall findings provide insights into the roles of MADS‐box gene family in evolving interspecific divergence in floral development between T. ciliata and T. sinensis. Collinearity analysis of MADS‐box genes in T. ciliata var. ciliata, T. sinensis, and A. thaliana.

Toona ciliata and Toona sinensis belong to the Toona genus of the Meliaceae family and are important timber species in China. T. ciliata is an endangered species at level II due to overcutting and a low rate of natural regeneration. T. sinensis was cultivated as an economic and nutritious tree for more than 2000 years. The two species differ in flower and leaf morphological traits, reproductive systems, and range size of natural distribution. To reveal the potential molecular basis of these divergences, we examined the similarities and differences in their whole genome sequences. Results indicate that T. ciliata had a higher number of expanded gene families than T. sinensis. The whole genome duplication (WGD) occurred before their speciation. The long-terminal repeats (LTRs) insertion was earlier in the T. ciliata genome (3.2985 ± 2.5007 Mya) than in the T. sinensis genome (3.1516 ± 2.2097 Mya). Twenty-five gene families in the T. ciliata genome were detected to be under positive selection compared with background branches of ten different land species. The T. ciliata genome was highly collinear with the T. sinensis genome, but had low collinearity with the genomes of more distant species. These genomic and evolutionary divergences are potentially associated with the differences between T. ciliata and T. sinensis in terms of their reproductive systems and ecological adaptation.

Bipolaris oryzae is the causative agent of rice brown spot disease, leading to serious economic yield losses all over the world. The present study aims to manage brown spot disease on susceptible rice cultivar PR 124 using botanical extracts of three meliaceae species. In vitro screening of botanical extracts revealed the dose dependent response of botanical extracts, though maximum mycelial inhibition occurred at 50% concentration. Ethanolic extracts showed a better inhibition percentage when compared to the aqueous extracts. Azadirachta indica exhibited the highest antifungal ability, followed by Melia azedarach and Toona ciliata. A field experiment conducted during two consecutive years (2021–22) revealed that pre-treatment with promising doses of botanical extracts followed by challenge inoculation 48 h after a foliar spray led to a significant reduction in the severity index, incidence, mean spot count, AUDPC and r value of treated plants over control. A significant increase in yield parameters was also recorded with the foliar application of botanical extracts as compared to un-inoculated (C1) and inoculated (C2) plots. The number of filled grains, test weight, panicle weight and fertility also increased as compared to control plants. The stimulation of the defence system and the antioxidant potential (phenols and lignin) coincided with the induction of endurance in susceptible cultivars. The results demonstrate that defence enzymes like PAL, TAL, glucanase and chitinase are expressed during the activation of a defence response induced by botanical extracts. A. indica was most effective at managing the disease development followed by M. azedarach and T. ciliata. Findings from this research are important for producing a biocide that is safe for the environment and could result in the effective management of this disease.