Biology subjects

Batista, D.

Publications and source records attributed to Batista, D..

9 recordsLinked to original sources

bioRxiv2026

A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained production of Arabica coffee for over 150 years. Here, we present a pseudo-phased, chromosome-level genome resource for H. vastatrix, isolate Hv178a, to guide research into disease management. The Hv178a genome assembly is 665 and 638 Mbp for haplotype A and B respectively, localised to 18 chromosomes. We determined that the genomes are highly repetitive at [~]90%, with a GC content of [~]33%. We present the full annotation of 13,760 and 17,998 protein coding genes, and we predicted 452 and 496 effectors in haplotype A and B respectively. Depth-based comparisons with 11 additional H. vastatrix isolates revealed increased chromosome 17 (chr17) copy number in Hv178a. Validation with qPCR supports a chr17 trisomy in Hv178a absent from the ancestral lineage and potentially explaining the observed change in virulence.

genomics↗

bioRxiv2025

The globally dispersed sun-coral species is _Tubastraea coccinea_ (Cnidaria: Anthozoa)

Species of the genus Tubastraea (sun corals) have dispersed globally over recent decades, but morphological trait identification has led to taxonomic confusion, with multiple authors proposing conflicting species identifications due to high morphological plasticity and overlapping diagnostic traits. We combined global-scale molecular phylogenetics with chromosome-level genome assemblies to resolve this taxonomic issue. Using mitochondrial and nuclear markers from 287 specimens across five ocean regions, including type localities in Bora Bora (T. coccinea) and Galapagos (T. tagusensis), we reconstructed phylogenetic relationships and inferred demographic history through approximate Bayesian computation. We also generated high-quality, chromosome-level genome assemblies for three morphologically distinct morphotypes from the Brazilian coastline. Phylogenetic and species delimitation analyses revealed two well-supported clades: a small, geographically restricted T. tagusensis clade confined to the Galapagos Islands, and a large cosmopolitan clade containing all worldwide samples, including T. coccinea from its type locality. Chromosome-level genomic analyses confirmed that the three morpho-types represent a single species, sharing a triploid karyotype of 14 chromosomes with extensive synteny and gene-tree discordance consistent with incomplete lineage sorting. Dispersed-route analyses identified the Centralwestern Pacific as the ancestral source, with at least three independent, humanmediated colonization events establishing populations in the Southwestern Atlantic, Gulf of Mexico, and Western Pacific. However, preliminary analysis suggests a Galapagos (Southeastern Pacific) origin rather than Centralwestern Pacific for the T. tagusensis and T. coccinea cluster. Our results definitively establish Tubastraea coccinea as the cosmopolitan species responsible for global dissemination, while T. tagusensis is endemic to the Galapagos and not involved in the worldwide dis-persion.

genetics↗

bioRxiv2024

Simulated larvae dispersion of the invasive sun-coral (Tubastrea spp.) along Rio de Janeiro's coast: the role of submesoscale filaments on offshore transport and connectivity

The spread of invasive species in marine ecosystems is a growing global concern, particularly in regions with high economic and ecological importance. sun corals (Tubastraea spp.) are scleractinians native to the Pacific Ocean that have spread along most of the Brazilian coast. This exotic species initially established populations in Rio de Janeiro, reaching high levels of abundance. Although the ecological aspects and impacts caused by this organism have been studied in detail, the natural mechanisms that drive its dispersal have attracted little attention. In this research, we focus on the offshore transport of sun coral larvae between Cabo de Sao Tome and Ilha Grande Bay, RJ, investigating how submesoscale oceanographic features such as filaments, eddies and upwelling influence connectivity among different population. High-resolution numerical simulations were used to model the coastal dynamics, incorporating the influence of the Brazil Current, wind-driven circulation, and submesoscale structures. Larval dispersal was examined under different wind scenarios, including northeasterly winds that drive southward currents which enhance offshore transport via submesoscale filaments. Results show that submesoscale features, particularly filaments emerged from upwelling regions, play a significant role on sun coral larvae dispersion. These features act as pathways that connect larvae from coastal to offshore oil exploration areas, highlighting the importance of both natural and anthropogenic processes for the dissemination of this invasive species. This research provides critical insights into the ecological mechanisms governing the spread of invasive marine species, emphasizing the need for integrated coastal management strategies. Understanding how physical processes drive larval transport is essential for developing targeted control measures to mitigate the impact of invasive species like sun coral on native ecosystems and local economies. Furthermore, the study underscores the importance of monitoring both natural and anthropogenic influences on marine bioinvasions, particularly in regions with significant offshore industrial activities.

ecology↗

bioRxiv2023

Mitochondria Exhibit Changes in Morphology/Function to Support Increased Glutamate Release in TauP301L Neurons Prior to Reduction in Presynaptic Vesicle Release

We have shown that tauopathy models display early-stage hyperexcitability due to increased presynaptic glutamate release that is mediated by an increase in vesicular glutamate transporter-1 (VGlut1). This hyperexcitability increases energy demand which in turn would increase demand on mitochondria. It is unclear, however, how early-stage presynaptic changes in glutamate release are supported by or influence the function of mitochondria. Using Large Area Scanning Electron Microscopy (LA-SEM) and fluorescence microscopy, we demonstrate that mitochondrial changes in morphology, structure, and function in CA1/CA3 hippocampal neurons decrease resting mitochondrial membrane potential in P301L mice. However, P301L mitochondria maintain a high membrane potential during levels of high activity, suggesting that they can support increased energy demand during hyperexcitability. These activity-dependent differences in membrane potential can be rescued by inhibiting ATP-dependent VGlut1 vesicle refilling. This indicates that the increased VGlut1 per vesicle observed in P301L mice contributes to the differences in mitochondria membrane potential. Notably, the mitochondrial dysfunction in P301L mice occurs before any observable alterations in presynaptic release mechanics, suggesting these changes may represent early therapeutic targets. Finally, we propose a model of increased glutamate-mediated changes in mitochondrial morphology and function in P301L neurons that represents a potentially targetable pathway to reduce or arrest neurodegeneration.

neuroscience↗

bioRxiv2022

A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained the sustainable production of Arabica coffee for over 150 years. The ability of H. vastatrix to overcome resistance in coffee cultivars and evolve new races is inexplicable for a -pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between H. vastatrix and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for H. vastatrix that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for H. vastatrix strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization.

genomics↗

bioRxiv2020

The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions

Corals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some species like Tubastraea coccinea and T. tagusensis have been spreading very fast replacing the native ones which affect the local environment and decrease biodiversity of corals and other organisms associated with them. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for both conservation and management of invasive species. In this circumstance, it is expected that genome sequencing would provide powerful insights that could lead to better strategies for prevention, management, and control of this and other invasive species. Here, we present three genomes of Tubastraea spp. in one of the most comprehensive biological studies of corals, that includes flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The genome of T. tagusensis is organized in 23 chromosomes pairs and has 1.1 Gb, the T. coccinea genome is organized in 22 chromosome pairs and has 806 Mb, and the Tubastraea sp. genome is organized in 21 chromosome pairs and has 795 Mb. The hybrid assembly of T. tagusensis using short and long-reads has a N50 of 227,978 bp, 7,996 contigs and high completeness estimated as 91.6% of BUSCO complete genes, of T. coccinea has a N50 of 66,396 bp, 17,214 contigs and 88.1% of completeness, and of Tubastraea sp. has a N50 of 82,672 bp, 12,922 contigs and also 88.1% of completeness. We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. We provide evidence for exclusive Scleractinia and Tubastraea gene content related to adhesion and immunity. The Tubastraea spp. genomes are a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral genus, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of coral species, whether invasive or threatened.

evolutionary biology↗

bioRxiv2019

A non-mosaic humanized mouse model of Down syndrome, trisomy of the long arm of human chromosome 21 in mouse chromosome background

Down syndrome (DS) is a complex human condition, and animal models trisomic for human chromosome 21 (HSA21) genes or orthologs provide insights into better understanding and treating DS. However, HSA21 orthologs are distributed into three mouse chromosomes, preventing us from generating mouse models trisomy of a complete set of HSA21 orthologs. The only existing humanized mouse DS model, Tc1, carries a HSA21 with over 20% of protein coding genes (PCGs) disrupted. More importantly, due to the human centromere, Tc1 is mosaic (a mix of euploid and trisomic cells), which makes every mouse unique and compromises interpretation of results. Here, we used mouse artificial chromosome (MAC) technology to "clone" the 34 MB long arm of HSA21 (HSA21q). Through multiple steps of microcell-mediated chromosome transfer we created a new humanized DS mouse model, Tc(HSA21q;MAC)1Yakaz ("TcMAC21"). Constitutive EGFP expression from the transchromosome and fluorescent in situ hybridization validate that TcMAC21, containing a hybrid chromosome of HSA21q and mouse centromere, is not mosaic. Whole genome sequencing shows that TcMAC21 contains a nearly complete copy of HSA21q with 93% of intact PCGs, while RNA-seq and additional mRNA/protein expression analyses confirm that PCGs are transcribed and regulated. A battery of tests show that TcMAC21 recapitulates many DS phenotypes including morphological anomalies in heart, craniofacial skeleton and brain, pathologies at molecular and cellular level, and impairments in learning, memory and synaptic plasticity. TcMAC21 is the most complete mouse model of DS extant and has potential for supporting a wide range of basic and preclinical research. Significance StatementIn the last 25 years, mouse models of trisomy 21 have supported research into Down syndrome, from defining the basis for developmental effects up to support for clinical trials. However, existing models have significant shortfalls, especially for preclinical studies. These deficiencies include incomplete or inappropriate representation of trisomic genes, absence of an extra chromosome, and mosaicism. Using cutting edge technologies we produced a mouse artificial chromosome containing the entire 34Mb long arm of human chromosome 21 and, with assisted reproductive technologies, established it in the germ line of mice. This trisomic mouse manifests developmental and functional features of Down syndrome, including hippocampal-based learning and memory deficits. This is the most complete model of Down syndrome produced to date.

genetics↗

bioRxiv2019

The draft genome of the invasive coral Tubastraea sp.

Corals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some coral species have been spreading very fast, replacing native species and affecting local biodiversity. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for management of invasive species. Here, we present the first Tubastraea sp. genome in one of the most comprehensive biological studies of a coral, that includes morphology, flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The Tubastraea sp. genome is organized in 23 chromosome pairs and has 1.4 Gb making it the largest coral and Cnidaria genome sequenced to date. The hybrid assembly using short and long-reads has a N50 of 180,044 pb, 12,320 contigs and high completeness estimated as 91.6% of BUSCO complete genes. We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. Gene content was estimated as about 94,000, a high number that warrants deeper scrutiny. The Tubastraea sp. genome is a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral species, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of corals species, whether invasive or threatened.

genomics↗

bioRxiv2019

Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework

Transparent evaluations of FAIRness are increasingly required by a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers. We propose a scalable, automatable framework to evaluate digital resources that encompasses measurable indicators, open source tools, and participation guidelines, which come together to accommodate domain relevant community-defined FAIR assessments. The components of the framework are: (1) Maturity Indicators - community-authored specifications that delimit a specific automatically-measurable FAIR behavior; (2) Compliance Tests - small Web apps that test digital resources against individual Maturity Indicators; and (3) the Evaluator, a Web application that registers, assembles, and applies community-relevant sets of Compliance Tests against a digital resource, and provides a detailed report about what a machine \"sees\" when it visits that resource. We discuss the technical and social considerations of FAIR assessments, and how this translates to our community-driven infrastructure. We then illustrate how the output of the Evaluator tool can serve as a roadmap to assist data stewards to incrementally and realistically improve the FAIRness of their resources.

bioinformatics↗