Biology subjects

Oliveira, L. S.

Publications and source records attributed to Oliveira, L. S..

6 recordsLinked to original sources

bioRxiv2026

COMPARATIVE GENOMIC ANALYSIS OF CORE AND ACCESSORY GENES IN RUST FUNGI REVEALS PATHOGENICITY-ASSOCIATED GENE FAMILIES IN Phakopsora pachyrhizi

Accessory genes are thought to contribute to fungal adaptation and pathogenicity by modulating host immunity, while core genes play crucial roles in maintaining fundamental biological processes. Rust fungi (order Pucciniales) are obligate biotrophic plant-pathogens and infect economically relevant crops. Here, we characterize core and accessory gene repertoires across rust fungi, with a particular focus on Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Across Pucciniales genomes, accessory genes represented the largest fraction of gene content ([~]44.6% on average), whereas core genes accounted for a smaller proportion ([~]18-35%). Notably, variations in accessory gene content among rust fungi are perhaps attributed to lineage-specific gene expansions and losses. Core gene content was positively correlated with total gene number across Pucciniales genomes, suggesting retention after gene duplication events, consistent with their essential biological functions. Among P. pachyrhizi genes expressed during soybean infection, core effectors were associated with cysteine-rich proteins, pectin-degrading enzymes, and SPFH/Band 7 family, while accessory effectors included phosphatidylethanolamine-binding proteins, trehalose phosphatases, and CFEM domain-containing proteins. The in-plant induced core and accessory genes in P. pachyrhizi also comprised multiple families of CAZymes (GH5/GH7 cellulases, CE5 cutinases, CE8 pectinesterases, CE4/GH18 chitin-modifying enzymes); proteases (aspartyl proteases, serine carboxypeptidases, alpha/beta hydrolases); transporters (amino acid permeases, ferric reductase-like transmembrane proteins, and OPT oligopeptide transporter), and transcription factors (bZIP, GATA zinc finger, STE-like, and homeobox KN). Our study highlights that core and accessory gene families have shaped P. pachyrhizi-soybean interactions, identifying promising targets for functional studies aimed at elucidating host-adaptation mechanisms in rust fungi.

genomics↗

bioRxiv2025

Absence of short-term axon initial segment plasticity in human, mouse, and rat cortical circuits

Maintaining neuronal output with respect to input in the physiological range relies on the ability of neurons to update their responsiveness to inputs dependent on changing activity levels. Termed homeostatic plasticity, the mechanisms that neurons employ to control their responsiveness are varied, and proposed to include structural changes to a key neuronal structure - the axon initial segment (AIS). As the site of action potential initiation, the AIS has been postulated to rapidly change its length in response to increased or decreased cellular and circuit activity. To date, AIS structural plasticity has only been tested in tissue cultures and rodent models. In our current study, we assess the ability of neurons to alter their AIS length over a variety of timescales in ex vivo rodent and human brain slices, human neurons derived from induced pluripotent stem cells, and in mice dark-reared during early life; using a combination of electrophysiology and immunohistochemistry. We find no evidence for changes to AIS length following depolarisation for up to 3 hours, despite positive controls confirming modulated activity. However, we do find that neuronal physiological properties are altered by changes in activity - but these are largely independent of action potential initiation associated with the AIS. In summary, we find no evidence supporting a role for AIS structural plasticity in mouse, rat, or human cortical neurons.

neuroscience↗

bioRxiv2025

Phylogenetic and population genetic analyses reveal patterns of divergence among isolates in the Ceratocystis manginecans complex

The taxonomic boundaries within the Ceratocystis manginecans complex have remained contentious due to limited morphological variation, interfertility in laboratory mating studies, and the application of different species concepts. However, recent studies have highlighted significant differences among isolates, such as host associations and biological traits, all with important implications for disease management. We examined the phylogenetic relationships, genetic diversity, and population structure of isolates treated broadly in the Ceratocystis manginecans complex, specifically those treated as C. eucalypticola and C. manginecans in various studies. This study included a comprehensive dataset of isolates from multiple hosts and regions, including both historical and recent outbreaks of Ceratocystis canker and wilt disease. Detailed morphological comparisons for representative isolates residing in discrete clades were conducted. Phylogenetic analyses of sequence data for seven gene regions, supported by multilocus genotyping of 16 SSR loci, identified two genetically distinct groups that broadly separated isolates having distinct ecological characteristics, the most relevant of which are infections primarily of roots or above ground tree parts. Morphological comparisons also provided support for the two groupings. Although the results supported the existence of two groups in the C. manginecans complex, there was also evidence of hybridization between isolates in the respective groups suggesting incomplete reproductive isolation, leading to taxonomic ambiguity. Isolates in the two groups are, therefore, treated as distinct lineages within the C. manginecans complex, recognizing their divergence while maintaining a conservative taxonomic approach.

evolutionary biology↗

bioRxiv2024

Generative Approaches for Nucleotide Sequences to Enhance Non-coding RNA Classification

Classifying non-coding RNA (ncRNA) sequences, particularly mirtrons, is essential for elucidating gene regulation mechanisms. However, the prevalent class imbalance in ncRNA datasets presents significant challenges, often resulting in overfitting and diminished generalization in machine learning models. In this study, GENerative Approaches for NUcleotide Sequences (GENNUS) is proposed, introducing novel data augmentation strategies using Generative Adversarial Networks (GANs) and Synthetic Minority Over-sampling Technique (SMOTE) to enhance ncRNA classification performance. Our GAN-based methods effectively generate high-quality synthetic data that capture the intricate patterns and diversity of real mirtron sequences, eliminating the need for extensive feature engineering. Through four experiments, it is demonstrated that models trained on a combination of real and GAN-generated data improve classification accuracy compared to traditional SMOTE techniques or only with real data. Our findings reveal that GANs enhance model performance and provide a richer representation of minority classes, thus improving generalization capabilities across various machine learning frameworks. This work highlights the transformative potential of synthetic data generation in addressing data limitations in genomics, offering a pathway for more effective and scalable ncRNA classification methodologies.

bioinformatics↗

bioRxiv2022

The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes

Asian soybean rust, caused by Phakopsora pachyrhizi, is one of the worlds most economically damaging agricultural diseases. Despite P. pachyrhizis impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizis genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.

microbiology↗

bioRxiv2022

Impact of sequencing technologies on long non-coding RNA computational identification

The correct annotation of non-coding RNAs, especially long non-coding RNAs (lncRNAs), is still an important critial challenge in genome analyses. One crucial issue in lncRNA transcript annotation is the transcriptome resource that supports lncRNA loci. Long-read technologies now bring the potential to improve the quality of transcriptome annotation. Consequently, long non-coding RNAs (lncRNA) are probably the most benefited class of transcripts that would have improved annotation using this novel technology. However, there is a gap regarding benchmarking studies that highlighted if the direct use of lncRNA predictors in long-reads makes more precise identification of these transcripts. Considering that these lncRNA tools were not trained with these reads, we want to address: how is the performance of these tools? Are they also able to efficiently identify lncRNAs? We could provide evidence of where and how to make potential better approaches for the lncRNA annotation by understanding these issues. Keywords: Non-coding RNAs, high-throughput sequencing technologies, coding, methods, benchmarking, tools, NGS, transcripts

bioinformatics↗