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Jax E, Franchini P, Sekar V, Ottenburghs J, Monné Parera D, Kellenberger RT, Magor KE, Müller I, Wikelski M, Kraus RHS. Comparative genomics of the waterfowl innate immune system. Mol Biol Evol 2022; 39:6649919. [PMID: 35880574 PMCID: PMC9356732 DOI: 10.1093/molbev/msac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets.
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Affiliation(s)
- Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy
| | - Vaishnovi Sekar
- Department of Biology, Lund University, Lund, Sweden.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Jente Ottenburghs
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands.,Forest Ecology and Forest Management Group, Wageningen University, Wageningen, The Netherlands
| | | | - Roman T Kellenberger
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katharine E Magor
- Department of Biological Sciences and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Inge Müller
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Robert H S Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
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Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Sci Rep 2021; 11:15771. [PMID: 34349207 PMCID: PMC8338973 DOI: 10.1038/s41598-021-95357-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.
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Levy H, Fiddaman SR, Vianna JA, Noll D, Clucas GV, Sidhu JKH, Polito MJ, Bost CA, Phillips RA, Crofts S, Miller GD, Pistorius P, Bonnadonna F, Le Bohec C, Barbosa A, Trathan P, Raya Rey A, Frantz LAF, Hart T, Smith AL. Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird. Mol Biol Evol 2020; 37:1708-1726. [PMID: 32096861 PMCID: PMC7253215 DOI: 10.1093/molbev/msaa040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.
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Affiliation(s)
- Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
| | - Daly Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Gemma V Clucas
- Cornell Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY
| | | | - Michael J Polito
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA
| | - Charles A Bost
- Centre d’Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS‐Université de La Rochelle, Villiers‐en‐Bois, France
| | | | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands, United Kingdom
| | - Gary D Miller
- Microbiology and Immunology, PALM, University of Western Australia, Crawley, Western Australia, Australia
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Francesco Bonnadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Céline Le Bohec
- Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
- Département de Biologie Polaire, Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Andrés Barbosa
- Museo Nacional de Ciencias Naturales, Departamento de Ecología Evolutiva, CSIC, Madrid, Spain
| | - Phil Trathan
- British Antarctic Survey, Cambridge, United Kingdom
| | - Andrea Raya Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Tierra del Fuego, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
- Wildlife Conservation Society, Buenos Aires, Argentina
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Kloch A, Biedrzycka A. Post-glacial phylogeography and variation in innate immunity loci in a sylvatic rodent, bank vole Myodes glareolus. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00016-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
AbstractIn the northern hemisphere, the spatial structure of many taxa has been shaped by migration patterns after the last glaciation, and phylogeography based on mtDNA variation may reflect the post-glacial demography. The mtDNA lineages are expected to differ in their adaptations to local conditions but little is known about the impact of these conditions on functional genetic variation. Here, we answer this question through an analysis of geographic variation and selection patterns in seven innate immunity genes in free-living bank voles Myodes glareolus from 10 localities across species range assigned to different lineages based on mtDNA. We found clear discrepancies between population structure in mtDNA and each of the studied innate immunity genes. There was no uniform pattern of spatial variation at immunity loci, they differed in the levels of polymorphism, and the results of neutrality tests were not consistent over loci. Each locus comprised a few common haplotypes shared between mitochondrial lineages and studied locations, plus numerous haplotypes unique for each studied site. Our results suggest that the diversity of innate immunity genes cannot be explained solely in terms of demographic processes, and that the observed polymorphism may be attributed to local selection. The strength and direction of selection differed between loci, even within the same gene family, which underlines how crucial it is to take a complex approach while studying the selection patterns acting on immune-related genes.
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Purifying selection shaping the evolution of the Toll-like receptor 2 TIR domain in brown hares (Lepus europaeus) from Europe and the Middle East. Mol Biol Rep 2020; 47:2975-2984. [PMID: 32236892 DOI: 10.1007/s11033-020-05382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular Toll/interleukin-1 receptor (TIR) domain important for downstream signal transduction. Here, we analyze the genetic variability of TIR nucleotide and amino-acid sequences of the TLR2 gene in 243 brown hares from Europe and the Middle East and tested for the presence of selection signals and spatial structuring. TLR2 TIR domain sequences were PCR amplified and sequenced, while genotyping was performed by phasing. Genetic diversity indices were calculated in DnaSP and Arlequin, while presence of selection signals was tested using MEGA and the Datamonkey web server. The presence of spatial patterns in TIR sequence distribution was tested by spatial Principal Component Analysis (sPCA) in adegenet. A total of 13 haplotypes were revealed with haplotype diversity of 0.424, and nucleotide diversity (π) of 0.00138. Two spatial clusters were revealed: "Anatolia/Middle East" and "Europe". In Anatolia the two most prevalent amino-acid variants, A and B (the latter being the most ancestral) were maintained at similar frequencies; but in Europe a shift in genotype frequencies was observed as well as a higher number of nonsynonymous substitutions giving rise to novel amino-acid protein variants originating from the evolutionarily younger protein variant. Molecular diversity (haplotype and nucleotide diversity) indices were significantly higher in the "Anatolia/Middle East" cluster. A signal of purifying selection was detected acting on the TIR sequences.
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Batra V, Maheshwarappa A, Dagar K, Kumar S, Soni A, Kumaresan A, Kumar R, Datta TK. Unusual interplay of contrasting selective pressures on β-defensin genes implicated in male fertility of the Buffalo (Bubalus bubalis). BMC Evol Biol 2019; 19:214. [PMID: 31771505 PMCID: PMC6878701 DOI: 10.1186/s12862-019-1535-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 10/22/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The buffalo, despite its superior milk-producing ability, suffers from reproductive limitations that constrain its lifetime productivity. Male sub-fertility, manifested as low conception rates (CRs), is a major concern in buffaloes. The epididymal sperm surface-binding proteins which participate in the sperm surface remodelling (SSR) events affect the survival and performance of the spermatozoa in the female reproductive tract (FRT). A mutation in an epididymal secreted protein, beta-defensin 126 (DEFB-126/BD-126), a class-A beta-defensin (CA-BD), resulted in decreased CRs in human cohorts across the globe. To better understand the role of CA-BDs in buffalo reproduction, this study aimed to identify the BD genes for characterization of the selection pressure(s) acting on them, and to identify the most abundant CA-BD transcript in the buffalo male reproductive tract (MRT) for predicting its reproductive functional significance. RESULTS Despite the low protein sequence homology with their orthologs, the CA-BDs have maintained the molecular framework and the structural core vital to their biological functions. Their coding-sequences in ruminants revealed evidence of pervasive purifying and episodic diversifying selection pressures. The buffalo CA-BD genes were expressed in the major reproductive and non-reproductive tissues exhibiting spatial variations. The Buffalo BD-129 (BuBD-129) was the most abundant and the longest CA-BD in the distal-MRT segments and was predicted to be heavily O-glycosylated. CONCLUSIONS The maintenance of the structural core, despite the sequence divergence, indicated the conservation of the molecular functions of the CA-BDs. The expression of the buffalo CA-BDs in both the distal-MRT segments and non-reproductive tissues indicate the retention the primordial microbicidal activity, which was also predicted by in silico sequence analyses. However, the observed spatial variations in their expression across the MRT hint at their region-specific roles. Their comparison across mammalian species revealed a pattern in which the various CA-BDs appeared to follow dissimilar evolutionary paths. This pattern appears to maintain only the highly efficacious CA-BD alleles and diversify their functional repertoire in the ruminants. Our preliminary results and analyses indicated that BuBD-129 could be the functional ortholog of the primate DEFB-126. Further studies are warranted to assess its molecular functions to elucidate its role in immunity, reproduction and fertility.
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Affiliation(s)
- Vipul Batra
- Animal Genomics Lab, National Dairy Research Institute, Karnal, 132001, India
| | | | - Komal Dagar
- Animal Genomics Lab, National Dairy Research Institute, Karnal, 132001, India
| | - Sandeep Kumar
- Animal Genomics Lab, National Dairy Research Institute, Karnal, 132001, India
| | - Apoorva Soni
- Animal Genomics Lab, National Dairy Research Institute, Karnal, 132001, India
| | - A Kumaresan
- Theriogenology Lab, SRS of NDRI, Bengaluru, 560030, India
| | - Rakesh Kumar
- Animal Genomics Lab, National Dairy Research Institute, Karnal, 132001, India
| | - T K Datta
- Animal Genomics Lab, National Dairy Research Institute, Karnal, 132001, India.
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Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps. PLoS Comput Biol 2019; 15:e1007426. [PMID: 31710623 PMCID: PMC6872172 DOI: 10.1371/journal.pcbi.1007426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 11/21/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Selective sweeps, the genetic footprint of positive selection, have been extensively studied in the past decades, with dozens of methods developed to identify swept regions. However, these methods suffer from both false positive and false negative reports, and the candidates identified with different methods are often inconsistent with each other. We propose that a biological cause of this problem can be population subdivision, and a technical cause can be incomplete, or inaccurate, modeling of the dynamic process associated with sweeps. Here we used simulations to show how these effects interact and potentially cause bias. In particular, we show that sweeps maybe misclassified as either hard or soft, when the true time stage of a sweep and that implied, or pre-supposed, by the model do not match. We call this "temporal misclassification". Similarly, "spatial misclassification (softening)" can occur when hard sweeps, which are imported by migration into a new subpopulation, are falsely identified as soft. This can easily happen in case of local adaptation, i.e. when the sweeping allele is not under positive selection in the new subpopulation, and the underlying model assumes panmixis instead of substructure. The claim that most sweeps in the evolutionary history of humans were soft, may have to be reconsidered in the light of these findings.
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Adrian J, Bonsignore P, Hammer S, Frickey T, Hauck CR. Adaptation to Host-Specific Bacterial Pathogens Drives Rapid Evolution of a Human Innate Immune Receptor. Curr Biol 2019; 29:616-630.e5. [PMID: 30744974 DOI: 10.1016/j.cub.2019.01.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/12/2018] [Accepted: 01/22/2019] [Indexed: 12/25/2022]
Abstract
The selective pressure by infectious agents is a major driving force in the evolution of humans and other mammals. Members of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family serve as receptors for bacterial pathogens of the genera Haemophilus, Helicobacter, Neisseria, and Moraxella, which engage CEACAMs via distinct surface adhesins. While microbial attachment to epithelial CEACAMs facilitates host colonization, recognition by CEACAM3, a phagocytic receptor expressed by granulocytes, eliminates CEACAM-binding bacteria. Sequence analysis of primate CEACAM3 orthologs reveals that this innate immune receptor is one of the most rapidly evolving human proteins. In particular, the pathogen-binding extracellular domain of CEACAM3 shows a high degree of non-synonymous versus synonymous nucleotide exchanges, indicating an exceptionally strong positive selection. Using CEACAM3 domains derived from different primates, we find that the amino acid alterations found in CEACAM3 translate into characteristic binding patterns for bacterial adhesins. One such amino acid residue is F62 in human and chimp CEACAM3, which is not present in other primates and which is critical for binding the OMP P1 adhesin of Haemophilus aegyptius. Incorporation of the F62-containing motif into gorilla CEACAM3 results in a gain-of-function phenotype with regard to phagocytosis of H. aegyptius. Moreover, CEACAM3 polymorphisms found in human subpopulations widen the spectrum of recognized bacterial adhesins, suggesting an ongoing multivariate selection acting on this innate immune receptor. The species-specific detection of diverse bacterial adhesins helps to explain the exceptionally fast evolution of CEACAM3 within the primate lineage and provides an example of Red Queen dynamics in the human genome.
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Affiliation(s)
- Jonas Adrian
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Patrizia Bonsignore
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Sebastian Hammer
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Tancred Frickey
- Forest Industry Informatics, Scion, Te Papa Tipu Innovation Park, 49 Sala Street, 3015 Rotorua, New Zealand; Konstanz Research School-Chemical Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Christof R Hauck
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany; Konstanz Research School-Chemical Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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10
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Whiteoak AM, Ideozu J, Alkathiry H, Tomlinson AJ, Delahay RJ, Cowen S, Mullineaux E, Gormley E, Birtles RJ, Lun ZR, Hide G. Investigation into the genetic diversity in toll-like receptors 2 and 4 in the European badger Meles meles. Res Vet Sci 2018; 119:228-231. [PMID: 30005397 DOI: 10.1016/j.rvsc.2018.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/23/2018] [Accepted: 06/28/2018] [Indexed: 01/14/2023]
Abstract
The Toll-like receptor (TLR) genes are a conserved family of genes central to the innate immune response to pathogen infection. They encode receptor proteins, recognise pathogen associated molecular patterns (PAMPs) and trigger initial immune responses. In some host-pathogen systems, it is reported that genetic differences, such as single nucleotide polymorphisms (SNPs), associate with disease resistance or susceptibility. Little is known about TLR gene diversity in the European badger (Meles meles). We collected DNA from UK badgers, carried out PCR amplification of the badger TLR2 gene and exon 3 of TLR4 and determined DNA sequences for individual badgers for TLR2 (n = 61) and TLR4 exon 3 (n = 59). No polymorphism was observed in TLR4. Three TLR2 amino acid haplotype variants were found. Ninety five percent of badgers were homozygous for one common haplotype (H1), the remaining three badgers had genotypes H1/H3, H1/H2 and H2/H2. By broad comparison with other species, diversity in TLR genes in badgers seems low. This could be due to a relatively localised sampling or inherent low genetic diversity. Further studies are required to assess the generality of the low observed diversity and the relevance to the immunological status of badgers.
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Affiliation(s)
- Andrew M Whiteoak
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK
| | - Justin Ideozu
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK
| | - Hadil Alkathiry
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK
| | - Alexandra J Tomlinson
- National Wildlife Management Centre, Animal and Plant Health Agency, Woodchester Park, Gloucestershire GL10 3UJ, UK
| | - Richard J Delahay
- National Wildlife Management Centre, Animal and Plant Health Agency, Woodchester Park, Gloucestershire GL10 3UJ, UK
| | - Sara Cowen
- Secret World Wildlife Rescue, New Road, East Huntspill, Highbridge TA9 3PZ, UK
| | | | - Eamonn Gormley
- School of Veterinary Medicine, Veterinary Science Centre, University College Dublin (UCD), Belfield, Dublin 4, Ireland
| | - Richard J Birtles
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK
| | - Zhao-Rong Lun
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK; State Key Laboratory of Biocontrol, School of Life Sciences, Key Laboratory of Tropical Diseases and Control of the Ministry of Education, Zhongshan Medical School, Sun Yat-Sen University, Guangzhou 510275, PR China; Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK
| | - Geoff Hide
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK; Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, M5 4WT, UK.
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Divergence of protein sensing (TLR 4, 5) and nucleic acid sensing (TLR 3, 7) within the reptilian lineage. Mol Phylogenet Evol 2017; 119:210-224. [PMID: 29196206 DOI: 10.1016/j.ympev.2017.11.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 10/22/2017] [Accepted: 11/27/2017] [Indexed: 11/21/2022]
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12
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David S, Aguiar P, Antunes L, Dias A, Morais A, Sakuntabhai A, Lavinha J. Variants in the non-coding region of the TLR2 gene associated with infectious subphenotypes in pediatric sickle cell anemia. Immunogenetics 2017; 70:37-51. [DOI: 10.1007/s00251-017-1013-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/07/2017] [Indexed: 12/14/2022]
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Early AM, Clark AG. Genomic signatures of local adaptation in the Drosophila immune response. Fly (Austin) 2017; 11:277-283. [PMID: 28586288 DOI: 10.1080/19336934.2017.1337612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
As environments and pathogen landscapes shift, host defenses must evolve to remain effective. Due to this selection pressure, among-species comparisons of genetic sequence data often find immune genes to be among the fastest evolving genes across the genome. The full extent and nature of these immune adaptations, however, remain largely unexplored. In a recent study, we analyzed patterns of selection within distinct components of the Drosophila melanogaster immune pathway. While we found evidence of positive selection within some immune processes, immune genes were not universally characterized by signatures of strong selection. On the contrary, we even found that some immune functions show greater than expected constraint. Overall these results highlight 2 major factors that appear to play an outsize role in determining a gene's evolutionary rate: the type of pathogen the gene targets and the gene's position within the immune network. These results join a growing body of literature that highlight the complexity of immune adaptation. Rather than there being uniformly strong selection across all immune genes, a combination of pathogen-specificity and host genetic constraints appear to play key roles in determining each immune gene's individual evolutionary trajectory.
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Affiliation(s)
- Angela M Early
- a Department of Molecular Biology and Genetics , Cornell University , Ithaca , NY.,b Infectious Disease and Microbiome Program , Broad Institute of MIT and Harvard , Cambridge , MA
| | - Andrew G Clark
- a Department of Molecular Biology and Genetics , Cornell University , Ithaca , NY
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14
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Das Ghosh D, Mukhopadhyay I, Bhattacharya A, Roy Chowdhury R, Mandal NR, Roy S, Sengupta S. Impact of genetic variations and transcriptional alterations of HLA class I genes on cervical cancer pathogenesis. Int J Cancer 2017; 140:2498-2508. [PMID: 28268260 DOI: 10.1002/ijc.30681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 02/23/2017] [Indexed: 01/21/2023]
Abstract
In a novel attempt to understand the variations in DNA sequences underlying HLA class I alleles associated with HPV16-related CaCx, we determined the alleles by reconstructing SNP-based haplotypes from resequencing of the most polymorphic exons 2 and 3 of HLA-A, HLA-B and HLA-C. We also determined the impact of SNPs and transcriptional alterations of the genes on CaCx. A high density of SNPs was identified from resequencing. HLA expression was determined by real-time PCR. We identified that even a single associated HLA allele had many underlying SNP-based haplotypes. Out of the most frequent (≥5%) HLA class I alleles, HLA-B*40:06 and HLA-B*15:02 respectively imparted significant risk towards and protection from CaCx as well as HPV16 infection. Employing median-joining networks to detect clusters of sequence-variations for specific HLA alleles, we found the protective SNP-based signature, GAATTTA, in all SNP-based haplotypes of HLA-B*15:02 allele. The signature was derived from seven SNPs within HLA-B which were newly associated with the disease. Contrarily, similarly derived risk-signature, TTGCGCC, mapped only to 52% of SNP-based haplotypes of HLA-B*40:06 allele. This indicated that all SNP-based haplotypes underlying a particular associated HLA allele might or might not have a single signature of risk/protection. HLA-A, HLA-B and HLA-C expressions were downregulated among CaCx cases compared to asymptomatic infections and HPV-negative controls. HLA-A and HLA-B were repressed in both cases harbouring episomal and integrated HPV16, whereas HLA-C in only the latter. Novel genetic variations and differential downregulation-patterns of HLA class I have a significant bearing on HPV16-related CaCx pathogenesis.
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Affiliation(s)
| | | | - Amrapali Bhattacharya
- Cancer Genomics and Epigenomics, National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, Kalyani, West Bengal, India
| | - Rahul Roy Chowdhury
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Nidhu Ranjan Mandal
- Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Sudipta Roy
- Department of Pathology, Sri Aurobindo Seva Kendra, Kolkata, West Bengal, India
| | - Sharmila Sengupta
- Cancer Genomics and Epigenomics, National Institute of Biomedical Genomics, Netaji Subhas Sanatorium, Kalyani, West Bengal, India
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15
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Ishengoma E, Agaba M. Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification. BMC Evol Biol 2017; 17:54. [PMID: 28209121 PMCID: PMC5314619 DOI: 10.1186/s12862-017-0901-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/02/2017] [Indexed: 11/17/2022] Open
Abstract
Background Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined. In addition, comparison of the patterning of key TLR motifs and domains between giraffe and related species was performed. The quantification of selection pressure and divergence on TLRs among terrestrial ungulates and cetaceans was also performed. Results Sequence analysis shows that giraffe has 94–99% nucleotide identity with okapi and cattle for all TLRs analyzed. Variations in the number of Leucine-rich repeats were observed in some of TLRs between giraffe, okapi and cattle. Patterning of key TLR domains did not reveal any significant differences in the domain architecture among giraffe, okapi and cattle. Molecular evolutionary analysis for selection pressure identifies positive selection on key sites for all TLRs examined suggesting that pervasive evolutionary pressure has taken place during the evolution of terrestrial ungulates and cetaceans. Analysis of positively selected sites showed some site to be part of Leucine-rich motifs suggesting functional relevance in species-specific recognition of pathogen associated molecular patterns. Notably, clade analysis reveals significant selection divergence between terrestrial ungulates and cetaceans in viral sensing TLR3. Mapping of giraffe TLR3 key substitutions to the structure of the receptor indicates that at least one of giraffe altered sites coincides with TLR3 residue known to play a critical role in receptor signaling activity. Conclusion There is overall structural conservation in TLRs among giraffe, okapi and cattle indicating that the mechanism for innate immune response utilizing TLR pathways may not have changed very much during the evolution of these species. However, a broader phylogenetic analysis revealed signatures of adaptive evolution among terrestrial ungulates and cetaceans, including the observed selection divergence in TLR3. This suggests that long term ecological dynamics has led to species-specific innovation and functional variation in the mechanisms mediating innate immunity in terrestrial ungulates and cetaceans. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0901-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edson Ishengoma
- School of Life Science and Biongineering, The Nelson Mandela African Institution of Sciences and Technology, P.O. Box 447, Arusha, Tanzania. .,Mkwawa University College of Education, University of Dar es Salaam, P.O. Box 2513, Iringa, Tanzania.
| | - Morris Agaba
- School of Life Science and Biongineering, The Nelson Mandela African Institution of Sciences and Technology, P.O. Box 447, Arusha, Tanzania.,Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, GPO00100, Kenya
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16
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Chapman JR, Hellgren O, Helin AS, Kraus RHS, Cromie RL, Waldenström J. The Evolution of Innate Immune Genes: Purifying and Balancing Selection on β-Defensins in Waterfowl. Mol Biol Evol 2016; 33:3075-3087. [DOI: 10.1093/molbev/msw167] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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17
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Babik W, Dudek K, Fijarczyk A, Pabijan M, Stuglik M, Szkotak R, Zieliński P. Constraint and adaptation in newt toll-like receptor genes. Genome Biol Evol 2014; 7:81-95. [PMID: 25480684 PMCID: PMC4316619 DOI: 10.1093/gbe/evu266] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Acute die-offs of amphibian populations worldwide have been linked to the emergence of viral and fungal diseases. Inter and intraspecific immunogenetic differences may influence the outcome of infection. Toll-like receptors (TLRs) are an essential component of innate immunity and also prime acquired defenses. We report the first comprehensive assessment of TLR gene variation for urodele amphibians. The Lissotriton newt TLR repertoire includes representatives of 13 families and is compositionally most similar to that of the anuran Xenopus. Both ancient and recent gene duplications have occurred in urodeles, bringing the total number of TLR genes to at least 21. Purifying selection has predominated the evolution of newt TLRs in both long (∼70 Ma) and medium (∼18 Ma) timescales. However, we find evidence for both purifying and positive selection acting on TLRs in two recently diverged (2-5 Ma) allopatric evolutionary lineages (Lissotriton montandoni and L. vulgaris graecus). Overall, both forms of selection have been stronger in L. v. graecus, while constraint on most TLR genes in L. montandoni appears relaxed. The differences in selection regimes are unlikely to be biased by demographic effects because these were controlled by means of a historical demographic model derived from an independent data set of 62 loci. We infer that TLR genes undergo distinct trajectories of adaptive evolution in closely related amphibian lineages, highlight the potential of TLRs to capture the signatures of different assemblages of pathogenic microorganisms, and suggest differences between lineages in the relative roles of innate and acquired immunity.
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Affiliation(s)
- Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Maciej Pabijan
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Michał Stuglik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Rafał Szkotak
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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