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1. Longitudinal positron emission tomography and postmortem analysis reveals widespread neuroinflammation in SARS-CoV-2 infected rhesus macaques

Author

Nieuwland, Juliana M., Nutma, Erik, Philippens, Ingrid H. C. H. M., Böszörményi, Kinga P., Remarque, Edmond J., Bakker, Jaco, Meijer, Lisette, Woerdman, Noor, Fagrouch, Zahra C., Verstrepen, Babs E., Langermans, Jan A. M., Verschoor, Ernst J., Windhorst, Albert D., Bontrop, Ronald E., de Vries, Helga E., Stammes, Marieke A., and Middeldorp, Jinte

Published
2023
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3. The molecular evolution of spermatogenesis across mammals

Author

Murat, Florent, Mbengue, Noe, Winge, Sofia Boeg, Trefzer, Timo, Leushkin, Evgeny, Sepp, Mari, Cardoso-Moreira, Margarida, Schmidt, Julia, Schneider, Celine, Mößinger, Katharina, Brüning, Thoomke, Lamanna, Francesco, Belles, Meritxell Riera, Conrad, Christian, Kondova, Ivanela, Bontrop, Ronald, Behr, Rüdiger, Khaitovich, Philipp, Pääbo, Svante, Marques-Bonet, Tomas, Grützner, Frank, Almstrup, Kristian, Schierup, Mikkel Heide, and Kaessmann, Henrik

Published
2023
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6. Imaging the immune sequelae of infection with SARS‐CoV‐2 in nonhuman primates by using two nanobody PET‐tracers.

Author

Koopman, Gerrit, Verhoeven, Tom, Mooij, Petra, Acar, Roja F., Harmand, Thibault, Flanagan, Laney, Bakker, Jaco, Böszörményi, Kinga P., Bontrop, Ronald E., Langermans, Jan A. M., Ploegh, Hidde L., Verschoor, Ernst J., Vugts, Danielle J., Pishesha, Novalia, and Stammes, Marieke A.

Subjects
ANTIGEN presenting cells, POSITRON emission tomography, NASAL mucosa, EMPLOYEE recruitment, LUNG diseases
Abstract

Infection with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) impacts multiple anatomical sites. Whether this is due to the virus itself or is a secondary effect caused by the influx and activation of immune cells is not known. Positron emission tomography (PET) with immunoglobulins can provide insights into which sites and cells are activated in a living animal. Our aim is to use two nanobodies as tools to monitor (1) the distribution of antigen presenting cells (APC) by virtue of their Mafa‐DR expression profile, (2) virus‐infected cells and viral particles using a nanobody against the SARS‐CoV‐2 spike protein. Two [89Zr]‐labeled nanobodies that target the SARS‐CoV‐2 spike protein and major histocompatability complex (MHC) class II antigens (Mafa‐DR), respectively, are used to monitor their distribution during an experimental SARS‐CoV‐2 infection in a nonhuman primate model. Scans are obtained before infection and on Day 3 and 10 post infection (pi) in two macaques each. The [89Zr]anti‐SARS‐CoV‐2 spike nanobody localized to SARS‐CoV‐2‐associated lung lesions and the nasal mucosa, while the [89Zr]anti‐human leukocyte antigen (HLA)‐DR nanobody was predominantly found in non‐affected lung tissue after infection. We also detected, pi, upregulation of the Mafa‐DR signal, indicative of recruitment of professional APCs, in the superior sagittal sinus. [89Zr]‐labeled nanobodies show recruitment of macrophages/monocytes in non‐lesional lung tissue in cynomolgus macaques after experimental infection with SARS‐CoV‐2, as well as accumulation of the spike protein in both lung lesions and the nasal mucosa during infection. These results show the possibility of in vivo monitoring the quality and quantity of immune responses during the initial stages of an infection. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Medical imaging of pulmonary disease in SARS-CoV-2-exposed non-human primates

Author

Stammes, Marieke A., Lee, Ji Hyun, Meijer, Lisette, Naninck, Thibaut, Doyle-Meyers, Lara A., White, Alexander G., Borish, H. Jacob, Hartman, Amy L., Alvarez, Xavier, Ganatra, Shashank, Kaushal, Deepak, Bohm, Rudolf P., le Grand, Roger, Scanga, Charles A., Langermans, Jan A.M., Bontrop, Ronald E., Finch, Courtney L., Flynn, JoAnne L., Calcagno, Claudia, Crozier, Ian, and Kuhn, Jens H.

Published
2022
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9. Origins of de novo genes in human and chimpanzee

Author

Ruiz-Orera, Jorge, Hernandez-Rodriguez, Jessica, Chiva, Cristina, Sabidó, Eduard, Kondova, Ivanela, Bontrop, Ronald, Marqués-Bonet, Tomàs, and Albà, M. Mar

Subjects
Quantitative Biology - Genomics
Abstract

The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process we have performed in-depth sequencing of the transcriptomes of four mammalian species, human, chimpanzee, macaque and mouse, and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new transcriptional multiexonic events in human and/or chimpanzee that are not observed in the rest of species. By comparative genomics we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. We also find that the coding potential of the new genes is higher than expected by chance, consistent with the presence of protein-coding genes in the dataset. Using available human tissue proteomics and ribosome profiling data we identify several de novo genes with translation evidence. These genes show significant purifying selection signatures, indicating that they are probably functional. Taken together, the data supports a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins., Comment: 25 pages, 4 figures, 2 tables

Published
2015

14. Extreme selective sweeps independently targeted the X chromosomes of the great apes

Author

Nam, Kiwoong, Munch, Kasper, Hobolth, Asger, Dutheil, Julien Yann, Veeramah, Krishna R, Woerner, August E, Hammer, Michael F, Mailund, Thomas, Schierup, Mikkel Heide, Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, O’Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Eichler, Evan E, and Marques-Bonet, Tomas

Subjects
Human Genome, Genetics, Animals, Computational Biology, Databases, Genetic, Genetic Variation, Genetics, Population, Hominidae, Models, Genetic, Polymorphism, Genetic, Selection, Genetic, Species Specificity, X Chromosome, Great Ape Genome Diversity Project, X-chromosome evolution, ampliconic genes, great apes, meiotic drive, selective sweeps
Abstract

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis.

Published
2015

18. Great ape genetic diversity and population history.

Author

Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, Veeramah, Krishna R, Woerner, August E, O'Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Munch, Kasper, Hobolth, Asger, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Mailund, Thomas, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Hammer, Michael F, Eichler, Evan E, and Marques-Bonet, Tomas

Subjects
Animals, Animals, Wild, Animals, Zoo, Hominidae, Gorilla gorilla, Humans, Pan paniscus, Pan troglodytes, Inbreeding, Genetics, Population, Population Density, Evolution, Molecular, Phylogeny, Polymorphism, Single Nucleotide, Genome, Africa, Asia, Southeastern, Gene Flow, Genetic Variation, General Science & Technology
Abstract

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Published
2013

19. Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

Author

Leffler, Ellen M, Gao, Ziyue, Pfeifer, Susanne, Ségurel, Laure, Auton, Adam, Venn, Oliver, Bowden, Rory, Bontrop, Ronald, Wall, Jeffrey D, Sella, Guy, Donnelly, Peter, McVean, Gilean, and Przeworski, Molly

Subjects
Genetics, Human Genome, Clinical Research, Animals, Base Sequence, Genetic Association Studies, Genome, Human, Haplotypes, Host-Pathogen Interactions, Humans, Molecular Sequence Data, Pan troglodytes, Pedigree, Polymorphism, Single Nucleotide, Selection, Genetic, General Science & Technology
Abstract

Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex, we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are noncoding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.

Published
2013

29. Differential DNA methylation of vocal and facial anatomy genes in modern humans

Author

Gokhman, David, Nissim-Rafinia, Malka, Agranat-Tamir, Lily, Housman, Genevieve, García-Pérez, Raquel, Lizano, Esther, Cheronet, Olivia, Mallick, Swapan, Nieves-Colón, Maria A., Li, Heng, Alpaslan-Roodenberg, Songül, Novak, Mario, Gu, Hongcang, Osinski, Jason M., Ferrando-Bernal, Manuel, Gelabert, Pere, Lipende, Iddi, Mjungu, Deus, Kondova, Ivanela, Bontrop, Ronald, Kullmer, Ottmar, Weber, Gerhard, Shahar, Tal, Dvir-Ginzberg, Mona, Faerman, Marina, Quillen, Ellen E., Meissner, Alexander, Lahav, Yonatan, Kandel, Leonid, Liebergall, Meir, Prada, María E., Vidal, Julio M., Gronostajski, Richard M., Stone, Anne C., Yakir, Benjamin, Lalueza-Fox, Carles, Pinhasi, Ron, Reich, David, Marques-Bonet, Tomas, Meshorer, Eran, and Carmel, Liran

Published
2020
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33. Nomenclature for the KIR of non-human species

Author

Robinson, James, Guethlein, Lisbeth A., Maccari, Giuseppe, Blokhuis, Jeroen, Bimber, Benjamin N., de Groot, Natasja G., Sanderson, Nicholas D., Abi-Rached, Laurent, Walter, Lutz, Bontrop, Ronald E., Hammond, John A., Marsh, Steven G. E., and Parham, Peter

Published
2018
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35. The KIR repertoire of a West African chimpanzee population is characterized by limited gene, allele, and haplotype variation

Author

de Groot, Natasja G., Heijmans, Corrine M.C., van der Wiel, Marit K.H., Bruijnesteijn, Jesse, Bontrop, Ronald E., de Groot, Natasja G., Heijmans, Corrine M.C., van der Wiel, Marit K.H., Bruijnesteijn, Jesse, and Bontrop, Ronald E.

Abstract

Introduction: The killer cell immunoglobulin-like receptors (KIR) play a pivotal role in modulating the NK cell responses, for instance, through interaction with major histocompatibility complex (MHC) class I molecules. Both gene systems map to different chromosomes but co-evolved during evolution. The human KIR gene family is characterized by abundant allelic polymorphism and copy number variation. In contrast, our knowledge of the KIR repertoire in chimpanzees is limited to 39 reported alleles, with no available population data. Only three genomic KIR region configurations have been mapped, and seventeen additional ones were deduced by genotyping. Methods: Previously, we documented that the chimpanzee MHC class I repertoire has been skewed due to an ancient selective sweep. To understand the depth of the sweep, we set out to determine the full-length KIR transcriptome – in our MHC characterized pedigreed West African chimpanzee cohort – using SMRT sequencing (PacBio). In addition, the genomic organization of 14 KIR haplotypes was characterized by applying a Cas9-mediated enrichment approach in concert with long-read sequencing by Oxford Nanopore Technologies. Results: In the cohort, we discovered 35 undescribed and 15 already recorded Patr-KIR alleles, and a novel hybrid KIR gene. Some KIR transcripts are subject to evolutionary conserved alternative splicing events. A detailed insight on the KIR region dynamics (location and order of genes) was obtained, however, only five new KIR region configurations were detected. The population data allowed to investigate the distribution of the MHC-C1 and C2-epitope specificity of the inhibitory lineage III KIR repertoire, and appears to be skewed towards C2. Discussion: Although the KIR region is known to evolve fast, as observed in other primate species, our overall conclusion is that the genomic architecture and repertoire in West African chimpanzees exhibit only limited to moderate levels of variation. Hence, the anci

Published
2023

36. Longitudinal positron emission tomography and postmortem analysis reveals widespread neuroinflammation in SARS-CoV-2 infected rhesus macaques

Author

Nieuwland, Juliana M, Nutma, Erik, Philippens, Ingrid H C H M, Böszörményi, Kinga P, Remarque, Edmond J, Bakker, Jaco, Meijer, Lisette, Woerdman, Noor, Fagrouch, Zahra C, Verstrepen, Babs E, Langermans, Jan A M, Verschoor, Ernst J, Windhorst, Albert D, Bontrop, Ronald E, de Vries, Helga E, Stammes, Marieke A, Middeldorp, Jinte, Nieuwland, Juliana M, Nutma, Erik, Philippens, Ingrid H C H M, Böszörményi, Kinga P, Remarque, Edmond J, Bakker, Jaco, Meijer, Lisette, Woerdman, Noor, Fagrouch, Zahra C, Verstrepen, Babs E, Langermans, Jan A M, Verschoor, Ernst J, Windhorst, Albert D, Bontrop, Ronald E, de Vries, Helga E, Stammes, Marieke A, and Middeldorp, Jinte

Abstract

BACKGROUND: Coronavirus disease 2019 (COVID-19) patients initially develop respiratory symptoms, but they may also suffer from neurological symptoms. People with long-lasting effects after acute infections with severe respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., post-COVID syndrome or long COVID, may experience a variety of neurological manifestations. Although we do not fully understand how SARS-CoV-2 affects the brain, neuroinflammation likely plays a role.METHODS: To investigate neuroinflammatory processes longitudinally after SARS-CoV-2 infection, four experimentally SARS-CoV-2 infected rhesus macaques were monitored for 7 weeks with 18-kDa translocator protein (TSPO) positron emission tomography (PET) using [18F]DPA714, together with computed tomography (CT). The baseline scan was compared to weekly PET-CTs obtained post-infection (pi). Brain tissue was collected following euthanasia (50 days pi) to correlate the PET signal with TSPO expression, and glial and endothelial cell markers. Expression of these markers was compared to brain tissue from uninfected animals of comparable age, allowing the examination of the contribution of these cells to the neuroinflammatory response following SARS-CoV-2 infection.RESULTS: TSPO PET revealed an increased tracer uptake throughout the brain of all infected animals already from the first scan obtained post-infection (day 2), which increased to approximately twofold until day 30 pi. Postmortem immunohistochemical analysis of the hippocampus and pons showed TSPO expression in cells expressing ionized calcium-binding adaptor molecule 1 (IBA1), glial fibrillary acidic protein (GFAP), and collagen IV. In the hippocampus of SARS-CoV-2 infected animals the TSPO+ area and number of TSPO+ cells were significantly increased compared to control animals. This increase was not cell type specific, since both the number of IBA1+TSPO+ and GFAP+TSPO+ cells was increased, as well as the TSPO+ area within collagen I

Published
2023

37. The molecular evolution of spermatogenesis across mammals

Author

Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Murat, Florent, Mbengue, Noe, Winge, Sofia Boeg, Trefzer, Timo, Leushkin, Evgeny, Sepp, Mari, Cardoso-Moreira, Margarida, Schmidt, Julia, Schneider, Celine, Mößinger, Katharina, Brüning, Thoomke, Lamanna, Francesco, Belles, Meritxell Riera, Conrad, Christian, Kondova, Ivanela, Bontrop, Ronald, Behr, Rüdiger, Khaitovich, Philipp, Pääbo, Svante, Marques-Bonet, Tomas, Grützner, Frank, Almstrup, Kristian, Schierup, Mikkel Heide, Kaessmann, Henrik, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Murat, Florent, Mbengue, Noe, Winge, Sofia Boeg, Trefzer, Timo, Leushkin, Evgeny, Sepp, Mari, Cardoso-Moreira, Margarida, Schmidt, Julia, Schneider, Celine, Mößinger, Katharina, Brüning, Thoomke, Lamanna, Francesco, Belles, Meritxell Riera, Conrad, Christian, Kondova, Ivanela, Bontrop, Ronald, Behr, Rüdiger, Khaitovich, Philipp, Pääbo, Svante, Marques-Bonet, Tomas, Grützner, Frank, Almstrup, Kristian, Schierup, Mikkel Heide, and Kaessmann, Henrik

Published
2023

39. The KIR repertoire of a West African chimpanzee population is characterized by limited gene, allele, and haplotype variation

Author

Sub Theoretical Biology, Theoretical Biology and Bioinformatics, de Groot, Natasja G., Heijmans, Corrine M.C., van der Wiel, Marit K.H., Bruijnesteijn, Jesse, Bontrop, Ronald E., Sub Theoretical Biology, Theoretical Biology and Bioinformatics, de Groot, Natasja G., Heijmans, Corrine M.C., van der Wiel, Marit K.H., Bruijnesteijn, Jesse, and Bontrop, Ronald E.

Published
2023

40. Longitudinal positron emission tomography and postmortem analysis reveals widespread neuroinflammation in SARS-CoV-2 infected rhesus macaques

Author

AISS Animal Welfare, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, AISS – Animal Welfare, Nieuwland, Juliana M, Nutma, Erik, Philippens, Ingrid H C H M, Böszörményi, Kinga P, Remarque, Edmond J, Bakker, Jaco, Meijer, Lisette, Woerdman, Noor, Fagrouch, Zahra C, Verstrepen, Babs E, Langermans, Jan A M, Verschoor, Ernst J, Windhorst, Albert D, Bontrop, Ronald E, de Vries, Helga E, Stammes, Marieke A, Middeldorp, Jinte, AISS Animal Welfare, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, AISS – Animal Welfare, Nieuwland, Juliana M, Nutma, Erik, Philippens, Ingrid H C H M, Böszörményi, Kinga P, Remarque, Edmond J, Bakker, Jaco, Meijer, Lisette, Woerdman, Noor, Fagrouch, Zahra C, Verstrepen, Babs E, Langermans, Jan A M, Verschoor, Ernst J, Windhorst, Albert D, Bontrop, Ronald E, de Vries, Helga E, Stammes, Marieke A, and Middeldorp, Jinte

Published
2023

41. The molecular evolution of spermatogenesis across mammals

Author

University of Heidelberg, German Research Foundation, Ministry of Science, Research and Art Baden-Württemberg, European Research Council, EMBO, Australian Research Council, Novo Nordisk Foundation, Marqués-Bonet, Tomàs [0000-0002-5597-3075], Murat, Florent, Mbengue, Noe, Boeg Winge, Sofia, Trefzer, Timo, Leushkin, Evgeny, Sepp, Mari, Cardoso-Moreira, Margarida, Schmidt, Julia, Schneider, Celine, Mößinger, Katharina, Brüning, Thoomke, Lamanna, Francesco, Riera Belles, Meritxell, Conrad, Christian, Kondova, Ivanela, Bontrop, Ronald, Behr, Rüdiger, Khaitovich, Philipp, Pääbo, Svante, Marqués-Bonet, Tomàs, Grützner, Frank, Almstrup, Kristian, Schierup, Mikkel Heide, Kaessmann, Henrik, University of Heidelberg, German Research Foundation, Ministry of Science, Research and Art Baden-Württemberg, European Research Council, EMBO, Australian Research Council, Novo Nordisk Foundation, Marqués-Bonet, Tomàs [0000-0002-5597-3075], Murat, Florent, Mbengue, Noe, Boeg Winge, Sofia, Trefzer, Timo, Leushkin, Evgeny, Sepp, Mari, Cardoso-Moreira, Margarida, Schmidt, Julia, Schneider, Celine, Mößinger, Katharina, Brüning, Thoomke, Lamanna, Francesco, Riera Belles, Meritxell, Conrad, Christian, Kondova, Ivanela, Bontrop, Ronald, Behr, Rüdiger, Khaitovich, Philipp, Pääbo, Svante, Marqués-Bonet, Tomàs, Grützner, Frank, Almstrup, Kristian, Schierup, Mikkel Heide, and Kaessmann, Henrik

Abstract

The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1,2,3,4,5,6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.

Published
2023

42. Correction to: Nomenclature report 2019: major histocompatibility complex genes and alleles of great and small ape and old and new world monkey species

Author

de Groot, Natasja G., Otting, Nel, Maccari, Giuseppe, Robinson, James, Hammond, John A., Blancher, Antoine, Lafont, Bernard A. P., Guethlein, Lisbeth A., Wroblewski, Emily E., Marsh, Steven G. E., Shiina, Takashi, Walter, Lutz, Vigilant, Linda, Parham, Peter, O’Connor, David H., and Bontrop, Ronald E.

Published
2020
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43. Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Author

Francescatto, Margherita, Lizio, Marina, Philippens, Ingrid, Pardo, Luba M., Bontrop, Ronald, Sakai, Mizuho, Watanabe, Shoko, Itoh, Masayoshi, Hasegawa, Akira, Lassmann, Timo, Severin, Jessica, Harshbarger, Jayson, Abugessaisa, Imad, Kasukawa, Takeya, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Kawaji, Hideya, Rizzu, Patrizia, and Heutink, Peter

Published
2018
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44. The molecular evolution of spermatogenesis across mammals

Author

Murat, Florent, primary, Mbengue, Noe, additional, Winge, Sofia Boeg, additional, Trefzer, Timo, additional, Leushkin, Evgeny, additional, Sepp, Mari, additional, Cardoso-Moreira, Margarida, additional, Schmidt, Julia, additional, Schneider, Celine, additional, Mößinger, Katharina, additional, Brüning, Thoomke, additional, Lamanna, Francesco, additional, Belles, Meritxell Riera, additional, Conrad, Christian, additional, Kondova, Ivanela, additional, Bontrop, Ronald, additional, Behr, Rüdiger, additional, Khaitovich, Philipp, additional, Pääbo, Svante, additional, Marques-Bonet, Tomas, additional, Grützner, Frank, additional, Almstrup, Kristian, additional, Schierup, Mikkel Heide, additional, and Kaessmann, Henrik, additional

Published
2022
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