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  1. Article ; Online: Protecting science in times of crises.

    Bravo, Ignacio G / Buton, François

    Anaesthesia, critical care & pain medicine

    2022  Volume 42, Issue 1, Page(s) 101187

    Language English
    Publishing date 2022-12-16
    Publishing country France
    Document type Editorial
    ISSN 2352-5568
    ISSN (online) 2352-5568
    DOI 10.1016/j.accpm.2022.101187
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  2. Article ; Online: Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: The showcase of polypyrimidine tract binding proteins.

    Bourret, Jérôme / Borvető, Fanni / Bravo, Ignacio G

    Journal of evolutionary biology

    2023  Volume 36, Issue 10, Page(s) 1375–1392

    Abstract: Gene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel ... ...

    Abstract Gene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel functions. Here, we focused our study on gene paralogs on the evolutionary history of the three polypyrimidine tract binding protein genes (PTBP) and their concurrent evolution of differential codon usage preferences (CUPrefs) in vertebrate species. PTBP1-3 show high identity at the amino acid level (up to 80%) but display strongly different nucleotide composition, divergent CUPrefs and, in humans and in many other vertebrates, distinct tissue-specific expression levels. Our phylogenetic inference results show that the duplication events leading to the three extant PTBP1-3 lineages predate the basal diversification within vertebrates, and genomic context analysis illustrates that local synteny has been well preserved over time for the three paralogs. We identify a distinct evolutionary pattern towards GC3-enriching substitutions in PTBP1, concurrent with enrichment in frequently used codons and with a tissue-wide expression. In contrast, PTBP2s are enriched in AT-ending, rare codons, and display tissue-restricted expression. As a result of this substitution trend, CUPrefs sharply differ between mammalian PTBP1s and the rest of PTBPs. Genomic context analysis suggests that GC3-rich nucleotide composition in PTBP1s is driven by local substitution processes, while the evidence in this direction is thinner for PTBP2-3. An actual lack of co-variation between the observed GC composition of PTBP2-3 and that of the surrounding non-coding genomic environment would raise an interrogation on the origin of CUPrefs, warranting further research on a putative tissue-specific translational selection. Finally, we communicate an intriguing trend for the use of the UUG-Leu codon, which matches the trends of AT-ending codons. Our results are compatible with a scenario in which a combination of directional mutation-selection processes would have differentially shaped CUPrefs of PTBPs in vertebrates: the observed GC-enrichment of PTBP1 in placental mammals may be linked to genomic location and to the strong and broad tissue-expression, while AT-enrichment of PTBP2 and PTBP3 would be associated with rare CUPrefs and thus, possibly to specialized spatio-temporal expression. Our interpretation is coherent with a gene subfunctionalisation process by differential expression regulation associated with the evolution of specific CUPrefs.
    Language English
    Publishing date 2023-09-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1465318-7
    ISSN 1420-9101 ; 1010-061X
    ISSN (online) 1420-9101
    ISSN 1010-061X
    DOI 10.1111/jeb.14212
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  3. Article ; Online: Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide.

    Daron, Josquin / Bravo, Ignacio G

    Viruses

    2021  Volume 13, Issue 9

    Abstract: ... ...

    Abstract The
    MeSH term(s) COVID-19/epidemiology ; COVID-19/virology ; Codon Usage ; Evolution, Molecular ; Genome, Viral ; Host-Pathogen Interactions/genetics ; Humans ; Mutation ; Pandemics ; SARS-CoV-2/genetics ; Selection, Genetic
    Language English
    Publishing date 2021-09-10
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13091800
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  4. Article: Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide

    Daron, Josquin / Bravo, Ignacio G.

    Viruses. 2021 Sept. 10, v. 13, no. 9

    2021  

    Abstract: The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential of ... ...

    Abstract The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential of coronaviruses, it is critical to unravel their evolutionary history of host species breadth, host-switch potential, adaptation and emergence, to identify viruses posing a pandemic risk in humans. We present here a comprehensive analysis of the composition and codon usage bias of the 82 Orthocoronavirinae members, infecting 47 different avian and mammalian hosts. Our results clearly establish that synonymous codon usage varies widely among viruses, is only weakly dependent on their primary host, and is dominated by mutational bias towards AU-enrichment and by CpG avoidance. Indeed, variation in GC3 explains around 34%, while variation in CpG frequency explains around 14% of total variation in codon usage bias. Further insight on the mutational equilibrium within Orthocoronavirinae revealed that most coronavirus genomes are close to their neutral equilibrium, the exception being the three recently infecting human coronaviruses, which lie further away from the mutational equilibrium than their endemic human coronavirus counterparts. Finally, our results suggest that, while replicating in humans, SARS-CoV-2 is slowly becoming AU-richer, likely until attaining a new mutational equilibrium.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; birds ; codon usage ; hosts ; humans ; pandemic ; risk ; viruses ; zoonoses
    Language English
    Dates of publication 2021-0910
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13091800
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Variability in codon usage in Coronaviruses is mainly driven by mutational bias and selective constraints on CpG dinucleotide

    Daron, Josquin / Bravo, Ignacio G.

    bioRxiv

    Abstract: The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third virus within the Orthocoronavirinae causing an emergent infectious disease in humans, the ongoing coronavirus disease 2019 pandemic (COVID-19). Due to the high zoonotic ... ...

    Abstract The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third virus within the Orthocoronavirinae causing an emergent infectious disease in humans, the ongoing coronavirus disease 2019 pandemic (COVID-19). Due to the high zoonotic potential of these viruses, it is critical to unravel their evolutionary history of host species shift, adaptation and emergence. Only such knowledge can guide virus discovery, surveillance and research efforts to identify viruses posing a pandemic risk in humans. We present a comprehensive analysis of the composition and codon usage bias of the 82 Orthocoronavirinae members, infecting 47 different avian and mammalian hosts. Our results clearly establish that synonymous codon usage varies widely among viruses and is only weakly dependent on the type of host they infect. Instead, we identify mutational bias towards AT-enrichment and selection against CpG dinucleotides as the main factors responsible of the codon usage bias variation. Further insight on the mutational equilibrium within Orthocoronavirinae revealed that most coronavirus genomes are close to their neutral equilibrium, the exception is the three recently-infecting human coronaviruses, which lie further away from the mutational equilibrium than their endemic human coronavirus counterparts. Finally, our results suggest that while replicating in humans SARS-CoV-2 is slowly becoming AT-richer, likely until attaining a new mutational equilibrium.
    Keywords covid19
    Language English
    Publishing date 2021-01-26
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.01.26.428296
    Database COVID19

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  6. Article ; Online: Evolution and diversity of nucleotide and dinucleotide composition in poxviruses.

    Molteni, Cristian / Forni, Diego / Cagliani, Rachele / Bravo, Ignacio G / Sironi, Manuela

    The Journal of general virology

    2023  Volume 104, Issue 10

    Abstract: Poxviruses ( ... ...

    Abstract Poxviruses (family
    MeSH term(s) Animals ; Humans ; Poxviridae/genetics ; Nucleotides ; Codon/genetics ; Evolution, Molecular ; Mammals/genetics ; Dinucleoside Phosphates ; Antiviral Agents
    Chemical Substances Nucleotides ; Codon ; Dinucleoside Phosphates ; Antiviral Agents
    Language English
    Publishing date 2023-10-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 219316-4
    ISSN 1465-2099 ; 0022-1317
    ISSN (online) 1465-2099
    ISSN 0022-1317
    DOI 10.1099/jgv.0.001897
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    In stock of ZB MED Cologne/Königswinter

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  7. Article ; Online: Origin and evolution of papillomavirus (onco)genes and genomes.

    Willemsen, Anouk / Bravo, Ignacio G

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2019  Volume 374, Issue 1773, Page(s) 20180303

    Abstract: Papillomaviruses (PVs) are ancient viruses infecting vertebrates, from fishes to mammals. Although the genomes of PVs are small and show conserved synteny, PVs display large genotypic diversity and ample variation in the phenotypic presentation of the ... ...

    Abstract Papillomaviruses (PVs) are ancient viruses infecting vertebrates, from fishes to mammals. Although the genomes of PVs are small and show conserved synteny, PVs display large genotypic diversity and ample variation in the phenotypic presentation of the infection. Most PV genomes contain two small early genes E6 and E7. In a bunch of closely related human papillomaviruses (HPVs), the E6 and E7 proteins provide the viruses with oncogenic potential. The recent discoveries of PVs without E6 and E7 in different fish species place a new root on the PV tree, and suggest that ancestral PVs consisted of the minimal PV backbone E1-E2-L2-L1. Bayesian phylogenetic analyses date the most recent common ancestor of the PV backbone to 424 million years ago (Ma). Common ancestry tests on extant E6 and E7 genes indicate that they share a common ancestor dating back to at least 184 Ma. In AlphaPVs infecting Old World monkeys and apes, the appearance of the E5 oncogene 53-58 Ma concurred with (i) a significant increase in substitution rate, (ii) a basal radiation and (iii) key gain of functions in E6 and E7. This series of events was instrumental to construct the extant phenotype of oncogenic HPVs. Our results assemble the current knowledge on PV diversity and present an ancient evolutionary timeline punctuated by evolutionary innovations in the history of this successful viral family. This article is part of the theme issue 'Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses'.
    MeSH term(s) Biological Evolution ; Genes, Viral ; Genome, Viral ; Oncogenes ; Papillomaviridae/genetics
    Language English
    Publishing date 2019-03-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2018.0303
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    Einzelsignatur: Show issues

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  8. Article ; Online: Two

    Bouzidi, Sarah / Puech, Julien / Fulla, Marta / González-Compta, Xavier / Pere, Hélène / Alemany, Laia / Veyer, David / Bravo, Ignacio G

    Microbiology resource announcements

    2024  Volume 13, Issue 4, Page(s) e0118423

    Abstract: We communicate here two ... ...

    Abstract We communicate here two complete
    Language English
    Publishing date 2024-03-05
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01184-23
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  9. Article ; Online: COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences.

    Bourret, Jérôme / Alizon, Samuel / Bravo, Ignacio G

    Genome biology and evolution

    2020  Volume 11, Issue 12, Page(s) 3523–3528

    Abstract: Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been developed to evaluate CUPrefs, either in absolute terms or with respect to a reference. We introduce ... ...

    Abstract Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been developed to evaluate CUPrefs, either in absolute terms or with respect to a reference. We introduce the normalized index COUSIN (for COdon Usage Similarity INdex), that compares the CUPrefs of a query against those of a reference and normalizes the output over a Null Hypothesis of random codon usage. The added value of COUSIN is to be easily interpreted, both quantitatively and qualitatively. An eponymous software written in Python3 is available for local or online use (http://cousin.ird.fr). This software allows for an easy and complete analysis of CUPrefs via COUSIN, includes seven other indices, and provides additional features such as statistical analyses, clustering, and CUPrefs optimization for gene expression. We illustrate the flexibility of COUSIN and highlight its advantages by analyzing the complete coding sequences of eight divergent genomes. Strikingly, COUSIN captures a bimodal distribution in the CUPrefs of human and chicken genes hitherto unreported with such precision. COUSIN opens new perspectives to uncover CUPrefs specificities in genomes in a practical, informative, and user-friendly way.
    MeSH term(s) Animals ; Bacteria ; Chickens ; Codon Usage ; Genome ; Humans ; Mice ; Plasmodium falciparum ; Reference Standards ; Software ; Species Specificity
    Language English
    Publishing date 2020-01-16
    Publishing country England
    Document type Letter ; Research Support, Non-U.S. Gov't
    ISSN 1759-6653
    ISSN (online) 1759-6653
    DOI 10.1093/gbe/evz262
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  10. Article: Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event.

    Borvető, Fanni / Bravo, Ignacio G / Willemsen, Anouk

    Virus evolution

    2020  Volume 6, Issue 1, Page(s) veaa038

    Abstract: Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus-host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and ... ...

    Abstract Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus-host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined the genomic impact of a recombination event between distantly related PVs infecting Cetartiodactyla (even-toed ungulates and cetaceans). Our phylogenetic analyses suggest that one single recombination was responsible for the generation of extant 'chimeric' PV genomes infecting cetaceans. By correlating the phylogenetic relationships to the genomic content, we observed important differences between the recombinant and non-recombinant cetartiodactyle PV genomes. Notably, recombinant PVs contain a unique set of conserved motifs in the upstream regulatory region (URR). We interpret these regulatory changes as an adaptive response to drastic changes in the PV genome. In terms of codon usage preferences (CUPrefs), we did not detect any particular differences between orthologous open reading frames in recombinant and non-recombinant PVs. Instead, our results are in line with previous observations suggesting that CUPrefs in PVs are rather linked to gene expression patterns as well as to gene function. We show that the non-coding URR of PVs infecting cetaceans, the central regulatory element in these viruses, exhibits signs of adaptation following a recombination event. Our results suggest that also in PVs, the evolution of gene regulation can play an important role in speciation and adaptation to novel environments.
    Language English
    Publishing date 2020-06-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veaa038
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