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Navratil, V.

Publications and source records attributed to Navratil, V..

10 recordsLinked to original sources
bioRxiv2026

Benchmarking and integration of viral prediction tools to uncover viral dark matter across divergent low abundance metagenomes

While existing benchmark studies have focused on viral detection tools using highly-abundant virus-enriched, their performance in low-abundance metagenomic environments remains unexplored. We aimed to benchmark eleven viral prediction tools and assess combinations of the best-performing-tools in low-abundance metagenomes. We generated an artificial dataset simulating the low-abundant metagenomic samples including human,bacterial and viral sequences, using complete-Refseq genomes. Viral sequences were fragmented into varying lengths and subjected to increased levels of in silico mutations to evaluate recall and F1 score of eleven tools tested individually. We further evaluated complementary tool combinations to improve sensitivity and specificity, and assessed the best-performing multi-tools formulations on low-abundance viromes from human lower respiratory tract and air metagenomic samples. DeepVirfinder(DVF) and DIAMOND achieved the highest recall (median of 67% and 58%, respectively) on the RefSeq artificial contigs dataset along increased levels of induced mutations. On the artificially mutated RefSeq dataset, the highest sensitivity and F1 scores were achieved by 4 two-tools combinations : DVF+DeepMicroclass,DVF+ViraLM,DVF+geNomad and DVF+DIAMOND, combined with Kraken2X-filtering to remove false-positive contigs classified as Eukaryota,Bacteria,or Archaea. Using Kraken2X-filtering, DVF+ViraLM and DVF+DeepMicroclass achieved the best sensitivity across real human airway and air datasets. These combinations expanded the previously identified viral repertoire using gold-standard methods, increasing the number of viral contigs with functionally annotated CDSs and revealing previously undetected viral diversity. Benchmarking of the eleven most used tools for viral prediction showed that the complementary combination approach, improves the detection of viral sequences while limiting false positives. This provides a robust strategy for uncovering divergent viral dark matter.

bioinformatics↗
bioRxiv2026

Unraveling viral identity: Avoiding the trap of endogenous sequences for viral surveillance of small ruminant oncogenic retroviruses

Small ruminants (sheep and goats) are one of the few mammals in which an exogenous retrovirus (XRV) and closely related endogenous retroviral elements (ERV) coexist within the same host genome. The betaretroviruses Jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus (ENTV) cause pulmonary and nasal adenocarcinomas, respectively, and share extensive sequence similarity with their endogenous counterparts. Consequently, molecular surveillance must rely on assays that can unequivocally distinguish true exogenous infection from ERV-derived templates; failure to do so compromises diagnosis, phylogenetic inference, and epidemiological conclusions. We retrieved all complete JSRV, ENTV-1/2, and related ERV genomes deposited in public repositories and performed a comprehensive alignment. Only a limited number of genomic segments were capable of distinguishing exogenous from endogenous sequences. We refer to these as discriminating regions (DRs). Phylogenies built using DRs revealed that several entries annotated as XRV are, in fact, ERV-derived or chimeric artefacts generated by short-amplicon reconstruction. A systematic literature review of over 100 articles identified 286 distinct primers and probes used for the XRV amplification. In-silico mapping of each oligonucleotide onto the full alignment showed that only 28 % reliably differentiate XRV from ERV. We experimentally validated the predictive power of this approach for 17 primer/probe sets, confirming that non-discriminating assays produce false-positive signals from endogenous templates. The misannotation of ERV sequences as exogenous viruses has resulting in the population of databases with dubious entries, fostering erroneous hypotheses such as vector-borne transmission of JSRV and ENTV. To address this issue, we propose a concise set of criteria for assay design, validation, and database annotation emphasizing DR targeting, specificity testing against endogenous templates, and transparent reporting. Although this framework was developed for small ruminants, it is readily applicable to any host-virus system in which exogenous viruses coexist with endogenous viral elements. This will strengthen viral surveillance, phylogenetics, and the One Health initiatives.

microbiology↗
bioRxiv2025

pylifemap: Mapping Data onto the Tree of Life

O_LIThe need to visualize data associated with NCBI Taxonomy Identifiers is growing in various biological fields ranging from comparative genomics to metagenomics and metabarcoding, and even for outreach. C_LIO_LINo tool today allows visualization of such data while still keeping the full vision of the whole taxonomy, possibly causing a biased view of the data at hand. C_LIO_LIHere we introduce pylifemap, a Python package that allows users to map their own data directly on the interactive taxonomic tree proposed by Lifemap. Through a simple syntax, layers (points, lines, icons, heatmaps, etc.) depicting any type of data are superimposed on the Lifemap basemap, producing an interactive map to inspect biological datasets. The produced visualizations can easily be shared with others through notebooks or standalone HTML files, or exported as static images. C_LIO_LIWe illustrate the utility of pylifemap in the exploration of two contrasting datasets: the IUCN Red List of Threatened Species and the output of a large-scale environmental metagenomics experiment. C_LI Data/Code for peer reviewpylifemap is available at PyPI and easily installable with pip or uv. The development version can be found at https://lifemap-tol.github.io/pylifemap/ along with extensive documentation and examples.

evolutionary biology↗
bioRxiv2024

A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats

BackgroundEndogenous retroviruses (ERV) are traces of ancestral retroviral germline infections that constitute a significant portion of mammalian genomes and function as LTR-retrotransposons. ERVs remain understudied in ruminants and usually focus on specific families, highlighting a need for comprehensive and thorough exploration of the ERV landscape in these species. ResultsWe characterized 23 de novo Class I and II ERV families across four reference assemblies of domestic and wild sheep and goats, and one assembly of cattle. Among these families, 15 were shared by the five ruminant species, while six were exclusive to small ruminants and two were exclusive to cattle. The presence of these families in other ruminant species revealed multiple endogenization events over 40 million years. We identified a total of 113,812 ERV insertions across the five genomes, representing between 0.5 and 1% of their genomes. Solo-LTRs account for 84.5% of the annotated copies demonstrating that most of the ERVs are relics of past events. Although Class I ERVs showed similar sequence divergence landscapes between species, Class II ERVs displayed contrasting evolutionary dynamics. Families II-3 and II-5 showed higher abundance and copy conservation in small ruminants. Family II-5 was closely related to circulating exogenous retroviruses and was identified with 22 copies sharing identical LTRs and 12 with complete coding capacities in the domestic goat. ConclusionsOur results indicate that two ERV families may have retain their transpositional activity within ruminants, particularly in domestic goats, illustrating distinct evolutionary dynamics among ruminant species. This work highlights the ongoing influence of ERVs on genomic landscapes and provides further insights into their evolutionary trajectories in ruminant genomes.

evolutionary biology↗
bioRxiv2024

Proteogenomic reconstruction of organ-specific metabolic networks in an environmental sentinel species, the amphipod Gammarus fossarum

Metabolic pathways are targets of environmental contaminants underlying a large variability of toxic effects throughout biodiversity. However, the systematic reconstruction of metabolic pathways remains limited in environmental sentinel species due to the lack of available genomic data in many taxa of animal diversity. In order to improve the knowledge of the metabolism of sentinel species, in this study we used a multi-omics approach to reconstruct the most comprehensive map of metabolic pathways for a crustacean model in biomonitoring, the amphipod Gammarus fossarum. We revisited the assembly of RNA-seq data by de novo approaches drastically reducing RNA contaminants and transcript redundancy. We also acquired extensive mass spectrometry shotgun proteomic data on several organs from G. fossarum males and females to identify organ-specific metabolic profiles. The G. fossarum metabolic pathway reconstruction (available through the metabolic database GamfoCyc) was performed by adapting the genomic tool CycADS and we identified 377 pathways representing 7,630 annotated enzymes, 2,610 enzymatic reactions and the expression of 858 enzymes was experimentally validated by proteomics. Our analysis shows organ-specific metabolic profiles, such as an elevated abundance in enzymes involved in ATP biosynthesis and fatty acid beta-oxidation indicative of the high-energy requirement of the gills, or the key anabolic and detoxification role of the hepatopancreatic caeca, as exemplified by the specific expression of the retinoid biosynthetic pathways and glutathione synthesis. In conclusion, the multi-omics data integration performed in this study provides new resources to investigate metabolic processes in crustacean amphipods and their role in mediating the effects of environmental contaminant exposures in sentinel species.

molecular biology↗
bioRxiv2022

Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify important host determinants of COVID-19

The COVID-19 pandemic is caused by SARS-CoV-2, a novel coronavirus that spilled from the bat reservoir. Despite numerous clinical trials and vaccines, the burden remains immense, and the host determinants of SARS-CoV-2 susceptibility and COVID-19 severity remain largely unknown. Signatures of positive selection detected by comparative functional-genetic analyses in primate and bat genomes can uncover important and specific adaptations that occurred at virus-host interfaces. Here, we performed high-throughput evolutionary analyses of 334 SARS- CoV-2 interacting proteins to identify SARS-CoV adaptive loci and uncover functional differences between modern humans, primates and bats. Using DGINN (Detection of Genetic INNovation), we identified 38 bat and 81 primate proteins with marks of positive selection. Seventeen genes, including the ACE2 receptor, present adaptive marks in both mammalian orders, suggesting common virus-host interfaces and past epidemics of coronaviruses shaping their genomes. Yet, 84 genes presented distinct adaptations in bats and primates. Notably, residues involved in ubiquitination and phosphorylation of the inflammatory RIPK1 have rapidly evolved in bats but not primates, suggesting different inflammation regulation versus humans. Furthermore, we discovered residues with typical virus-host arms-race marks in primates, such as in the entry factor TMPRSS2 or the autophagy adaptor FYCO1, pointing to host-specific in vivo important interfaces that may be drug targets. Finally, we found that FYCO1 sites under adaptation in primates are those associated with severe COVID-19, supporting their importance in pathogenesis and replication. Overall, we identified functional adaptations involved in SARS- CoV-2 infection in bats and primates, critically enlightening modern genetic determinants of virus susceptibility and severity. Key findingsO_LIEvolutionary history of 334 SARS-CoV-2 interacting proteins (VIPs) in bats and primates identifying how the past has shaped modern viral reservoirs and humans - results publicly-available in an online resource. C_LIO_LIIdentification of 81 primate and 38 bat VIPs with signatures of adaptive evolution. The common ones among species delineate a core adaptive interactome, while the ones displaying distinct evolutionary trajectories enlighten host lineage-specific determinants. C_LIO_LIEvidence of primate specific adaptation of the entry factor TMPRSS2 pointing to its host- specific in vivo importance and predicting molecular interfaces. C_LIO_LIFYCO1 sites associated with severe COVID-19 in human (GWAS) display hallmarks of ancient adaptive evolution in primates, highlighting its importance in SARS-CoV-2 replication or pathogenesis and differences with the bat reservoir. C_LIO_LIIdentification of adaptive evolution in the bats multifunctional RIPK1 at residues that may differentially regulate inflammation. C_LI

evolutionary biology↗
bioRxiv2022

Type B and Type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD

During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs (primarily human viruses) have diverged over long time scales. Identifying their common and distinctive features is an effective approach to increase knowledge about the molecular details of influenza infection. The virus-encoded RNA-dependent RNA polymerases (FluPolB and FluPolA) are PB1-PB2-PA heterotrimers that perform transcription and replication of the viral genome in the nucleus of infected cells. Initiation of viral mRNA synthesis requires a direct association of FluPol with the host RNA polymerase II (RNAP II), in particular the repetitive C-terminal domain (CTD) of the major RNAP II subunit, to enable "cap-snatching" whereby 5-capped oligomers derived from nascent RNAP II transcripts are pirated to prime viral transcription. Here, we present the first high-resolution co-crystal structure of FluPolB bound to a CTD mimicking peptide at a binding site crossing from PA to PB2. By performing structure-based mutagenesis of FluPolB and FluPolA followed by a systematic investigation of FluPol-CTD binding, FluPol activity and viral phenotype, we demonstrate that IBVs and IAVs have evolved distinct binding interfaces to recruit the RNAP II CTD, despite the CTD sequence being highly conserved across host species. We find that the PB2 627 subdomain, a major determinant of FluPol-host cell interactions and IAV host-range, is involved in CTD-binding for IBVs but not for IAVs, and we show that FluPolB and FluPolA bind to the host RNAP II independently of the CTD. Altogether, our results strongly suggest that the CTD-binding modes of IAV and IBV represent avian- and human-optimized binding modes, respectively, and that their divergent evolution was shaped by the broader interaction network between the FluPol and the host transcriptional machinery. Authors summaryDuring seasonal influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs) and can cause severe outcomes. The influenza polymerase is a key drug target and it is therefore important to understand the common and distinctive molecular features of IBV and IAV polymerases. To achieve efficient transcription and replication in the nucleus of infected cells, influenza polymerases closely cooperate with the cellular RNA polymerase II (RNAP II) and interact with the repetitive C-terminal domain (CTD) of its major subunit. Here we gained new insights into the way IBV and IAV polymerases interact with the CTD of RNAP II. High-resolution structural data was used to perform structure-based mutagenesis of IBV and IAV polymerases followed by a systematic investigation of their interaction with RNAP II, transcription/replication activity and viral phenotype. Strikingly, we found that IBVs and IAVs have evolved distinct interfaces to interact with the host transcriptional machinery, in particular with the CTD of RNAP II. We provide evidence that these differences may have evolved as a consequence of the differences in IBV and IAV host range. Our findings are of significant importance with regard to the development of broad-spectrum antivirals that target the virus-host interface.

microbiology↗
bioRxiv2021

Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors

Transposable elements (TEs) are middle-repeated DNA sequences that can move along chromosomes using internal coding and regulatory regions. By their ability to move and because they are repeated, TEs can promote mutations. Especially they can alter the expression pattern of neighboring genes and have been shown to be involved in the mammalian regulatory network evolution. Human and mouse share more than 95% of their genomes and are affected by comparable diseases, which makes the mouse a perfect model in cancer research. However not much investigation concerning the mouse TE content has been made on this topics. In human cancer condition, a global activation of TEs can been observed which may ask the question of their impact on neighboring gene functioning. In this work, we used RNA sequences of highly aggressive pancreatic tumors from mouse to analyze the gene and TE deregulation happening in this condition compared to pancreas from healthy animals. Our results show that several TE families are deregulated and that the presence of TEs is associated with the expression divergence of genes in the tumor condition. These results illustrate the potential role of TEs in the global deregulation at work in the cancer cells.

genomics↗
bioRxiv2021

Large-scale deregulation of gene expression by artificial light at night in tadpoles of common toads

Artificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by potentially disturbing circadian timekeeping systems. Although gene-specific approaches have already shown the deleterious effect of ALAN on the circadian clock, immunity and reproduction, large-scale transcriptomic approaches with ecologically relevant light levels are still lacking to assess the global impact of ALAN on biological processes. Moreover, studies have focused mainly on variations in gene expression during the night in the presence of ALAN but never during the day. In a controlled laboratory experiment, transcriptome sequencing of Bufo bufo tadpoles revealed that ALAN affected gene expression at both night and daytime with a dose-dependent effect and globally induced a downregulation of genes. ALAN effects were detected at very low levels of illuminance (0.1 lux) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results indicate that a broad range of physiological pathways is impacted at the molecular level by very low levels of ALAN potentially resulting in reduced survival under environmental immune challenges.

ecology↗