1
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Hilbert ZA, Haffener PE, Young HJ, Schwiesow MJW, Leffler EM, Elde NC. Rapid evolution of glycan recognition receptors reveals an axis of host-microbe arms races beyond canonical protein-protein interfaces. Genome Biol Evol 2023:evad119. [PMID: 37390614 DOI: 10.1093/gbe/evad119] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023] Open
Abstract
Detection of microbial pathogens is a primary function of many mammalian immune proteins. This is accomplished through the recognition of diverse microbial-produced macromolecules including proteins, nucleic acids and carbohydrates. Pathogens subvert host defenses by rapidly changing these structures to avoid detection, placing strong selective pressures on host immune proteins that repeatedly adapt to remain effective. Signatures of rapid evolution have been identified in numerous immunity proteins involved in the detection of pathogenic protein substrates, but whether similar signals can be observed in host proteins engaged in interactions with other types of pathogen-derived molecules has received less attention. This focus on protein-protein interfaces has largely obscured the study of fungi as contributors to host-pathogen conflicts, despite their importance as a formidable class of vertebrate pathogens. Here, we provide evidence that mammalian immune receptors involved in the detection of microbial glycans have been subject to recurrent positive selection. We find that rapidly evolving sites in these genes cluster in key functional domains involved in carbohydrate recognition. Further, we identify convergent patterns of substitution and evidence for balancing selection in one particular gene, MelLec, which plays a critical role in controlling invasive fungal disease. Our results also highlight the power of evolutionary analyses to reveal uncharacterized interfaces of host-pathogen conflict by identifying genes, like CLEC12A, with strong signals of positive selection across mammalian lineages. These results suggest that the realm of interfaces shaped by host-microbe conflicts extends beyond the world of host-viral protein-protein interactions and into the world of microbial glycans and fungi.
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Affiliation(s)
- Zoë A Hilbert
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Paige E Haffener
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Hannah J Young
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Mara J W Schwiesow
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Ellen M Leffler
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
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2
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Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM, Macharia AW, Hubbart C, Jeffreys AE, Rowlands K, Nguyen T, Gonçalves S, Ariani CV, Stalker J, Pearson RD, Amato R, Drury E, Sirugo G, d'Alessandro U, Bojang KA, Marsh K, Peshu N, Saelens JW, Diakité M, Taylor SM, Conway DJ, Williams TN, Rockett KA, Kwiatkowski DP. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature 2021; 602:106-111. [PMID: 34883497 PMCID: PMC8810385 DOI: 10.1038/s41586-021-04288-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations. A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.
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Affiliation(s)
- Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Muminatou Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Edward Francis Small Teaching Hospital (formerly Royal Victoria Teaching Hospital), Independence Drive, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Thuy Nguyen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Jim Stalker
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA
| | | | | | - Giorgio Sirugo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Umberto d'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kalifa A Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford, UK
| | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - David J Conway
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial College, London, London, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
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3
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Amuzu DS, Rockett KA, Leffler EM, Ansah F, Amoako N, Morang'a CM, Hubbart C, Rowlands K, Jeffreys AE, Amenga-Etego LN, Kwiatkowski DP, Awandare GA. High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies. Exp Biol Med (Maywood) 2020; 246:916-928. [PMID: 33325748 PMCID: PMC8022085 DOI: 10.1177/1535370220968545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Glycophorins are the most abundant sialoglycoproteins on the surface of human erythrocyte membranes. Genetic variation in glycophorin region of human chromosome 4 (containing GYPA, GYPB, and GYPE genes) is of interest because the gene products serve as receptors for pathogens of major public health interest, including Plasmodiumsp., Babesiasp., Influenza virus, Vibrio cholerae El Tor Hemolysin, and Escherichia coli. A large structural rearrangement and hybrid glycophorin variant, known as Dantu, which was identified in East African populations, has been linked with a 40% reduction in risk for severe malaria. Apart from Dantu, other large structural variants exist, with the most common being deletion of the whole GYPB gene and its surrounding region, resulting in multiple different deletion forms. In West Africa particularly, these deletions are estimated to account for between 5 and 15% of the variation in different populations, mostly attributed to the forms known as DEL1 and DEL2. Due to the lack of specific variant assays, little is known of the distribution of these variants. Here, we report a modification of a previous GYPB DEL1 assay and the development of a novel GYPB DEL2 assay as high-throughput PCR-RFLP assays, as well as the identification of the crossover/breakpoint for GYPB DEL2. Using 393 samples from three study sites in Ghana as well as samples from HapMap and 1000 G projects for validation, we show that our assays are sensitive and reliable for genotyping GYPB DEL1 and DEL2. To the best of our knowledge, this is the first report of such high-throughput genotyping assays by PCR-RFLP for identifying specific GYPB deletion types in populations. These assays will enable better identification of GYPB deletions for large genetic association studies and functional experiments to understand the role of this gene cluster region in susceptibility to malaria and other diseases.
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Affiliation(s)
- Dominic Sy Amuzu
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Nicholas Amoako
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
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4
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Abstract
A new study reports genome-wide variation in 163 vervet monkeys from across their taxonomic and geographic ranges. The analysis suggests a complex history of admixture and identifies signals of repeated evolutionary selection, some of which may be linked to response to simian immunodeficiency virus.
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Affiliation(s)
- Ellen M Leffler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK, and the Wellcome Trust Sanger Institute, Hinxton, UK
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5
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Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017; 356:science.aam6393. [PMID: 28522690 DOI: 10.1126/science.aam6393] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/08/2017] [Indexed: 12/29/2022]
Abstract
The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
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Affiliation(s)
- Ellen M Leffler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - George B J Busby
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Katja Kivinen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kalifa A Bojang
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia
| | - David J Conway
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Muminatou Jallow
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia.,Royal Victoria Teaching Hospital, Independence Drive, Post Office Box 1515, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia
| | - Edith C Bougouma
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | | | - David Modiano
- University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | - Eric Achidi
- Department of Medical Laboratory Sciences, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon
| | - Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon
| | - Kevin Marsh
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford OX3 7FZ, UK
| | - Carolyne M Ndila
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya
| | - Norbert Peshu
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya
| | - Thomas N Williams
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya.,Faculty of Medicine, Department of Medicine, Imperial College, Exhibition Road, London SW7 2AZ, UK
| | - Chris Drakeley
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,National Institute for Medical Research, Mwanza Research Centre, Mwanza City, Tanzania
| | - Hugh Reyburn
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Eleanor Riley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - David Kachala
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi
| | - Malcolm Molyneux
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Vysaul Nyirongo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi
| | - Terrie Taylor
- Blantyre Malaria Project, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.,College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Nicole Thornton
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Louise Tilley
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Shane Grimsley
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Eleanor Drury
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jim Stalker
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Victoria Cornelius
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Anna E Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. .,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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6
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Singhal S, Leffler EM, Sannareddy K, Turner I, Venn O, Hooper DM, Strand AI, Li Q, Raney B, Balakrishnan CN, Griffith SC, McVean G, Przeworski M. Stable recombination hotspots in birds. Science 2015; 350:928-32. [PMID: 26586757 PMCID: PMC4864528 DOI: 10.1126/science.aad0843] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have recombination hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, most hotspots are shared between the two species, and their conservation seems to extend over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution.
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Affiliation(s)
- Sonal Singhal
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Department of Systems Biology, Columbia University, New York, NY 10032, USA.
| | - Ellen M Leffler
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Keerthi Sannareddy
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Isaac Turner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Oliver Venn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Daniel M Hooper
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alva I Strand
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Qiye Li
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Brian Raney
- Center for Biomolecular Science and Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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7
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Leffler EM, Gao Z, Pfeifer S, Ségurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella G, Donnelly P, McVean G, Przeworski M. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 2013; 339:1578-82. [PMID: 23413192 DOI: 10.1126/science.1234070] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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.
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Affiliation(s)
- Ellen M Leffler
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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8
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Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski M. Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol 2012; 10:e1001388. [PMID: 22984349 PMCID: PMC3439417 DOI: 10.1371/journal.pbio.1001388] [Citation(s) in RCA: 317] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.
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Affiliation(s)
- Ellen M. Leffler
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (EML); (MP)
| | - Kevin Bullaughey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Daniel R. Matute
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Wynn K. Meyer
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Laure Ségurel
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Molly Przeworski
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (EML); (MP)
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9
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Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel L, Street T, Leffler EM, Bowden R, Aneas I, Broxholme J, Humburg P, Iqbal Z, Lunter G, Maller J, Hernandez RD, Melton C, Venkat A, Nobrega MA, Bontrop R, Myers S, Donnelly P, Przeworski M, McVean G. A fine-scale chimpanzee genetic map from population sequencing. Science 2012; 336:193-8. [PMID: 22422862 PMCID: PMC3532813 DOI: 10.1126/science.1216872] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but with exceptions, particularly in regions of chromosomal rearrangements and around the site of ancestral fusion in human chromosome 2. At fine scales, chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes. The hotspot-specifying protein PRDM9 shows extensive variation among Western chimpanzees, and there is little evidence that any sequence motifs are enriched in hotspots. The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition.
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Affiliation(s)
- Adam Auton
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Genetics, Albert Einstein College of Medicine, New York, New York, USA
| | - Adi Fledel-Alon
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Susanne Pfeifer
- Department of Statistics, 1 South Parks Road, University of Oxford, Oxford, OX1 3TG, UK
| | - Oliver Venn
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Laure Ségurel
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Teresa Street
- Department of Statistics, 1 South Parks Road, University of Oxford, Oxford, OX1 3TG, UK
| | - Ellen M. Leffler
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Statistics, 1 South Parks Road, University of Oxford, Oxford, OX1 3TG, UK
- Oxford Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Ivy Aneas
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - John Broxholme
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Julian Maller
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Statistics, 1 South Parks Road, University of Oxford, Oxford, OX1 3TG, UK
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143-0912, USA
| | - Cord Melton
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Marcelo A. Nobrega
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Ronald Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Center, Lange Kleiweg 139 2288 GJ, Rijswijk, Netherlands
| | - Simon Myers
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Statistics, 1 South Parks Road, University of Oxford, Oxford, OX1 3TG, UK
| | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Statistics, 1 South Parks Road, University of Oxford, Oxford, OX1 3TG, UK
| | - Molly Przeworski
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Statistics, 1 South Parks Road, University of Oxford, Oxford, OX1 3TG, UK
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10
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Abstract
Chlamydomonas exhibits force transduction in association with its flagellar surface; this can be visualized by the saltatory movements of attached polystyrene microspheres. This flagellar surface motility has been quantitated by determining the percentage of attached microspheres in motion at the time of observation (60% in the case of control cells at 25 degrees C). A number of experimental treatments reversibly inhibit flagellar surface motility. These include an increase in sodium or potassium chloride concentration, a decrease in temperature, or a decrease in the free calcium concentration in the medium. Many of the conditions that result in inhibition of flagellar surface motility also result in an induction of flagellar resorption. Although both flagellar stability and flagellar surface motility are dependent on the availability of calcium, the two processes are separable; under appropriate conditions, flagellar surface motility can occur at normal levels on flagella that are resorbing. Inhibition of protein synthesis results in a gradual loss of both the binding of microspheres to the flagellum and the flagellar surface motility. After resumption of protein synthesis, both binding and movement return to control levels. The effect of the inhibition of protein synthesis is interpreted in terms of selective turnover of certain components within the intact flagellum, one or more of these components being necessary for the binding of the microspheres and their subsequent movement. If this turnover is inhibited by keeping the cells below 5 degrees C, the absence of protein synthesis no longer has an effect on microsphere attachment and motility, when measured immediately after warming the cells to 25 degrees C.
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