Biology subjects

Venancio, T. M.

Publications and source records attributed to Venancio, T. M..

At least 19 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

Integrative phylogenomic and pangenome landscape of Bacillus: insights from 10,000 genomes into taxonomy, functional potential, and biotechnological applications

The genus Bacillus comprises Gram-positive, endospore-forming rods with a ubiquitous distribution across terrestrial, aquatic, and aerial environments, as well as associations with plants, animals, and food. To explore its diversity, we conducted an integrated phylogenomic and pangenome analysis using 10,839 publicly available RefSeq genomes (67 type strain genomes). Taxonomic delimitation combining genomic-distance metrics (Mash/ANI), network analyses, and a label-propagation algorithm assigned 10,276 genomes to operational communities, revealing novel complexes within B. cereus sensu lato and other clades. A robust phylogeny reconstructed from 103 representative genomes corroborated the ANI-based groupings. Forty-eight communities ([≥]10 genomes) were further analyzed for pangenome openness, showing a strong negative correlation between the saturation coefficient () and genomic fluidity ({varphi}) ({rho} = -0.636), indicating that open pangenomes exhibit high gene-content variability. Functional profiling revealed 135 antifungal genes and 15 secondary metabolite clusters, highlighting B. velezensis, B. amyloliquefaciens, and B. subtilis as rich reservoirs of hydrolytic enzymes, NRPS/PKS systems, and nutrient-competition traits. Additionally, 135 resistance determinants and 115 virulence factors were identified, mainly within B. cereus sensu lato. Biofertilization genes related to phosphorus, nitrogen, siderophore, potassium, and sulfur metabolism were broadly conserved, underscoring the genus biotechnological potential.

microbiology↗

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

Genomic insights into the genus Pantoea: biotechnological potential and lifestyle diversity

Pantoea is a genus of Gram-negative bacteria isolated from diverse environments. Over time, it has drawn considerable attention for its potential to promote plant growth. However, its biotechnological application is complicated by high genomic plasticity, which underlies both its beneficial traits and its ability to cause disease in a wide range of plants, as well as occasional opportunistic infections in humans, raising biosafety concerns. In this study, we conducted a comparative genomic analysis of all publicly available Pantoea genomes. Our goals were to refine taxonomic classifications and to identify genes linked to biotechnological potential, virulence, and antibiotic resistance, thereby clarifying lifestyle strategies within the genus. We found that plant growth-promoting genes are widely conserved, particularly those involved in phosphate solubilization, phytohormone biosynthesis, and siderophore production. In contrast, traits such as nitrogen fixation and ACC deaminase activity were restricted to specific species. The resistome analysis revealed intrinsic resistance mechanisms conserved across the genus, primarily involving diverse efflux pump families and {beta}-lactamases conferring resistance to cephalosporins. In parallel, the pan-GWAS highlighted lifestyle-defining genetic markers, including the hrp/hrc genes encoding type III secretion system components, pepM (phosphoenolpyruvate mutase) associated with the production of a phytotoxin, and ibeB, an invasin linked to clinical infections. Together, our findings underscore both the biotechnological potential of Pantoea and the importance of genetic markers for distinguishing beneficial from pathogenic lifestyles, supporting the safe application of selected strains in biotechnology.

microbiology↗

bioRxiv2025

Transcription-based dissection of floral identity and trichome biosynthesis pathways in Cannabis sativa L.

Cannabis sativa L. has a long history of medicinal and industrial use, with female flowers being the primary source of bioactive compounds such as cannabinoids and terpenoids, which are synthesized in glandular trichomes. Despite its importance, the genetic mechanisms governing flower development, sex determination, and the biosynthesis of these valuable secondary metabolites remain only partially understood. In this study, we conducted an in-depth transcriptomic and comparative genomic analysis to elucidate the molecular networks underlying these key traits. By integrating 117 RNA-Seq datasets and performing phylogenetic analyses across nine distinct C. sativa genomes, we identified 31 orthogroups of MADS-box transcription factors. Expression profiling of these genes revealed distinct sets of candidates associated with male and female flower identity, consistent with the established ABCDE model of floral development. Specifically, genes from the AP3, PI/GLO, and MIKCS clades showed preferential expression in male flowers, while genes from the AGL6, FLC-like, and Bsister clades were highly expressed in female flowers. Furthermore, our investigation into genes related to pollen development highlighted the significant role of sugar metabolism and transport in male fertility. Finally, our analysis of cannabinoid and terpenoid biosynthetic genes confirmed their pronounced expression in trichomes and highlighted a key distinction: while the upstream polyketide, MEV, and MEP pathways and the terpenoid pathway showed conserved expression across chemotypes, the cannabinoid pathway exhibited chemotype-specific expression profiles. Collectively, our findings provide a comprehensive molecular framework for understanding floral development and secondary metabolism in C. sativa, offering valuable targets for future functional studies and advanced breeding programs aimed at optimizing desirable agronomic and medicinal traits.

plant biology↗

bioRxiv2025

Investigating Cannabis sativa L. gene expression through housekeeping genes and gene coexpression networks

Cannabis sativa L. is a versatile crop with applications ranging from medicinal products to industrial materials. Despite growing interest in cannabis transcriptomics, comprehensive studies of gene expression in this species remain limited. Here, we explore cannabis transcriptomics through two complementary approaches: the identification and prioritization of housekeeping (HK) genes for qRT-PCR normalization and the construction of a genome-wide gene coexpression network (GCN) using publicly available RNA-Seq data. Based on expression stability criteria (i.e. log mean TPM [≥] 6, log variance < 0.3), we proposed the optimal HK genes and designed qRT-PCR primers for them. Primer specificity was verified in silico using the Jamaican Lion mother + Y genome. In parallel, to explore the non HK gene expression, we constructed a GCN comprising 32 coexpression modules, which was then analyzed for tissue-specific expression patterns, transcription factor (TF), and functional enrichment. Several modules were significantly correlated with cannabis tissues such as flowers and bast fibres and were linked to key processes, including photoperiod sensitivity, stress responses, and vegetative-to-reproductive phase transitions. Together, our results help understand the functions and maximize the use of HK genes in molecular biology and reveal coexpression modules that constitute critical genetic circuits underlying cannabis physiology.

plant biology↗

bioRxiv2025

Unravelling the role of epigenetic regulators during embryonic development of Rhipicephalus micropolus

Epigenetic modifications are long-lasting changes to the genome that influence a cells transcriptional potential, thereby altering its function. These modifications can trigger adaptive responses that impact protein expression and various cellular processes, including differentiation and growth. The primary epigenetic mechanisms identified to date include DNA and RNA methylation, histone modifications, and microRNA-mediated regulation of gene expression. The intricate crosstalk among these mechanisms makes epigenetics a compelling field for the development of novel control strategies, particularly through the use of epigenetic drugs targeting arthropod vectors such as ticks. In this study, we identified the Rhipicephalus microplus orthologs of canonical histone-modifying enzymes, along with components of the machinery responsible for m5C and 6mA-DNA, and m6A-RNA methylations. We further characterized their transcriptional profiles and enzymatic activities during embryonic development. To explore the functional consequences of epigenetic regulation in R. microplus, we evaluated the effects of various epigenetic inhibitors on the BME26 tick embryonic cell line. Molecular docking simulations were performed to predict the binding mode of these inhibitors to tick enzymes, followed by in vitro assessment of their effects on cell viability and morphology. Tick cells exposed to these inhibitors exhibited phenotypic and molecular alterations. Notably, we observed higher levels of DNA methylation in the mitochondrial genome compared to nuclear DNA. Inhibition of DNA methylation using 5-azacytidine (5-AZA) was associated with increased activity of the mitochondrial electron transport chain and ATP synthesis, but reduced cellular proliferation. Our findings highlight the importance of epigenetic regulation during tick embryogenesis and suggest that targeting these pathways may offer a novel and promising strategy for tick control. HighlightsO_LIR. microplus presents a complete set of epigenetic enzymes that modify histones, DNA and RNA C_LIO_LIEpigenetic regulation is highly dynamic, and functionally significant during R. microplus embryogenesis C_LIO_LIInhibition of DNA methylation leads to overactivation of the mitochondrial electron transport chain C_LI

molecular biology↗

bioRxiv2024

Multiomic analysis of genes related to oil traits in legumes provide insights into lipid metabolism and oil richness in soybean

Soybean (Glycine max) and common bean (Phaseolus vulgaris) diverged approximately 19 million years ago. While these species share a whole-genome duplication (WGD), the Glycine lineage experienced a second, independent WGD. Despite the significance of these WGDs, their impact on gene families related to oil-traits remains poorly understood. Here, we report an in-depth investigation of oil-related gene families in soybean, common bean, and twenty-eight other legume species. We adopted a systematic approach that included transcriptome and co-expression analysis, identification of orthologous groups, gene duplication modes and evolutionary rates, and family expansions and contractions. We curated a list of oil candidate genes and found that 91.5% of the families containing these genes expanded in soybean in comparison to common bean. Notably, we observed an expansion of triacylglycerol (TAG) biosynthesis ([~]3:1) and an erosion of TAG degradation ([~]1.4:1) families in soybean in comparison to common bean. In addition, TAG degradation genes were two-fold more expressed in common bean than in soybean, suggesting that oil degradation is also important for the sharply contrasting seed oil contents in these species. We found 17 transcription factor hub genes that are likely regulators of lipid metabolism. Finally, we inferred expanded and contracted families and correlated these patterns with oil content found in different legume species. In summary, our results do not only shed light on the evolution of oil metabolism genes in soybean, but also present multifactorial evidence supporting the prioritization of candidates for crop improvement.

plant biology↗

bioRxiv2024

Comparative metagenomic profiling of seed-borne microbiomes in a landrace and a hybrid maize variety

The plant seed-borne microbiome comprises microorganisms vertically inherited from the mother plant. This microbiome is often linked to early-life protection and seedling growth promotion. Here, we compare the seed-borne bacteriomes of a commercial hybrid and a landrace maize variety. The landrace variety displays a more diverse seed-borne microbiome, featuring a variety of taxa across samples. In contrast, the microbiome of the hybrid variety is less diverse and more uniform across samples. Although both microbiomes lack a functional nitrogen fixation apparatus, we found a remarkably distinct presence of genes associated with phytohormone production and phosphate solubilization, particularly in the landrace variety. In addition, we recovered 18 metagenome-assembled genomes (MAGs), including four from potentially novel species. Collectively, our results allow a better understanding of the contrasting diversity between maize varieties and open important perspectives for designing synthetic microbial communities for agroecosystems.

plant biology↗

bioRxiv2023

Relating Ecological Diversity to Genetic Discontinuity across Bacterial Species

Bacterial genetic discontinuity, representing abrupt breaks in genomic identity among species, is crucial for grasping microbial diversity and evolution. Advances in genomic sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring systematically the degree to which bacterial diversity exists as a continuum or is sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aimed to quantify the genetic discontinuity ({delta}) and investigate how this metric is related to ecology. We harnessed a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which varied depending on the taxa in question. By delving into pangenome characteristics, we uncovered a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes were associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detected key features that impact genetic discontinuity prediction. Our study enhances the understanding of bacterial genetic patterns and their ecological implications, offering insights into species boundaries for prokaryotes.

genomics↗

bioRxiv2023

The Soybean Expression Atlas v2: a comprehensive database of over 5000 RNA-seq samples

Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamic of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a 4-fold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.

plant biology↗

bioRxiv2022

Comparative genomics and phylogenomics of Campylobacter unveil potential novel species and provide insights into niche segregation

Campylobacter is a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies on Campylobacter generally focus on specific pathogenic species such as C. coli and C. jejuni. Currently, there are thousands of publicly available Campylobacter genomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all available Campylobacter genomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III of C. coli is in fact a novel species (referred here as Campylobacter spp12). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinct Campylobacter species. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics of Campylobacter species with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that the Campylobacter genus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.

microbiology↗

bioRxiv2022

Discovering and prioritizing candidate resistance genes against soybean pests by integrating GWAS and gene coexpression networks

Soybean is one of the most important legume crops worldwide. Soybean pests have considerable impact on crop yield. Here, we integrated publicly available genome-wide association studies and transcriptomic data to prioritize candidate resistance genes against the insects Aphis glycines and Spodoptera litura, and the nematode Heterodera glycines. We identified 171, 7, and 228 high-confidence candidate resistance genes against A. glycines, S. litura, and H. glycines, respectively. We found some overlap of candidate genes between insect species, but not between insects and H. glycines. Although 15% of the prioritized candidate genes encode proteins of unknown function, the vast majority of the candidates are related to plant immunity processes, such as transcriptional regulation, signaling, oxidative stress, recognition, and physical defense. Based on the number of resistance alleles, we selected the ten most promising accessions against each pest species in the soybean USDA germplasm. The most resistant accessions do not reach the maximum theoretical resistance potential, indicating that they might be further improved to increase resistance in breeding programs or through genetic engineering. Finally, the coexpression networks generated here are available in a user-friendly web application (https://soypestgcn.venanciogroup.uenf.br/) and an R/Shiny package (https://github.com/almeidasilvaf/SoyPestGCN) that serve as a public resource to explore soybean-pest interactions at the transcriptional level.

plant biology↗

bioRxiv2021

Zika virus infection drives epigenetic modulation of immunity by the histone acetyltransferase CBP of Aedes aegypti

Epigenetic mechanisms are responsible for a wide range of biological phenomena in insects, controlling embryonic development, growth, aging and nutrition. Despite this, the role of epigenetics in shaping insect-pathogen interactions has received little attention. Gene expression in eukaryotes is regulated by histone acetylation/deacetylation, an epigenetic process mediated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this study, we explored the role of the Aedes aegypti histone acetyltransferase CBP (AaCBP) after infection with Zika virus (ZIKV), focusing on the two main immune tissues, the midgut and fat body. We showed that the expression and activity of AaCBP could be positively modulated by blood meal and ZIKV infection. Nevertheless, Zika-infected mosquitoes that were silenced for AaCBP revealed a significant reduction in the acetylation of H3K27 (CBP target marker), followed by downmodulation of the expression of immune genes, higher titers of ZIKV and lower survival rates. Importantly, in Zika-infected mosquitoes that were treated with sodium butyrate, a histone deacetylase inhibitor, their capacity to fight virus infection was rescued. Our data point to a direct correlation among histone hyperacetylation by AaCBP, upregulation of antimicrobial peptide genes and increased survival of Zika-infected-A. aegypti. Author summaryPathogens have coevolved with mosquitoes to optimize transmission to hosts. As natural vectors, mosquitoes are permissive to and allow systemic and persistent arbovirus infection, which intriguingly does not result in dramatic pathological sequelae that affect their lifespan. In this regard, mosquitoes have evolved mechanisms to tolerate persistent infection and develop efficient antiviral strategies to restrict viral replication to nonpathogenic levels. There is a great deal of evidence supporting the implication of epigenetics in the modulation of the biological interaction between hosts and pathogens. This study reveals that Zika virus infection positively modulates the expression and activity of A. aegypti histone acetyltransferase CBP (AaCBP). This study shows that AaCBP plays a role in the activation of immune-responsive genes to limit Zika virus replication. This first description that Zika virus infection has epigenomic consequences in the regulation of A. aegypti immunity opens a new avenue for research on mosquito factors that can drive vector competence.

molecular biology↗

bioRxiv2021

Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens

Soybean is one of the most important legume crops worldwide. However, soybean yield is dramatically affected by fungal diseases, leading to economic losses of billions of dollars yearly. Here, we integrated publicly available genome-wide association studies and transcriptomic data to prioritize candidate genes associated with resistance to Cadophora gregata, Fusarium graminearum, Fusarium virguliforme, Macrophomina phaseolina, and Phakopsora pachyrhizi. We identified 188, 56, 11, 8, and 3 high-confidence candidates for resistance to F. virguliforme, F. graminearum, C. gregata, M. phaseolina and P. pachyrhizi, respectively. The prioritized candidate genes are highly conserved in the pangenome of cultivated soybeans and are heavily biased towards fungal species-specific defense response. The vast majority of the prioritized candidate resistance genes are related to plant immunity processes, such as recognition, signaling, oxidative stress, systemic acquired resistance, and physical defense. Based on the number of resistance alleles, we selected the five most resistant accessions against each fungal species in the soybean USDA germplasm. Interestingly, the most resistant accessions do not reach the maximum theoretical resistance potential. Hence, they can be further improved to increase resistance in breeding programs or through genetic engineering. Finally, the coexpression network generated here is available in a user-friendly web application (https://soyfungigcn.venanciogroup.uenf.br/) and an R/Shiny package (https://github.com/almeidasilvaf/SoyFungiGCN) that serve as a public resource to explore soybean-pathogenic fungi interactions at the transcriptional level.

plant biology↗

bioRxiv2021

Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification

The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, containing more than 254 species. Although type strains have been employed to estimate Pseudomonas diversity, they represent a small fraction of the genomic diversity at a genus level. We used 10,035 available Pseudomonas genomes, including 210 type strains, to build a genomic distance network to estimate the number of species through community identification. We identified taxonomic inconsistencies with several type strains and found that 25.65% of the Pseudomonas genomes deposited on Genbank are misclassified. The phylogenetic tree using single-copy genes from representative genomes in each species cluster in the distance network revealed at least 14 Pseudomonas groups, including P. alcaligenes group proposed here. We show that Pseudomonas is likely an admixture of different genera and should be further divided. This study provides an overview of Pseudomonas diversity from a network and phylogenomic perspective that may help reduce the propagation of mislabeled Pseudomonas genomes.

microbiology↗

bioRxiv2021

Genome sequencing of the vermicompost strain Stenotrophomonas maltophilia UENF-4GII and population structure analysis of the S. maltophilia Sm3 genogroup

The Stenotrophomonas maltophilia complex (Smc) is a cosmopolitan bacterial group that has been proposed an emergent multidrug-resistant pathogen. Taxonomic studies support the genomic heterogeneity of Smc, which comprises genogroups exhibiting a range of phenotypically distinct strains from different sources. Here, we report the genome sequencing and in-depth analysis of S. maltophilia UENF-4GII, isolated from vermicompost. This genome harbors a unique region encoding a penicillin-binding protein (pbpX) that was carried by a transposon, as well as horizontally-transferred genomic islands involved in anti-phage defense via DNA modification, and pili glycosylation. We also analyzed all available Smc genomes to investigate genes associated with resistance and virulence, niche occupation, and population structure. S. maltophilia UENF-4GII belongs to genogroup 3 (Sm3), which comprises three phylogenetic clusters (PC). Pan-GWAS analysis uncovered 471 environment-associated and 791 PC-associated genes, including antimicrobial resistance (e.g. blaL1 and blaR1) and virulence determinants (e.g. treS and katG) that provide insights on the resistance and virulence potential of Sm3 strains. Together, the results presented here provide the grounds for more detailed clinical and ecological investigations of S. maltophilia.

microbiology↗