Biology subjects

Venancio, T. M.

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

35 records · Page 2Linked to original sources

bioRxiv2021

Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

Soybean is one of the major sources of edible protein and oil. Oil content is a quantitative trait that is significantly determined by genetic and environmental factors. Over the past 30 years, a large volume of soybean genetic, genomic, and transcriptomic data have been accumulated. Nevertheless, integrative analyses of such data remain scarce, in spite of their importance for crop improvement. We hypothesized that the co-occurrence of genomic regions for oil-related traits in different studies may reveal more stable regions encompassing important genetic determinants of oil content and quality in soybean. We integrated publicly available data, obtained with distinct techniques, to discover and prioritize candidate genes involved in oil biosynthesis and regulation in soybean. We detected key fatty acid biosynthesis genes (e.g., BCCP and ACCase, FADs, KAS family proteins) and several transcripton factors, which are likely regulators of oil biosynthesis. In addition, we identified new candidates for seed oil accumulation and quality, such as Glyma.03G213300 and Glyma.19G160700, which encode a translocator protein and a histone acetyltransferase, respectively. Further, oil and protein genomic hotspots are strongly associated with breeding and not with domestication, suggesting that soybean domestication prioritized other traits. The genes identified here are promising targets for breeding programs and for the development of soybean lines with increased oil content and quality.

plant biology↗

bioRxiv2021

cageminer: an R/Bioconductor package to prioritize candidate genes by integrating GWAS and gene coexpression networks

SummaryAlthough genome-wide association studies (GWAS) identify variants associated with traits of interest, they often fail in identifying causative genes underlying a given phenotype. Integrating GWAS and gene coexpression networks can help prioritize high-confidence candidate genes, as the expression profiles of trait-associated genes can be used to mine novel candidates. Here, we present cageminer, the first R package to prioritize candidate genes through the integration of GWAS and coexpression networks. Genes are considered high-confidence candidates if they pass all three filtering criteria implemented in cageminer, namely physical proximity to SNPs, coexpression with known trait-associated genes, and significant changes in expression levels in conditions of interest. Prioritized candidates can also be scored and ranked to select targets for experimental validation. By applying cageminer to a real data set, we demonstrate that it can effectively prioritize candidates, leading to >99% reductions in candidate gene lists. Availability and implementationThe package is available at Bioconductor (http://bioconductor.org/packages/cageminer).

bioinformatics↗

bioRxiv2021

Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus

Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter, as well as root dry matter, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.

microbiology↗

bioRxiv2021

BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction

SummaryCurrently, standard network analysis workflows rely on many different packages, often requiring users to have a solid statistics and programming background. Here, we present BioNERO, an R package that aims to integrate all aspects of network analysis workflows, including expression data preprocessing, gene coexpression and regulatory network inference, functional analyses, and intra and interspecies network comparisons. The state-of-the-art methods implemented in BioNERO ensure that users can perform all analyses with a single package in a simple pipeline, without needing to learn a myriad of package-specific syntaxes. BioNERO offers a user-friendly framework that can be easily incorporated in systems biology pipelines. Availability and implementationThe package is available at Bioconductor (http://bioconductor.org/packages/BioNERO).

bioinformatics↗

bioRxiv2021

Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses

Plant pathogenesis-related (PR) proteins are a large group of proteins, classified in 17 families, that are induced by pathological conditions. Here, we characterized the soybean PR-1 (GmPR-1) gene repertoire at the sequence, structural and expression levels. We found 24 GmPR-1 genes, clustered in two phylogenetic groups. GmPR-1 genes are under strong purifying selection, particularly those that emerged by tandem duplications. GmPR-1 promoter regions are abundant in cis-regulatory elements associated with major stress-related transcription factor families, namely WRKY, ERF, HD-Zip, C2H2, NAC, and GATA. We observed that 23 GmPR-1 genes are induced by stress conditions or exclusively expressed upon stress. We explored 1972 transcriptome samples, including 26 stress conditions, revealing that most GmPR-1 genes are differentially expressed in a plethora of biotic and abiotic stresses. Our findings highlight stress-responsive GmPR-1 genes with potential biotechnological applications, such as the development of transgenic lines with increased resistance to biotic and abiotic stresses.

plant biology↗

bioRxiv2020

Phylogenetic and population structure analyses uncover pervasive misclassification and help assessing the biosafety of Pseudomonas putida for biotechnological applications

The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and safety for environmental applications.

microbiology↗

bioRxiv2020

Exploring the complexity of soybean (Glycine max) transcriptional regulation using global gene co-expression networks

Soybean (Glycine max (L.) Merr.) is one of the most important crops worldwide, constituting a major source of protein and edible oil. Gene co-expression networks (GCN) have been extensively used to study transcriptional regulation and evolution of genes and genomes. Here, we report a soybean GCN using 1,284 publicly available RNA-Seq samples from 15 distinct tissues. We found modules that are differentially regulated in specific tissues, comprising processes such as photosynthesis, gluconeogenesis, lignin metabolism, and response to biotic stress. We identified transcription factors among intramodular hubs, which probably integrate different pathways and shape the transcriptional landscape in different conditions. The top hubs for each module tend to encode proteins with critical roles, such as succinate dehydrogenase and RNA polymerase subunits. Importantly, gene essentiality was strongly correlated with degree centrality and essential hubs enriched in genes involved in nucleic acids metabolism and regulation of cell replication. By using a using a guilt-by-association approach, we predicted functions for 93 of 106 hubs without functional description in soybean. Most of the duplicated genes had different transcriptional profiles, supporting their functional divergence, although paralogs originating from whole-genome duplications (WGD) are more often preserved in the same module than those from other mechanisms. Together, our results highlight the importance of GCN analysis in unraveling key functional aspects of the soybean genome, in particular those associated with hub genes and WGD events.

plant biology↗

bioRxiv2019

Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past five years generated an enormous amount of RNA-seq data, encompassing various tissues, developmental conditions, and genotypes. In this study, we have collected data from 1,298 publicly available soybean transcriptome samples, processed the raw sequencing reads, and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52,737/56,044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground, and seed/seed-related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1,349 genes showed heavily biased expression patterns towards particular tissues. A transcript-level analysis revealed that 95% (70,963/74,490) of the known transcripts overlap with those reported here, whereas 3,256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user-friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.

plant biology↗

bioRxiv2019

Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae)

Transcription factors (TF) are essential for proper plant growth and development. Several legumes, particularly soybean, are rich sources of protein and oil, with great impact in the economy of several countries. Here we report a phylogenomic analysis of major TF families in legumes and their potential association with important traits such as nitrogen fixation and seed development. We used TF DNA-binding domains to systematically screen the genomes of 15 legume and 5 non-legume species. The percentage of TFs ranged from 3-8% of the gene complements. TF orthologous groups (OG) in extant species were used to estimate OG sizes in ancestor nodes using a gene birth-death model, which allowed us to identify lineage-specific expansions. Together, OG analysis and rate of synonymous substitutions (Ks) between gene pairs show that major TF expansions are strongly associated with known whole-genome duplication (WGD) events in the legume ([~]58 mya) and Glycine ([~]13 mya) lineages, which account for a large fraction of the Ph. vulgaris and Gl. max TF repertoires. Out of the 3407 Gl. max TFs, 1808 and 676 can be traced back to a single homeolog in Ph. vulgaris and Vi vinifera, respectively. We found a trend for TFs expanded in legumes to be preferentially transcribed in roots and nodules, suggesting their recruitment early in the evolution of nodulation in the legume clade. We also found TF expansions in the Glycine WGD that were followed by gene loss in the wild soybean Gl. soja, including genes located within important quantitative trait loci. Together, our findings strongly support the roles of two WGDs in shaping the TF repertoires in the legume and Glycine lineages, which are likely related to important aspects of legume and soybean biology.

plant biology↗

bioRxiv2019

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies

Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. Here, we report the genome of a non-clinical E. bugandensis strain. We used this and other several publicly available E. bugandensis genomes to obtain the species pangenome, investigate the conservation of important genes, and elucidate general population structure features of the species. Core- and whole-genome multilocus sequence typing (cgMLST and wgMLST, respectively) allowed the detection of five E. bugandensis phylogroups (PG-A to E). We found important antimicrobial resistance and virulence determinants associated with specific PGs, notably PG-A and PG-E. IncFII was the most prevalent plasmid replicon type in this species. We uncovered several extended-spectrum {beta}-lactamases, including blaCTX-M-55 and blaNDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of blaNDM-5 revealed the resemblance of this plasmid with other IncX plasmids isolated from other bacteria from the same country. Further, three distinctive siderophore producing operons were found in the E. bugandensis pangenome: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). The latter operon is conserved in all PG-E isolates. Collectively, our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.

genomics↗

bioRxiv2019

Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes

Klebsiella aerogenes is an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens, K. aerogenes population structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidate K. aerogenes clonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure of K. aerogenes based on 97 publicly available genomes by using both, multilocus sequence typing and single nucleotide polymorphisms extracted from core genome. We also assessed virulence and resistance profiles using VFDB and CARD, respectively. We show that K. aerogenes has an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least ten CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow and extended spectrum {beta}-lactamases. Regarding the population structure, we identified two clusters based on virulence profile due to the presence of the toxin-encoding clb operon and the siderophore production genes, irp and ybt. Notably, CC3 comprises the majority of K. aerogenes isolates associated with hospital outbreaks, emphasizing the importance of its constant monitoring. Collectively, our results can be useful in the development of new therapeutic and surveillance strategies worldwide.

genomics↗

bioRxiv2018

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor

Gibberellins (GA) are key positive regulators of seed germination. Although the GA effects on seed germination have been studied in a number of species, little is known about the transcriptional reprogramming modulated by GA during this phase in species other than Arabidopsis thaliana. Here we report the transcriptome analysis of soybean embryonic axes during germination in the presence of paclobutrazol (PBZ), a GA biosynthesis inhibitor. We found a number of differentially expressed cell wall metabolism genes, supporting their roles in cell expansion during germination. Several genes involved in the biosynthesis and signaling of other phytohormones were also modulated, indicating an intensive hormonal crosstalk at the embryonic axis. We have also found 26 photosynthesis genes that are up-regulated by PBZ at 24 hours of imbibition (HAI) and down-regulated at 36 HAI, which led us to suggest that this is part of a strategy to implement an autotrophic growth program in the absence of GA-driven mobilization of reserves. Finally, 30 transcription factors (mostly from the MYB, bHLH and bZIP families) that are down-regulated by PBZ and are likely downstream GA targets that will drive transcriptional changes during germination.

plant biology↗

bioRxiv2018

Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a Gram-negative species found in a wide range of environments, including soil. Here we describe the genome sequencing and assessment of plant-growth promoting abilities of S. marcescens UENF-22GI (SMU), a strain isolated from mature cattle manure vermicompost. In vitro, SMU is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with SMU remarkably increased seedling growth and biomass under greenhouse conditions. The SMU genome has 5 Mb, assembled in 17 scaffolds comprising 4,662 genes (4,528 are protein-coding). No plasmids were identified. SMU is phylogenetically placed within a clade comprised almost exclusively of environmental strains. We were able to find the genes and operons that are likely responsible for all the interesting plant-growth promoting features that were experimentally described. Genes involved other interesting properties that were not experimentally tested (e.g. tolerance against metal contamination) were also identified. The SMU genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to the SMU competitiveness against other bacteria. Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for Agriculture.

microbiology↗

bioRxiv2017

Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) in land plants

Gibberellic acid (gibberellins, GA) controls key developmental processes in the life-cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 52 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots, which provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (typically with low GA levels). Taken together, our results support that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by specific mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.

plant biology↗

bioRxiv2017

A Duplication Lost In Sugarcane Hybrids Revealed By Chloroplast Genome Assembly Of Wild Species Saccharum officinarum

Sugarcane is a crop of paramount importance for sustainable energy. Modern sugarcane cultivars are derived from interspecific crosses between the two wild species Saccharum officinarum and Saccharum spontaneum and this event occurred very early in the sugarcane domestication history. This hybridization allowed the generation of cultivars with complex aneuploidy genomes containing 100-130 chromosomes that are unequally inherited - ~80% from S. officinarum, ~10% from S. spontaneum and ~10% from inter-specific crosses. Several studies have highlighted the importance of chloroplast genomes (cpDNA) to investigate hybridization events in plant lineages. Few sugarcane cpDNAs have been assembled and published, including those from sugarcane hybrids. However, cpDNAs of wild Saccharum species remains unexplored. In the present study, we used whole-genome sequencing data to survey the chloroplast genome of the wild sugarcane species S. officinarum. Illumina sequencing technology was used for assembly 142,234 bp of S.officinarum cpDNA with 2,065,893 reads and 1043x of coverage. The analysis of the S. officinarum cpDNA revealed a notable difference in the LSC region of wild and cultivated sugarcanes. Chloroplasts of sugarcane cultivars showed a loss of a duplicated fragment with 1,031 bp in the beginning of the LSC region, which decreased the chloroplast gene content in hybrids. Based on these results, we propose the comparative analysis of organelle genomes as a very important tool for deciphering and understanding hybrid Saccharum lineages.

genomics↗

bioRxiv2017

De novo transcriptome sequencing and comparative analysis of midgut tissues of four non-model insects pertaining to Hemiptera, Coleoptera, Diptera and Lepidoptera

Despite the great morphological diversity of insects, there is a regularity in their digestive functions, which is apparently related to their physiology. In the present work we report the de novo midgut transcriptomes of four non-model insects from four distinct orders: Spodoptera frugiperda (Lepidoptera), Musca domestica (Diptera), Tenebrio molitor (Coleoptera) and Dysdercus peruvianus (Hemiptera). We employed a computational strategy to merge assemblies obtained with two different algorithms, which substantially increased the quality of the final transcriptomes. Unigenes were annotated and analyzed using the eggNOG database, which allowed us to assign some level of functional and evolutionary information to 79.7% to 93.1% of the transcriptomes. We found interesting transcriptional patterns, such as: i) the intense use of lysozymes in digestive functions of M. domestica larvae, which are streamlined and adapted to feed on bacteria; ii) the up-regulation of orthologous UDP-glycosyl transferase and cytochrome P450 genes in the whole midguts different species, supporting the presence of an ancient defense frontline to counter xenobiotics; iii) evidence supporting roles for juvenile hormone binding proteins in the midgut physiology, probably as a way to activate genes that help fight anti-nutritional substances (e.g. protease inhibitors). The results presented here shed light on the digestive and structural properties of the digestive systems of these distantly related species. Furthermore, the produced datasets will also be useful for scientists studying these insects.

genomics↗

bioRxiv2017

Evolution And Multiple Roles Of The Pancrustacea Specific Transcription Factor zelda In Insects

Gene regulatory networks (GRN) evolve as a result of the coevolutionary process acting on transcription factors and the cis-regulatory modules (CRMs) they bind. The zinc-finger transcription factor (TF) zelda (zld) is essential for maternal zygotic transition (MZT) in Drosophila melanogaster, where it directly binds over thousand CRMs to regulate chromatin accessibility. D. melanogaster displays a long germ type of embryonic development, where all segments are simultaneously generated along the whole egg. However, it remains unclear if zld is also involved in MZT of short-germ insects (including those from basal lineages) or in other biological processes. Here we show that zld is an innovation of the Pancrustacea lineage, being absent in more distant arthropods (e.g. chelicerates) and other organisms. To better understand zlds ancestral function, we thoroughly investigated its roles in a short-germ beetle, Tribolium castaneum, using molecular biology and computational approaches. Our results demonstrate roles for zld not only during the MZT, but also in posterior segmentation and patterning of imaginal disc derived structures. Further, we also demonstrate that zld is critical for posterior segmentation in the hemipteran Rhodnius prolixus, indicating this function predates the origin of holometabolous insects and was subsequently lost in long-germ insects. Our results unveil new roles of zld in maintaining pluripotent state of progenitor cells at the posterior region and suggest that changes in expression of zld (and probably other pioneer TFs) are critical in the evolution of insect GRNs.

genetics↗