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Bascón-Cardozo K, Bours A, Manthey G, Durieux G, Dutheil JY, Pruisscher P, Odenthal-Hesse L, Liedvogel M. Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap. Genome Biol Evol 2024; 16:evad233. [PMID: 38198800 PMCID: PMC10781513 DOI: 10.1093/gbe/evad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium-based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.
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Affiliation(s)
- Karen Bascón-Cardozo
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Andrea Bours
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Georg Manthey
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
| | - Gillian Durieux
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Julien Y Dutheil
- Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Peter Pruisscher
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Department of Zoology, Stockholm University, Stockholm SE-106 91, Sweden
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Miriam Liedvogel
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg 26129, Germany
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Bours A, Pruisscher P, Bascón-Cardozo K, Odenthal-Hesse L, Liedvogel M. The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons. Sci Rep 2023; 13:16471. [PMID: 37777595 PMCID: PMC10542752 DOI: 10.1038/s41598-023-43090-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can move around the genome, and as such are a source of genomic variability. Based on their characteristics we can annotate TEs within the host genome and classify them into specific TE types and families. The increasing number of available high-quality genome references in recent years provides an excellent resource that will enhance the understanding of the role of recently active TEs on genetic variation and phenotypic evolution. Here we showcase the use of a high-quality TE annotation to understand the distinct effect of recent and ancient TE insertions on the evolution of genomic variation, within our study species the Eurasian blackcap (Sylvia atricapilla). We investigate how these distinct TE categories are distributed along the genome and evaluate how their coverage across the genome is correlated with four genomic features: recombination rate, gene coverage, CpG island coverage and GC content. We found within the recent TE insertions an accumulation of LTRs previously not seen in birds. While the coverage of recent TE insertions was negatively correlated with both GC content and recombination rate, the correlation with recombination rate disappeared and turned positive for GC content when considering ancient TE insertions.
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Affiliation(s)
- Andrea Bours
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
| | - Peter Pruisscher
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Karen Bascón-Cardozo
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Miriam Liedvogel
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany.
- Institute of Avian Research "Vogelwarte Helgoland", 26386, Wilhelmshaven, Germany.
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Van Breedam E, Buyle-Huybrecht T, Govaerts J, Meysman P, Bours A, Boeren M, Di Stefano J, Caers T, De Reu H, Dirkx L, Schippers J, Bartholomeus E, Lebrun M, Sadzot-Delvaux C, Rybakowska P, Alarcón-Riquelme ME, Marañón C, Laukens K, Delputte P, Ogunjimi B, Ponsaerts P. Lack of strong innate immune reactivity renders macrophages alone unable to control productive Varicella-Zoster Virus infection in an isogenic human iPSC-derived neuronal co-culture model. Front Immunol 2023; 14:1177245. [PMID: 37287975 PMCID: PMC10241998 DOI: 10.3389/fimmu.2023.1177245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023] Open
Abstract
With Varicella-Zoster Virus (VZV) being an exclusive human pathogen, human induced pluripotent stem cell (hiPSC)-derived neural cell culture models are an emerging tool to investigate VZV neuro-immune interactions. Using a compartmentalized hiPSC-derived neuronal model allowing axonal VZV infection, we previously demonstrated that paracrine interferon (IFN)-α2 signalling is required to activate a broad spectrum of interferon-stimulated genes able to counteract a productive VZV infection in hiPSC-neurons. In this new study, we now investigated whether innate immune signalling by VZV-challenged macrophages was able to orchestrate an antiviral immune response in VZV-infected hiPSC-neurons. In order to establish an isogenic hiPSC-neuron/hiPSC-macrophage co-culture model, hiPSC-macrophages were generated and characterised for phenotype, gene expression, cytokine production and phagocytic capacity. Even though immunological competence of hiPSC-macrophages was shown following stimulation with the poly(dA:dT) or treatment with IFN-α2, hiPSC-macrophages in co-culture with VZV-infected hiPSC-neurons were unable to mount an antiviral immune response capable of suppressing a productive neuronal VZV infection. Subsequently, a comprehensive RNA-Seq analysis confirmed the lack of strong immune responsiveness by hiPSC-neurons and hiPSC-macrophages upon, respectively, VZV infection or challenge. This may suggest the need of other cell types, like T-cells or other innate immune cells, to (co-)orchestrate an efficient antiviral immune response against VZV-infected neurons.
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Affiliation(s)
- Elise Van Breedam
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Tamariche Buyle-Huybrecht
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Jonas Govaerts
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Andrea Bours
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Marlies Boeren
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Julia Di Stefano
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Thalissa Caers
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Hans De Reu
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Flow Cytometry and Cell Sorting Core Facility (FACSUA), Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Laura Dirkx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Jolien Schippers
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Marielle Lebrun
- Laboratory of Virology and Immunology, Interdisciplinary Research Institute in the Biomedical Sciences GIGA-Infection, Inflammation and Immunity, University of Liège, Liège, Belgium
| | - Catherine Sadzot-Delvaux
- Laboratory of Virology and Immunology, Interdisciplinary Research Institute in the Biomedical Sciences GIGA-Infection, Inflammation and Immunity, University of Liège, Liège, Belgium
| | - Paulina Rybakowska
- Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, Parque Tecnológico de la Salud (PTS), Granada, Spain
| | - Marta E. Alarcón-Riquelme
- Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, Parque Tecnológico de la Salud (PTS), Granada, Spain
| | - Concepción Marañón
- Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, Parque Tecnológico de la Salud (PTS), Granada, Spain
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Peter Delputte
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
- Infla-Med, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research & Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Flow Cytometry and Cell Sorting Core Facility (FACSUA), Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
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