Biology subjects

Dias, H. M.

Publications and source records attributed to Dias, H. M..

8 recordsLinked to original sources

bioRxiv2025

Unmmaped RNA-Seq reads from inoculated sugarcane reveals long non-coding RNAs related to retrotransposons and suggest microbiome modulation

BackgroundTranscriptome studies have contributed to the understanding of protein coding and non-coding gene expression of several organisms. They also provide knowledge into host responses to pathogen infections. Not common yet is to detect transcripts from multiple interacting organisms present in a given sample. In addition, transcriptome studies with complex polyploid hybrid genomes and not completely sequenced, such as the one of sugarcane, remains a challenge. In such studies, a considerable set of reads may not align on any reference genome but still hold significant relevance to the study, allowing to gather information beyond the complex organism itself. ResultsA complete transcriptome analysis of sugarcane inoculated with a pathogen, with and without the addition of a beneficial bacteria, generated a subset of reads that did not map to their respective genome references. Here, we report a pipeline based on the assembly of a collection of unmapped reads that potentially interfere with the gene expression of the associated microbiome, as well as the identification of long non-coding RNAs related to transposable elements present in a host-pathogen interaction. In addition, the detection of transcripts of naturally occurring microorganisms in sugarcane allowed the identification of its microbiome at the species level. Further studies support changes in microorganism transcription levels according to the biotic stress the plant was conditioned. ConclusionA quick and practical pipeline is proposed to study unmapped reads to infer relevant information that would remain otherwise unnoticed. New sequences from hybrid sugarcane transcriptome, such as long non-coding genes related to known retrotransposons are described. Also, changes in microbiome gene expression provides insights to the microbiome alterations and bring knowledge to the sugarcane "pathobiome".

bioinformatics↗

bioRxiv2025

Influence of plant genotype on nodule microbiome composition and function in seasonal yellow pea varieties

Background and AimsLegume root nodules host symbiotic rhizobia essential for nitrogen fixation but also harbor diverse non-rhizobial taxa that remain poorly characterized. Yellow pea (Pisum sativum) cultivars adapted to distinct seasonal growth (spring and winter) offer an opportunity to explore whether host genotype influences nodule microbiome composition and function. This study investigates the taxonomic and functional profiles of nodule-associated microbial communities in seasonal yellow pea varieties. MethodsA field experiment with 6 field pea cultivars (spring and winter types) was conducted in South Dakota. Surface-sterilized root nodules were subjected to full-length 16S rRNA gene sequencing using Oxford Nanopore technology. Reads were quality filtered, organellar sequences removed, and taxonomic classification performed with the EMU pipeline. Microbial diversity, community structure, and core taxa were analyzed using R, with predicted functions inferred by FAPROTAX. ResultsThe nodule microbiome was dominated by Rhizobium, accounting for up to 98% of classified reads. After excluding Rhizobium, non-rhizobial diversity revealed a conserved core microbiome shared across cultivars, including cyanobacteria with potential phototrophic and diazotrophic traits. Minor seasonal differences were observed, with winter cultivars exhibiting higher evenness and specific associations. ConclusionYellow pea nodules harbor a stable, cyanobacteria-enriched core microbiome, largely consistent across seasonal cultivars. Season-specific microbial patterns suggest potential host-genotype influences, warranting further validation.

plant biology↗

bioRxiv2024

Bridging Genomic Gaps: The Pan-Grass Syntenic Gene Set in Grass Crop Evolution

Understanding orthologous and homeologous relationships among genes can inform our understanding of how evolution and artificial selection have shaped the genomes of related species to adapt to different niches and produce different phenotypes. High-confidence information on orthologous relationships can also increase the impact of the functional characterization in one species by ensuring this information is available to researchers studying orthologs in other species. The grasses are ecologically and economically critical plants, and many genes are conserved in syntenic blocks between species. Here we leverage that conserved gene order to create and describe the Pan-Grass Syntenic Gene Set (PGSGS), a curated database of orthologous and homeologous relationships among the genes of 17 grass species, including both major and orphan crops as well as wild grasses. As a demonstration of the utility of the PGSGS, the dynamics of chromosome structure and gene content changes after polypoidy in several grass lineages are analyzed. This dataset serves as a seminal foundation for improving our understanding of genome evolution subsequent to polyploidy, as well as encouraging and enabling integration of functional genetic and functional genomic information across the grasses, the original promise of the "grasses as a single genetic system" model. SIGNIFICANCE STATEMENTThe Pan-Grass Syntenic Gene Set (PGSGS) leverages our understanding of the genomic background of major grass species, including rice, maize, sorghum, wheat, barley, millet, and sugarcane. It represents a milestone for deciphering the genetic foundations of essential traits such as yield, disease resistance, and environmental adaptability - key factors contributing to agriculture and food security. Scrutinizing pan-syntenic genes unveils the intricate interplay of diverse gene acquisition and loss mechanisms, potentially speeding molecular breeding knowledge transference. The PGSGS emerges as a valuable resource for gene annotation, with implications for improving grass crops.

genomics↗

bioRxiv2024

The Genetic Puzzle of Multicopy Genes: Challenges and Troubleshooting

BackgroundStudies with multicopy genes impose challenges related to gene redundancy and sequence similarity among copies. Recent advances in molecular biology and genomics tools associated with dedicated databases facilitate their study. Thus, the present work emphasizes the need for rigorous methodologies and standardized approaches to interpret RT-qPCR results accurately. ResultsThe present work in Physcomitrium patens provides a comprehensive five-step protocol, using thiamine thiazole synthase (THI1) and sucrose 6-phosphate phosphohydrolase (S6PP) genes as proof of concept, to showcase a systematic workflow for studying multicopy genes. Beyond examining genes of interest, we highlight the critical role of choosing appropriate internal controls in the analytical process for accurately interpreting gene expression patterns. We emphasized the importance of identifying the most relevant orthologous gene, recognizing the inherent challenges in determining the most functional copy for subsequent studies. Our objective is to enhance comprehension of gene redundancy by dissecting multicopy genes genomic landscape and its characteristics. Furthermore, we address the decision-making process surrounding the quantification of expression levels of multicopy genes. ConclusionsThe study of multicopy genes discloses early events of functional adaptation. We emphasize the significance of multicopy genes in plant biology and provide a practical protocol for their study. Plant systems are strongly influenced by light/dark cycles, and the challenges inherent to this process are acknowledged. In conclusion, our comprehensive approach aims to advance the understanding of multicopy gene dynamics, offering practical methodologies and contributing valuable insights to the scientific community.

molecular biology↗

bioRxiv2023

Comprehensive analysis of the Aquaporin genes in Eucalyptus grandis suggests potential targets for drought stress tolerance

This study delves into the comprehensive analysis of AQP genes in Eucalyptus grandis, providing insights into their genomic abundance, diversification, expression patterns across tissues, and responses to drought stress. We identified 53 AQP genes in the Eucalyptus grandis genome, categorized into four subfamilies: AQP-NIP, AQP-SIP, AQP-PIP, and AQP-TIP. This abundance of AQP genes is a reflection of gene duplications, both tandem and whole-genome, which have shaped their expansion. The chromosomal distribution of these genes reveals their widespread presence across the genome, with some subfamilies exhibiting more tandem duplications, suggesting distinct roles and evolutionary pressures. Sequence analysis uncovered characteristic motifs specific to different AQP subfamilies, demonstrating the diversification of protein and targeting. The expression profiles of AQP genes in various tissues in both Arabidopsis thaliana and Eucalyptus grandis showcased variations, with root tissues showing higher expression levels. Notably, AQP-PIP genes consistently exhibited robust expression across tissues, highlighting their importance in maintaining water regulation within plants. Furthermore, the study investigated the response of AQP genes to drought stress and rehydration, revealing differential expression patterns. EgAQP-NIP and EgAQP-TIP genes were up-regulated during drought stress, emphasizing their role in osmotic equilibrium and water transport. Conversely, EgAQP-PIP genes showed down-regulation during drought stress but were up-regulated upon rehydration, indicating their involvement in water movement across cell membranes. Overall, this research contributes to our understanding of AQP genes in Eucalyptus grandis, shedding light on their genomic evolution, expression patterns, and responses to environmental challenges, particularly drought stress. This information can be valuable for future studies aimed at enhancing the drought resilience of woody perennial plants like Eucalyptus grandis.

plant biology↗

bioRxiv2023

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually necessitates access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast datasets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and crucial cofactor in primary metabolic pathways. We conducted a comprehensive search for THI1 information within public repositories with careful curation to achieve this. Our searches reveal an evolutionary trend of 702 THI1 homologs of Archaea and Eukarya, with a detailed focus on plants. The green lineage of these organisms preserved the THI4 protein domain throughout its diversification by incorporating the N-terminus and targeting chloroplasts. Furthermore, evolutionary pressures and lifestyle appear to be associated with retention of TPP-riboswitch sites and consequent dual post-transcriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even successive rounds of genome duplications. Additionally, we identified the diversification of cis-regulatory sites in plants with the conservation of biological processes associated with the initial stages of seed development and preservation of the transcriptional pattern during the diurnal cycle. Our data mining of 484 transcriptome datasets supports this finding and brings a new look at public repositories and evolutionary trends to THI1.

plant biology↗

bioRxiv2023

Comparative GWAS identifies a role for Mendel green pea gene in the nonphotochemical quenching kinetics of sorghum, maize, and arabidopsis

Photosynthetic organisms must cope with rapid fluctuations in light intensity. Nonphotochemical quenching (NPQ) enables the dissipation of excess light energy as heat under high light conditions, whereas its relaxation under low light maximizes photosynthetic productivity. We quantified variation in NPQ kinetics across a large sorghum (Sorghum bicolor) association panel in four environments, uncovering significant genetic control for NPQ. A genome-wide association study (GWAS) identified 20 unique regions in the sorghum genome associated with NPQ. We detected strong signals from the sorghum ortholog of Arabidopsis thaliana SUPPRESSOR OF VARIEGATION3 (SVR3) involved in plastid-nucleus signaling and tolerance to cold. By integrating GWAS results for NPQ across maize (Zea mays) and sorghum association panels, we identified a second gene, NON-YELLOWING 1 (NYE1), originally identified by Gregor Mendel in pea (Pisum sativum) and involved in the degradation of photosynthetic pigments in light-harvesting complexes, along with OUTER ENVELOPE PROTEIN 37 (OEP37), that encodes a transporter in chloroplast envelope. Analysis of nye1 insertion alleles in A. thaliana confirmed the effect of this gene on NPQ kinetics across monocots and eudicots. We extended our comparative genomics GWAS framework across the entire maize and sorghum genomes, identifying four additional loci involved in NPQ kinetics. These results provide a baseline for engineering crops with improved NPQ kinetics and increasing the accuracy and speed of candidate gene identification for GWAS in species with high linkage disequilibrium.

plant biology↗

bioRxiv2020

Evidence-based gene expression modulation correlates with transposable element knock-down

BackgroundTransposable elements (TEs) are major components of plant genomes. Despite being regarded as "junk DNA" at first, TEs play important roles for the organisms they are found in. The most obvious and easily recognizable effects caused by TEs result from their mobility, which can disrupt coding sequences or promoter regions. However, with the recent advances in transcriptomics, it is becoming increasingly evident that TEs can act as an additional layer of gene expression regulation through a number of processes, which can involve production of non-coding RNAs. Here, we describe how Tnt1, a stress-responsive LTR-retrotransposon, interferes with gene expression and modulate a number of developmental aspects in tobacco. ResultsThrough an RNAi approach, we generated tobacco (HP) lines knocked-down for Tnt1 expression. Quantitative RT-PCR experiments confirm that Tnt1 is downregulated in HP lines after ethylene exposure. A RNA-seq experiment was performed and through two independent bioinformatic approaches (with different stringencies) we found 932 and 97 differentially expressed genes in HP lines. A number of phenotypes were observed in such lines, namely lesion mimicry in leaves, underdevelopment of the root system, overproduction of root hairs and early loss of seed viability. Folding prediction of part of the Tnt1 mRNA reveals putative stem-loop secondary structures containing transcriptional regulation sequences, suggesting it could be a source of small RNAs. We also propose a model to explain the Tnt1 expression in both homeostatic and stress conditions, and how it could interact with stress-responsive genes. ConclusionsOur results are consistent that interferences with Tnt1 transcript levels correlate with transcriptomic and phenotypic changes, suggesting a functional role for this element during plant development and stress response.

molecular biology↗