Biology subjects

Quintanilha-Peixoto, G.

Publications and source records attributed to Quintanilha-Peixoto, G..

4 recordsLinked to original sources

bioRxiv2026

Gene loss dynamics and T3PKS conservation shape the evolution and pathogenicity of Rosellinia necatrix

Fungal pathogens exhibit remarkable genome plasticity, driven by polyploidy, genome duplication, transposable elements, and niche adaptation. Gene losses often occur in dispensable regions, including in the remarkably dynamic secondary metabolite gene clusters (SMGCs). Within the diverse family Xylariaceae, comprising endophytes, saprotrophs, and phytopathogens, the broad-spectrum pathogen Rosellinia necatrix is of major concern, causing white root rot in numerous crops worldwide. Its strategy involves the root infection of weakened plants, tissue colonization, and saprotrophic survival in soil; yet, the genetic basis of this versatility remains poorly understood. Herein, we applied comparative genomics across Xylariaceae to investigate the molecular determinants of R. necatrix pathogenicity. We uncovered widespread gene losses in R. necatrix, particularly in SMGCs, candidate effectors, and transporter families (MFS and ABC transporters), suggesting a streamlining of its metabolic repertoire during adaptation to diverse hosts. We also identified two highly conserved type III polyketide synthases (T3PKS) across the family, predicted to encode chalcone synthases. Structural modeling and docking analyses support their role in chalcone-related biosynthesis, pointing to an unexpected link between fungal metabolism and plant-associated compounds. Variation in SMGC and carbohydrate-active enzyme (CAZy) repertoires across Xylariaceae further suggests a hemibiotrophic potential for R. necatrix, reconciling its capacity for both latent colonization and aggressive necrosis. Our findings establish niche specificity as a key driver of genome reduction in R. necatrix and reveal conserved metabolic innovations across Xylariaceae. By integrating gene loss dynamics with secondary metabolism, this work provides new insights into fungal adaptation and pathogenicity, with implications for disease management in perennial and annual crops.

genomics↗

bioRxiv2025

Genomic plasticity of the Azospirillum genus in a biotechnological context

Extensive agriculture and the use of chemical fertilizers cause notable environmental impacts on multiple levels, from reducing soil microbiota diversity to groundwater contamination. In this context, the usage of plant growth-promoting bacteria (PGPB) presents a sustainable alternative to enhance crop production while mitigating these adverse effects. Azospirillum, a bacterial genus renowned for its beneficial capabilities, particularly phytohormone production, is a key component of many commercial inoculants. In this work, we performed a comparative genomic analysis of all publicly available Azospirillum genomes and four novel isolates belonging to our microbial collection. Our analysis identified a species complex within the genus, which we designate the A. brasilense species complex, comprising species already used in commercial bioconsortia. This complex is characterized by a core set of exclusive genes linked to chemotaxis and host-recognition capability. Furthermore, we also validated the biosafety of the A. brasilense species complex and confirmed the plant growth-promoting potential of our novel isolates, highlighting their suitability for developing new biofertilizers.

microbiology↗

bioRxiv2025

Uncovering the Molecular Regulation of Seed Development and Germination in Endangered Legume Paubrasilia echinata Through Proteomic and Polyamine Analyses

Understanding the molecular regulation of seed maturation and germination is essential for plant conservation and agricultural applications. Here, we provide novel insights into the proteomic and polyamine dynamics of seeds from Paubrasilia echinata, an endangered legume, at 4, 6, and 8 weeks after anthesis. Using a sequential protein extraction approach combined with a species-specific protein database, we identified over 2,000 proteins, uncovering key regulators of maturation, stress tolerance, and germination. Seeds that reached maturity at 6 weeks displayed a high accumulation of proteasome components, translation machinery, and stress-associated proteins, notably late embryogenesis abundant (LEA) and heat shock proteins (HSPs), underscoring their role in seed development. Polyamine profiling showed that high putrescine levels were associated with early development and reduced germination, while spermidine and spermine were correlated with maturation, tolerance to desiccation, and germination. The decreases in certain proteins and polyamines during the transition to germination reveal dynamic regulatory shifts essential for the establishment of seedlings. These molecular signatures reveal dynamic metabolic and regulatory changes that facilitate the transition from seed development to germination. These findings reveal previously uncharacterized mechanisms of seed maturation and early germination in P. echinata and provide information on seed biology, ex situ conservation, and propagation strategies for endangered legumes.

plant biology↗

bioRxiv2025

Gene family expansions and nodule-specific expression patterns reveal the recruitment of Beta-Glucosidases and Cytochrome P450 genes to nodulation in soybean

Nodulation is a symbiotic interaction between legumes and rhizobia that is essential for biological nitrogen fixation and regulated by complex gene networks, which are partially shaped by whole-genome duplication (WGD) events. Although many core nodulation genes have been identified, the contribution of lineage-specific gene expansions and WGD-derived duplicates remains poorly understood. In this study, we performed a genome-wide analysis of gene family expansions in legumes and integrated expression data from over 5,000 soybean RNA-Seq samples to identify genes involved in nodulation. Our analysis not only recovered well-characterized nodulation genes among the most expanded families but also revealed several differentially expressed genes in nodules, including nodulins, aspartic proteases, NLP proteins, and GRAS transcription factors. Notably, we identified previously unreported {beta}-glucosidase and cytochrome P450 genes with high nodule-specific expression, suggesting their involvement as novel components of the nodulation machinery.

plant biology↗