Biology subjects

Monteiro-Vitorello, C. B.

Publications and source records attributed to Monteiro-Vitorello, C. B..

5 recordsLinked to original sources

bioRxiv2025

Germination-stage transcriptomics of the grapevine rust fungus Neophysopella tropicalis reveals protein effectors with plant immunity-suppressing activity

Germination of urediniospores represents a critical early stage in the life cycle of Neophysopella tropicalis, the causal agent of Asian grapevine leaf rust in Brazil. Rust fungi deploy diverse effector proteins to manipulate host immunity and establish infection. This study identified and functionally characterized secreted proteins expressed during early fungal development using RNA-seq analysis of in-vitro-germinated urediniospores. Effectorome analysis revealed 386 putative secreted proteins with hallmarks of fungal effectors, designated as N. tropicalis effector candidates (NtECs). Fifteen highly expressed NtECs were selected for expression profiling by RT-qPCR across infection stages. Fluorescence microscopy with WGA-FITC staining defined key phases of pathogenesis. Although identified during germination, seven NtECs showed elevated transcript accumulation during the penetration and early biotrophic phases, suggesting roles in host entry and establishment. To evaluate immune-suppressing activity, nine NtECs were delivered into Nicotiana benthamiana using the Type III Secretion System of Pseudomonas fluorescens EtHAn. Three effectors (NtEC-05, -09, and -10) strongly suppressed AvrB-triggered cell death, and three others (NtEC-11, -12, and -13) showed moderate suppression. This work provides the first characterization of N. tropicalis effectors, offering insights into rust pathogenesis and supporting future effector-informed strategies for grapevine resistance. HighlightThe grapevine rust fungus Neophysopella tropicalis deploys effectors whose expression aligns with early infection and immune suppression, revealing key virulence mechanisms and guiding effector-informed strategies for grapevine rust resistance.

pathology↗

bioRxiv2025

Soil Determines Microbial Functionality and Genotype Guides Endophytic Recruitment to Adaptability in Sugarcane Systems

Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-hour sprouted buds grown for 10 months, were analyzed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil-genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia, Leifsonia, and Mycobacterium), associated with nitrogen fixation, hormone production, and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas, Bacillus and Klebsiella) linked to nutrient acquisition and defense responses. Both genotypes exhibited enhanced expression of defense- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, including a potential "cry for help" mechanism in IACSP-5503, reflecting adaptation under nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.

genetics↗

bioRxiv2025

Integrative Multi-Omics Analysis Reveals Stress-Specific Molecular Architectures in Soybean under Drought and Rust Infection

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, represents a major constraint to soybean cultivation, with yield losses approaching 90% in the absence of effective control strategies. When coupled with the increasing incidence of drought driven by climate change, the co-occurrence of these biotic and abiotic pressures imposes a complex challenge for crop resilience. In this study, we explored the molecular responses of soybean (Glycine max) to concurrent water limitation and ASR infection through an integrative analysis of transcriptomic and metabolomic datasets. To capture both linear and conditional relationships among molecular features, we employed Weighted Gene Co-expression Network Analysis (WGCNA) alongside Copula Graphical Models (CGMs). WGCNA identified 17 gene co-expression modules exhibiting significant correlations with 27 annotated metabolites. Among these, abscisic acid showed consistent associations with drought-responsive modules enriched in central metabolic pathways and transcription factors such as Dof and bHLH. In contrast, modules linked to fungal infection were correlated with dipeptides and D-galacturonic acid, implicating early defense signaling and cell wall remodeling. The CGM framework further revealed sparse, condition-specific networks of differentially expressed genes and metabolites directly associated with each stressor, including genes encoding a dirigent-like protein, pentatricopeptide repeat proteins, and a nucleoredoxin, as well as metabolites such as inosine, Epi-dihydrophaseic acid and 2-oxoadipic acid. Notably, no gene or metabolite was found to be directly responsive to both stresses, underscoring the modular and stress-specific architecture of soybean defense. Together, these results highlight a hierarchical regulatory structure and demonstrate the value of combining correlation-based and dependency-driven models to identify candidate targets for multi-stress resilience breeding.

plant biology↗

bioRxiv2025

Updated chromosome-level genome assembly of Sporisorium scitamineum with improved accuracy and completeness

In 2015, we published the complete genome assembly of Sporisorium scitamineum, the fungal pathogen responsible for sugarcane smut disease, generated from PacBio long-read sequencing and polished with Illumina short reads. Since then, the tools for genome assembly have improved considerably, including advances in sequencing technologies and bioinformatics workflows, motivating us to revisit our original assembly. Here, we present an updated genome version, using newly generated high-quality Illumina short-read data and DeepVariant-based polishing, resulting in corrections at approximately 5,500 genomic positions. BUSCO benchmarking in protein mode demonstrated increased genome completeness from the original 94.2% to 99.3%, indicating substantial improvements in both accuracy and gene annotation reliability. Additionally, comparison with publicly available assemblies reveals that most sequence polymorphisms occur in isolates belonging to the Asian lineage, consistent with earlier population-level studies. This enhanced genome assembly provides a significantly improved reference resource, enabling more robust genetic, evolutionary, and functional studies of this economically important sugarcane pathogen.

bioinformatics↗

bioRxiv2025

Transcriptome Profiling of Resistance Genes Analogs in Soybean's Cross-Tolerance to Water Limitation and Rust Stress

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is the most destructive foliar disease of soybean, with yield losses up to 90%. With climate change intensifying drought and expanding disease incidence, it is critical to understand how combined abiotic and biotic stresses influence plant defense. We investigated the transcriptomic response of a susceptible soybean cultivar to ASR infection under normal and water-limited conditions at four infection stages (12, 24, 72, and 192 hours after-inoculation). We observed a biphasic expression of defense-related genes, particularly resistance gene analogs (RGAs), with an early peak at 12 hours and a late resurgence at 192 hours. Combined stress induced a greater number of differentially expressed genes (DEGs) than rust alone, especially at early infection. Among the differentially expressed RGAs (RGADEs), over 64% belonged to the TM-LRR class, and NBS-LRR genes were the most enriched at known ASR resistance loci, particularly Rpp2. Water limitation strongly modulated gene expression at late stages, revealing stress-specific transcriptional reprogramming. These findings reveal cross-tolerance mechanisms in soybean, highlight the temporal dynamics of RGADEs under dual stress, and provide targets for developing cultivars with improved resilience to both rust and water scarcity.

plant biology↗