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Hedtke SM, Post RJ, Feleke SM, Gebretsadik FS, Boakye DA, Krueger A, Grant WN, Wilding CS. Cytotaxonomic characterization and estimation of migration patterns of onchocerciasis vectors (Simulium damnosum sensu lato) in northwestern Ethiopia based on RADSeq data. PLoS Negl Trop Dis 2024; 18:e0011868. [PMID: 38175836 DOI: 10.1371/journal.pntd.0011868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/17/2024] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND While much progress has been made in the control and elimination of onchocerciasis across Africa, the extent to which vector migration might confound progress towards elimination or result in re-establishment of endemism in areas where transmission has been eliminated remains unclear. In Northern Ethiopia, Metema and Metekel-two foci located near the Sudan border-exhibit continuing transmission. While progress towards elimination has been faster in Metema, there remains a problematic hotspot of transmission. Whether migration from Metekel contributes to this is currently unknown. METHODOLOGY/PRINCIPLE FINDINGS To assess the role of vector migration from Metekel into Metema, we present a population genomics study of 151 adult female vectors using 47,638 RADseq markers and mtDNA CoI sequencing. From additional cytotaxonomy data we identified a new cytoform in Metema, closely related to S. damnosum s.str, here called the Gondar form. RADseq data strongly indicate the existence of two distinctly differentiated clusters within S. damnosum s.l.: one genotypic cluster found only in Metema, and the second found predominantly in Metekel. Because blackflies from both clusters were found in sympatry (in all four collection sites in Metema), but hybrid genotypes were not detected, there may be reproductive barriers preventing interbreeding. The dominant genotype in Metema was not found in Metekel while the dominant genotype in Metekel was found in Metema, indicating that (at the time of sampling) migration is primarily unidirectional, with flies moving from Metekel to Metema. There was strong differentiation between clusters but little genetic differentiation within clusters, suggesting migration and gene flow of flies within the same genetic cluster are sufficient to prevent genetic divergence between sites. CONCLUSIONS/SIGNIFICANCE Our results confirm that Metekel and Metema represent different transmission foci, but also indicate a northward movement of vectors between foci that may have epidemiological importance, although its significance requires further study.
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Affiliation(s)
- Shannon M Hedtke
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Rory J Post
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
- Disease Control Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Fikre Seife Gebretsadik
- Neglected Tropical Disease Prevention and Control Program, Federal Ministry of Health, Addis Ababa, Ethiopia
| | - Daniel A Boakye
- Parasitology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Andreas Krueger
- Military Hospital Hamburg, Department Tropical Medicine, Hamburg, Germany
| | - Warwick N Grant
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
| | - Craig S Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
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Dyer NA, Lucas ER, Nagi SC, McDermott DP, Brenas JH, Miles A, Clarkson CS, Mawejje HD, Wilding CS, Halfon MS, Asma H, Heinz E, Donnelly MJ. Mechanisms of transcriptional regulation in Anopheles gambiae revealed by allele specific expression. bioRxiv 2023:2023.11.22.568226. [PMID: 38045426 PMCID: PMC10690255 DOI: 10.1101/2023.11.22.568226] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Malaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved by elevated expression of detoxifying enzymes that metabolize the insecticide. In diploid organisms, gene expression is regulated both in cis, by regulatory sequences on the same chromosome, and by trans acting factors, affecting both alleles equally. Differing levels of transcription can be caused by mutations in cis-regulatory modules (CRM), but few of these have been identified in mosquitoes. We crossed bendiocarb resistant and susceptible Anopheles gambiae strains to identify cis-regulated genes that might be responsible for the resistant phenotype using RNAseq, and cis-regulatory module sequences controlling gene expression in insecticide resistance relevant tissues were predicted using machine learning. We found 115 genes showing allele specific expression in hybrids of insecticide susceptible and resistant strains, suggesting cis regulation is an important mechanism of gene expression regulation in Anopheles gambiae. The genes showing allele specific expression included a higher proportion of Anopheles specific genes on average younger than genes those with balanced allelic expression.
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Affiliation(s)
- Naomi A Dyer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Eric R Lucas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Sanjay C Nagi
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Daniel P McDermott
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Jon H Brenas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Alistair Miles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Chris S Clarkson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Henry D Mawejje
- Infectious Diseases Research Collaboration (IDRC), Plot 2C Nakasero Hill Road, P.O.Box 7475, Kampala, Uganda
| | - Craig S Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Marc S Halfon
- Department of Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo-State University of New York, 955 Main Street, Buffalo, New York 14203, USA
| | - Hasiba Asma
- Department of Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo-State University of New York, 955 Main Street, Buffalo, New York 14203, USA
| | - Eva Heinz
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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Howarth ERI, Szott ID, Witham CL, Wilding CS, Bethell EJ. Genetic polymorphisms in the serotonin, dopamine and opioid pathways influence social attention in rhesus macaques (Macaca mulatta). PLoS One 2023; 18:e0288108. [PMID: 37531334 PMCID: PMC10395878 DOI: 10.1371/journal.pone.0288108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 03/09/2023] [Accepted: 06/20/2023] [Indexed: 08/04/2023] Open
Abstract
Behaviour has a significant heritable component; however, unpicking the variants of interest in the neural circuits and molecular pathways that underpin these has proven difficult. Here, we present a comprehensive analysis of the relationship between known and new candidate genes from identified pathways and key behaviours for survival in 109 adult rhesus macaques (Macaca mulatta). Eight genes involved in emotion were analysed for variation at a total of nine loci. Genetic data were then correlated with cognitive and observational measures of behaviour associated with wellbeing and survival using MCMC-based Bayesian GLMM in R, to account for relatedness within the macaque population. For four loci the variants genotyped were length polymorphisms (SLC6A4 5-hydroxytryptamine transporter length-polymorphic repeat (5-HTTLPR), SLC6A4 STin polymorphism, Tryptophan 5-hydroxylase 2 (TPH2) and Monoamine oxidase A (MAOA)) whilst for the other five (5-hydroxytryptamine receptor 2A (HTR2A), Dopamine Receptor D4 (DRD4), Oxytocin receptor (OXTR), Arginine vasopressin receptor 1A (AVPR1a), Opioid receptor mu(μ) 1 (OPRM1)) SNPs were analysed. STin genotype, DRD4 haplotype and OXTR haplotype were significantly associated with the cognitive and observational measures of behaviour associated with wellbeing and survival. Genotype for 5-HTTLPR, STin and AVPR1a, and haplotype for HTR2A, DRD4 and OXTR were significantly associated with the duration of behaviours including fear and anxiety. Understanding the biological underpinnings of individual variation in negative emotion (e.g., fear and anxiety), together with their impact on social behaviour (e.g., social attention including vigilance for threat) has application for managing primate populations in the wild and captivity, as well as potential translational application for understanding of the genetic basis of emotions in humans.
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Affiliation(s)
- Emmeline R. I. Howarth
- Research Centre in Brain and Behaviour, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
- Department of Biological Sciences, University of Chester, Chester, United Kingdom
| | - Isabelle D. Szott
- Research Centre in Brain and Behaviour, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Claire L. Witham
- Centre for Macaques, Harwell Institute, Medical Research Council, Salisbury, United Kingdom
| | - Craig S. Wilding
- Biodiversity and Conservation Group, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Emily J. Bethell
- Research Centre in Brain and Behaviour, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
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Trissi N, Troczka BJ, Ozsanlav-Harris L, Singh KS, Mallott M, Aishwarya V, O'Reilly A, Bass C, Wilding CS. Differential regulation of the Tor gene homolog drives the red/green pigmentation phenotype in the aphid Myzuspersicae. Insect Biochem Mol Biol 2023; 153:103896. [PMID: 36587809 DOI: 10.1016/j.ibmb.2022.103896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
In some aphid species, intraspecific variation in body colour is caused by differential carotenoid content: whilst green aphids contain only yellow carotenoids (β-, γ-, and β,γ-carotenes), red aphids additionally possess red carotenoids (torulene and 3,4-didehydrolycopene). Unusually, within animals who typically obtain carotenoids from their diet, ancestral horizontal gene transfer of carotenoid biosynthetic genes from fungi (followed by gene duplication), have imbued aphids with the intrinsic gene repertoire necessary to biosynthesise carotenoids. In the pea aphid, Acyrthosiphon pisum a lycopene (phytoene) desaturase gene (Tor) underpins the red/green phenotype, with this locus present in heterozygous form in red individuals but absent in green aphids, resulting in them being unable to convert lycopene into the red compounds 3,4-didehydrolycopene and torulene. The green peach aphid, Myzus persicae, separated from the pea aphid for ≈45MY also exists as distinct colour variable morphs, with both red and green individuals present. Here, we examined genomic data for both red and green morphs of M. persicae and identified an enlarged (compared to A. pisum) repertoire of 16 carotenoid biosynthetic genes (11 carotenoid desaturases and five carotenoid cyclase/synthase genes). From these, we identify the homolog of A. pisum Tor (here called carotene desaturase 2 or CDE-2) and show through 3D modelling that this homolog can accommodate the torulene precursor lycopene and, through RNA knockdown feeding experiments, demonstrate that disabling CDE-2 expression in red M. persicae clones results in green-coloured offspring. Unlike in A. pisum, we show that functional CDE-2 is present in the genomes of both red and green aphids. However, expression differences between the two colour morphs (350-700 fold CDE-2 overexpression in red clones), potentially driven by variants identified in upstream putative regulatory elements, underpin this phenotype. Thus, whilst aphids have a common origin of their carotenoid biosynthetic pathway, two aphid species separated for over 40MY have evolved very different drivers of intraspecific colour variation.
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Affiliation(s)
- Nasser Trissi
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Bartlomiej J Troczka
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Luke Ozsanlav-Harris
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Kumar Saurabh Singh
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Mark Mallott
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | | | - Andrias O'Reilly
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK.
| | - Craig S Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.
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Vendrami DLJ, Hoffman JI, Wilding CS. Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species. Genes (Basel) 2022; 14:14. [PMID: 36672754 PMCID: PMC9858869 DOI: 10.3390/genes14010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria-Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus.
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Affiliation(s)
- David L. J. Vendrami
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33615 Bielefeld, Germany
| | - Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33615 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Craig S. Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
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6
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Wilding CS. Regulating resistance: CncC:Maf, antioxidant response elements and the overexpression of detoxification genes in insecticide resistance. Curr Opin Insect Sci 2018; 27:89-96. [PMID: 30025640 DOI: 10.1016/j.cois.2018.04.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/12/2018] [Accepted: 04/09/2018] [Indexed: 05/24/2023]
Abstract
Although genetic and genomic tools have greatly furthered our understanding of resistance-associated mutations in molecular target sites of insecticides, the genomic basis of transcriptional regulation of detoxification loci in insect pests and vectors remains relatively unexplored. Recent work using RNAi, reporter assays and comparative genomics are beginning to reveal the molecular architecture of this response, identifying critical transcription factors and their binding sites. Central to this is the insect ortholog of the mammalian transcription factor Nrf2, Cap 'n' Collar isoform-C (CncC) which as a heterodimer with Maf-S regulates the transcription of phase I, II and III detoxification loci in a range of insects, with CncC knockdown or upregulation directly affecting phenotypic resistance. CncC:Maf binds to specific antioxidant response element sequences upstream of detoxification genes to initiate transcription. Recent work is now identifying these binding sites for resistance-associated loci and, coupled with genome sequence data and reporter assays, enabling identification of polymorphisms in the CncC:Maf binding site which regulate the insecticide resistance phenotype.
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Affiliation(s)
- Craig S Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK.
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7
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Edmunds C, Post RJ, Wilding CS, Rae R. A survey investigating the diversity and distribution of entomopathogenic nematodes in the UK and the first confirmed UK record of Steinernema carpocapsae. NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Summary
Entomopathogenic nematodes (EPN) of the families Steinernematidae and Heterorhabditidae are lethal insect parasites that have been commercialised as biological control agents. EPN have been isolated from across the world but it has been more than 20 years since the last survey of the UK, and species like Steinernema carpocapsae have never been found here and positively identified through molecular biology. We collected 518 soil samples from a diverse range of habitats across the UK and baited them with Galleria mellonella to isolate EPN. Dead G. mellonella were placed in White traps and emergent EPN underwent DNA barcoding analyses. From the 518 samples, 3.5% were positive for EPN. No Heterorhabditis species were found, but seven isolates of S. glaseri, one isolate of S. feltiae, eight isolates of S. affine and two isolates of S. carpocapsae were found. This was the first confirmed record of S. carpocapsae in the UK.
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Affiliation(s)
- Cassandra Edmunds
- Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Rory J. Post
- Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Craig S. Wilding
- Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Robbie Rae
- Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
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Gomes B, Wilding CS, Weetman D, Sousa CA, Novo MT, Savage HM, Almeida APG, Pinto J, Donnelly MJ. Limited genomic divergence between intraspecific forms of Culex pipiens under different ecological pressures. BMC Evol Biol 2015; 15:197. [PMID: 26377220 PMCID: PMC4573496 DOI: 10.1186/s12862-015-0477-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 06/01/2015] [Accepted: 09/03/2015] [Indexed: 01/01/2023] Open
Abstract
Background Divergent selection can be a major driver of ecological speciation. In insects of medical importance, understanding the speciation process is both of academic interest and public health importance. In the West Nile virus vector Culex pipiens, intraspecific pipiens and molestus forms vary in ecological and physiological traits. Populations of each form appear to share recent common ancestry but patterns of genetic differentiation across the genome remain unknown. Here, we undertook an AFLP genome scan on samples collected from both sympatric and allopatric populations from Europe and the USA to quantify the extent of genomic differentiation between the two forms. Results The forms were clearly differentiated but each exhibited major population sub-structuring between continents. Divergence between pipiens and molestus forms from USA was higher than in both inter- and intra-continental comparisons with European samples. The proportion of outlier loci between pipiens and molestus (≈3 %) was low but consistent in both continents, and similar to those observed between sibling species of other mosquito species which exhibit contemporary gene flow. Only two of the outlier loci were shared between inter-form comparisons made within Europe and USA. Conclusion This study supports the molestus and pipiens status as distinct evolutionary entities with low genomic divergence. The low number of shared divergent loci between continents suggests a relatively limited number of genomic regions determining key typological traits likely to be driving incipient speciation and/or adaptation of molestus to anthropogenic habitats. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0477-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bruno Gomes
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008, Lisbon, Portugal. .,Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Craig S Wilding
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK. .,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, L3 3AF, UK.
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Carla A Sousa
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008, Lisbon, Portugal.
| | - Maria T Novo
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008, Lisbon, Portugal.
| | - Harry M Savage
- Centers for Disease Control and Prevention, 3156 Rampart Road, Fort Collins, CO, 80521, USA.
| | - António P G Almeida
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008, Lisbon, Portugal.
| | - João Pinto
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008, Lisbon, Portugal.
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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Weetman D, Mitchell SN, Wilding CS, Birks DP, Yawson AE, Essandoh J, Mawejje HD, Djogbenou LS, Steen K, Rippon EJ, Clarkson CS, Field SG, Rigden DJ, Donnelly MJ. Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae. Mol Ecol 2015; 24:2656-72. [PMID: 25865270 PMCID: PMC4447564 DOI: 10.1111/mec.13197] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [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] [Received: 01/02/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 12/27/2022]
Abstract
Functionally constrained genes are ideal insecticide targets because disruption is often fatal, and resistance mutations are typically costly. Synaptic acetylcholinesterase (AChE) is an essential neurotransmission enzyme targeted by insecticides used increasingly in malaria control. In Anopheles and Culex mosquitoes, a glycine–serine substitution at codon 119 of the Ace-1 gene confers both resistance and fitness costs, especially for 119S/S homozygotes. G119S in Anopheles gambiae from Accra (Ghana) is strongly associated with resistance, and, despite expectations of cost, resistant 119S alleles are increasing significantly in frequency. Sequencing of Accra females detected only a single Ace-1 119S haplotype, whereas 119G diversity was high overall but very low at non-synonymous sites, evidence of strong purifying selection driven by functional constraint. Flanking microsatellites showed reduced diversity, elevated linkage disequilibrium and high differentiation of 119S, relative to 119G homozygotes across up to two megabases of the genome. Yet these signals of selection were inconsistent and sometimes weak tens of kilobases from Ace-1. This unexpected finding is attributable to apparently ubiquitous amplification of 119S alleles as part of a large copy number variant (CNV) far exceeding the size of the Ace-1 gene, whereas 119G alleles were unduplicated. Ace-1 CNV was detectable in archived samples collected when the 119S allele was rare in Ghana. Multicopy amplification of resistant alleles has not been observed previously and is likely to underpin the recent increase in 119S frequency. The large CNV compromised localization of the strong selective sweep around Ace-1, emphasizing the need to integrate CNV analysis into genome scans for selection.
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Affiliation(s)
- David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Sara N Mitchell
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Craig S Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Daniel P Birks
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Alexander E Yawson
- Biotechnology and Nuclear Agriculture Research Institute, Ghana Atomic Energy Commission, Kwabenya, Accra, Ghana.,Department of Molecular Biology and Biotechnology, University of Cape Coast, Cape Coast, Ghana
| | - John Essandoh
- Department of Wildlife and Entomology, University of Cape Coast, Cape Coast, Ghana
| | | | - Luc S Djogbenou
- Institut Regional de Sante Publique de Ouidah, Ouidah, Benin.,Universite d'Abomey-Calavi, Cotonou, Benin
| | - Keith Steen
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Emily J Rippon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Christopher S Clarkson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Stuart G Field
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, USA
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.,Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VLM, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DST, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MKN, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GWC, Tojo M, Topalis P, Tubio JMC, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MAT, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 2014; 347:1258522. [PMID: 25554792 DOI: 10.1126/science.1258522] [Citation(s) in RCA: 362] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.
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Affiliation(s)
- Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA.
| | - Robert M Waterhouse
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Mohammad R Abai
- Department of Medical Entomology and Vector Control, School of Public Health and Institute of Health Researches, Tehran University of Medical Sciences, Tehran, Iran
| | - Sergey S Aganezov
- George Washington University, Department of Mathematics and Computational Biology Institute, 45085 University Drive, Ashburn, VA 20147, USA
| | - Max A Alekseyev
- George Washington University, Department of Mathematics and Computational Biology Institute, 45085 University Drive, Ashburn, VA 20147, USA
| | - James E Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Amon
- National Vector Borne Disease Control Programme, Ministry of Health, Tafea Province, Vanuatu
| | - Bruno Arcà
- Department of Public Health and Infectious Diseases, Division of Parasitology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic-Pomona, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Gleb Artemov
- Tomsk State University, 36 Lenina Avenue, Tomsk, Russia
| | - Lauren A Assour
- Department of Computer Science and Engineering, Eck Institute for Global Health, 211B Cushing Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hamidreza Basseri
- Department of Medical Entomology and Vector Control, School of Public Health and Institute of Health Researches, Tehran University of Medical Sciences, Tehran, Iran
| | - Aaron Berlin
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Bruce W Birren
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Stephanie A Blandin
- Inserm, U963, F-67084 Strasbourg, France. CNRS, UPR9022, IBMC, F-67084 Strasbourg, France
| | - Andrew I Brockman
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Thomas R Burkot
- Faculty of Medicine, Health and Molecular Science, Australian Institute of Tropical Health Medicine, James Cook University, Cairns 4870, Australia
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Clara S Chan
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Joanna C Chiu
- Department of Entomology and Nematology, One Shields Avenue, University of California-Davis, Davis, CA 95616, USA
| | - Mikkel Christensen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlo Costantini
- Institut de Recherche pour le Développement, Unités Mixtes de Recherche Maladies Infectieuses et Vecteurs Écologie, Génétique, Évolution et Contrôle, 911, Avenue Agropolis, BP 64501 Montpellier, France
| | - Victoria L M Davidson
- Division of Biology, Kansas State University, 271 Chalmers Hall, Manhattan, KS 66506, USA
| | - Elena Deligianni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Nikolaou Plastira 100 GR-70013, Heraklion, Crete, Greece
| | - Tania Dottorini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Vicky Dritsou
- Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Stacey B Gabriel
- Genomics Platform, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou 01 BP 2208, Burkina Faso
| | - Andrew B Hall
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Mira V Han
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Thaung Hlaing
- Department of Medical Research, No. 5 Ziwaka Road, Dagon Township, Yangon 11191, Myanmar
| | - Daniel S T Hughes
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Adam M Jenkins
- Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
| | - Xiaofang Jiang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Evdoxia G Kakani
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - Maryam Kamali
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Petri Kemppainen
- Computational Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Ryan C Kennedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Ioannis K Kirmitzoglou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Bioinformatics Research Laboratory, Department of Biological Sciences, New Campus, University of Cyprus, CY 1678 Nicosia, Cyprus
| | - Lizette L Koekemoer
- Wits Research Institute for Malaria, Faculty of Health Sciences, and Vector Control Reference Unit, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, Johannesburg, South Africa
| | - Njoroge Laban
- National Museums of Kenya, P.O. Box 40658-00100, Nairobi, Kenya
| | - Nicholas Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mara K N Lawniczak
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Manolis Lirakis
- Department of Biology, University of Crete, 700 13 Heraklion, Greece
| | - Neil F Lobo
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert M MacCallum
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Chunhong Mao
- Virginia Bioinformatics Institute, 1015 Life Science Circle, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Charles Mbogo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Jenny McCarthy
- Department of Biological Sciences, California State Polytechnic-Pomona, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Kristin Michel
- Division of Biology, Kansas State University, 271 Chalmers Hall, Manhattan, KS 66506, USA
| | - Sara N Mitchell
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02115, USA
| | - Wendy Moore
- Department of Entomology, 1140 East South Campus Drive, Forbes 410, University of Arizona, Tucson, AZ 85721, USA
| | - Katherine A Murphy
- Department of Entomology and Nematology, One Shields Avenue, University of California-Davis, Davis, CA 95616, USA
| | - Anastasia N Naumenko
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Eva M Novoa
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Samantha O'Loughlin
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Chioma Oringanje
- Department of Entomology, 1140 East South Campus Drive, Forbes 410, University of Arizona, Tucson, AZ 85721, USA
| | - Mohammad A Oshaghi
- Department of Medical Entomology and Vector Control, School of Public Health and Institute of Health Researches, Tehran University of Medical Sciences, Tehran, Iran
| | - Nazzy Pakpour
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Philippos A Papathanos
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Ashley N Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Michael Povelones
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Anil Prakash
- Regional Medical Research Centre NE, Indian Council of Medical Research, P.O. Box 105, Dibrugarh-786 001, Assam, India
| | - David P Price
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
| | - Ashok Rajaraman
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Lisa J Reimer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - David C Rinker
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Antonis Rokas
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37235, USA. Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Tanya L Russell
- Faculty of Medicine, Health and Molecular Science, Australian Institute of Tropical Health Medicine, James Cook University, Cairns 4870, Australia
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou 01 BP 2208, Burkina Faso
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Terrance Shea
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Frederic Simard
- Institut de Recherche pour le Développement, Unités Mixtes de Recherche Maladies Infectieuses et Vecteurs Écologie, Génétique, Évolution et Contrôle, 911, Avenue Agropolis, BP 64501 Montpellier, France
| | - Michel A Slotman
- Department of Entomology, Texas A&M University, College Station, TX 77807, USA
| | - Pradya Somboon
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Claudio J Struchiner
- Fundação Oswaldo Cruz, Avenida Brasil 4365, RJ Brazil. Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gregg W C Thomas
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Marta Tojo
- Department of Physiology, School of Medicine, Center for Research in Molecular Medicine and Chronic Diseases, Instituto de Investigaciones Sanitarias, University of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Nikolaou Plastira 100 GR-70013, Heraklion, Crete, Greece
| | - José M C Tubio
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Maria F Unger
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA
| | - John Vontas
- Department of Biology, University of Crete, 700 13 Heraklion, Greece
| | - Catherine Walton
- Computational Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Craig S Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Judith H Willis
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Yi-Chieh Wu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Department of Computer Science, Harvey Mudd College, Claremont, CA 91711, USA
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, Hewitt Hall, Irvine, CA 92697, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Flaminia Catteruccia
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - George K Christophides
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Frank H Collins
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA
| | - Robert S Cornman
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK. Malaria Programme, Wellcome Trust Sanger Institute, Cambridge CB10 1SJ, UK
| | - Scott J Emrich
- Department of Computer Science and Engineering, Eck Institute for Global Health, 211B Cushing Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael C Fontaine
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA. Centre of Evolutionary and Ecological Studies (Marine Evolution and Conservation group), University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, Netherlands
| | - William Gelbart
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA. School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Immo A Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
| | - Paul I Howell
- Centers for Disease Control and Prevention, 1600 Clifton Road NE MSG49, Atlanta, GA 30329, USA
| | - Fotis C Kafatos
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Daniel Lawson
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Christos Louis
- Department of Biology, University of Crete, 700 13 Heraklion, Greece. Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Nikolaou Plastira 100 GR-70013, Heraklion, Crete, Greece. Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Shirley Luckhart
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Marc A T Muskavitch
- Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA. Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA
| | - José M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, 12735 Twinbrook Parkway, Rockville, MD 20852, USA
| | - Michael A Riehle
- Department of Entomology, 1140 East South Campus Drive, Forbes 410, University of Arizona, Tucson, AZ 85721, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhijian Tu
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Laurence J Zwiebel
- Departments of Biological Sciences and Pharmacology, Institutes for Chemical Biology, Genetics and Global Health, Vanderbilt University and Medical Center, Nashville, TN 37235, USA
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.
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Weetman D, Steen K, Rippon EJ, Mawejje HD, Donnelly MJ, Wilding CS. Contemporary gene flow between wild An. gambiae s.s. and An. arabiensis. Parasit Vectors 2014; 7:345. [PMID: 25060488 PMCID: PMC4124135 DOI: 10.1186/1756-3305-7-345] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 03/31/2014] [Accepted: 07/21/2014] [Indexed: 11/10/2022] Open
Abstract
Background In areas where the morphologically indistinguishable malaria mosquitoes Anopheles gambiae Giles and An. arabiensis Patton are sympatric, hybrids are detected occasionally via species-diagnostic molecular assays. An. gambiae and An. arabiensis exhibit both pre- and post-reproductive mating barriers, with swarms largely species-specific and male F1 (first-generation) hybrids sterile. Consequently advanced-stage hybrids (back-crosses to parental species), which would represent a route for potentially-adaptive introgression, are expected to be very rare in natural populations. Yet the use of one or two physically linked single-locus diagnostic assays renders them indistinguishable from F1 hybrids and levels of interspecific gene flow are unknown. Methods We used data from over 350 polymorphic autosomal SNPs to investigate post F1 gene flow via patterns of genomic admixture between An. gambiae and An. arabiensis from eastern Uganda. Simulations were used to investigate the statistical power to detect hybrids with different levels of crossing and to identify the hybrid category significantly admixed genotypes could represent. Results A range of admixture proportions were detected for 11 field-collected hybrids identified via single-locus species-diagnostic PCRs. Comparison of admixture data with simulations indicated that at least seven of these hybrids were advanced generation crosses, with backcrosses to each species identified. In addition, of 36 individuals typing as An. gambiae or An. arabiensis that exhibited outlying admixture proportions, ten were identified as significantly mixed backcrosses, and at least four of these were second or third generation crosses. Conclusions Our results show that hybrids detected using standard diagnostics will often be hybrid generations beyond F1, and that in our study area around 5% (95% confidence intervals 3%-9%) of apparently ‘pure’ species samples may also be backcrosses. This is likely an underestimate because of rapidly-declining detection power beyond the first two backcross generations. Post-F1 gene flow occurs at a far from inconsequential rate between An. gambiae and An. arabiensis, and, especially for traits under strong selection, could readily lead to adaptive introgression of genetic variants relevant for vector control. Electronic supplementary material The online version of this article (doi:10.1186/1756-3305-7-345) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Craig S Wilding
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
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Abdalla H, Wilding CS, Nardini L, Pignatelli P, Koekemoer LL, Ranson H, Coetzee M. Insecticide resistance in Anopheles arabiensis in Sudan: temporal trends and underlying mechanisms. Parasit Vectors 2014; 7:213. [PMID: 24886129 PMCID: PMC4026821 DOI: 10.1186/1756-3305-7-213] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [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: 12/23/2013] [Accepted: 04/08/2014] [Indexed: 12/03/2022] Open
Abstract
Background Malaria vector control in Sudan relies mainly on indoor residual spraying (IRS) and the use of long lasting insecticide treated bed nets (LLINs). Monitoring insecticide resistance in the main Sudanese malaria vector, Anopheles arabiensis, is essential for planning and implementing an effective vector control program in this country. Methods WHO susceptibility tests were used to monitor resistance to insecticides from all four WHO-approved classes of insecticide at four sentinel sites in Gezira state over a three year period. Insecticide resistance mechanisms were studied using PCR and microarray analyses. Results WHO susceptibility tests showed that Anopheles arabiensis from all sites were fully susceptible to bendiocarb and fenitrothion for the duration of the study (2008–2011). However, resistance to DDT and pyrethroids was detected at three sites, with strong seasonal variations evident at all sites. The 1014 F kdr allele was significantly associated with resistance to pyrethroids and DDT (P < 0.001) with extremely high effects sizes (OR > 7 in allelic tests). The 1014S allele was not detected in any of the populations tested. Microarray analysis of the permethrin-resistant population of An. arabiensis from Wad Medani identified a number of metabolic genes that were significantly over-transcribed in the field-collected resistant samples when compared to the susceptible Sudanese An. arabiensis Dongola strain. These included CYP6M2 and CYP6P3, two genes previously implicated in pyrethroid resistance in Anopheles gambiae s.s, and the epsilon-class glutathione-S-transferase, GSTe4. Conclusions These data suggest that both target-site mechanisms and metabolic mechanisms play an important role in conferring pyrethroid resistance in An. arabiensis from Sudan. Identification in An. arabiensis of candidate loci that have been implicated in the resistance phenotype in An. gambiae requires further investigation to confirm the role of these genes.
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Affiliation(s)
| | | | | | | | | | | | - Maureen Coetzee
- Wits Research Institute for Malaria, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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13
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Mitchell SN, Rigden DJ, Dowd AJ, Lu F, Wilding CS, Weetman D, Dadzie S, Jenkins AM, Regna K, Boko P, Djogbenou L, Muskavitch MAT, Ranson H, Paine MJI, Mayans O, Donnelly MJ. Metabolic and target-site mechanisms combine to confer strong DDT resistance in Anopheles gambiae. PLoS One 2014; 9:e92662. [PMID: 24675797 PMCID: PMC3968025 DOI: 10.1371/journal.pone.0092662] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [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] [Received: 09/24/2013] [Accepted: 02/24/2014] [Indexed: 11/22/2022] Open
Abstract
The development of resistance to insecticides has become a classic exemplar of evolution occurring within human time scales. In this study we demonstrate how resistance to DDT in the major African malaria vector Anopheles gambiae is a result of both target-site resistance mechanisms that have introgressed between incipient species (the M- and S-molecular forms) and allelic variants in a DDT-detoxifying enzyme. Sequencing of the detoxification enzyme, Gste2, from DDT resistant and susceptible strains of An. gambiae, revealed a non-synonymous polymorphism (I114T), proximal to the DDT binding domain, which segregated with strain phenotype. Recombinant protein expression and DDT metabolism analysis revealed that the proteins from the susceptible strain lost activity at higher DDT concentrations, characteristic of substrate inhibition. The effect of I114T on GSTE2 protein structure was explored through X-ray crystallography. The amino acid exchange in the DDT-resistant strain introduced a hydroxyl group nearby the hydrophobic DDT-binding region. The exchange does not result in structural alterations but is predicted to facilitate local dynamics and enzyme activity. Expression of both wild-type and 114T alleles the allele in Drosophila conferred an increase in DDT tolerance. The 114T mutation was significantly associated with DDT resistance in wild caught M-form populations and acts in concert with target-site mutations in the voltage gated sodium channel (Vgsc-1575Y and Vgsc-1014F) to confer extreme levels of DDT resistance in wild caught An. gambiae.
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Affiliation(s)
- Sara N. Mitchell
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew J. Dowd
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Fang Lu
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Craig S. Wilding
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Samuel Dadzie
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Adam M. Jenkins
- Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Kimberly Regna
- Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Pelagie Boko
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Luc Djogbenou
- Institut Régional de Santé Publique de Ouidah/Université d’Abomey-Calavi, Cotonou, Bénin
| | - Marc A. T. Muskavitch
- Boston College, Chestnut Hill, Massachusetts, United States of America
- Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Hilary Ranson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Mark J. I. Paine
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail: (MJD); (OM)
| | - Martin J. Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- * E-mail: (MJD); (OM)
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Bass C, Zimmer CT, Riveron JM, Wilding CS, Wondji CS, Kaussmann M, Field LM, Williamson MS, Nauen R. Gene amplification and microsatellite polymorphism underlie a recent insect host shift. Proc Natl Acad Sci U S A 2013; 110:19460-5. [PMID: 24218582 PMCID: PMC3845143 DOI: 10.1073/pnas.1314122110] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [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: 11/18/2022] Open
Abstract
Host plant shifts of herbivorous insects may be a first step toward sympatric speciation and can create new pests of agriculturally important crops; however, the molecular mechanisms that mediate this process are poorly understood. Certain races of the polyphagous aphid Myzus persicae have recently adapted to feed on tobacco (Myzus persicae nicotianae) and show a reduced sensitivity to the plant alkaloid nicotine and cross-resistance to neonicotinoids a class of synthetic insecticides widely used for control. Here we show constitutive overexpression of a cytochrome P450 (CYP6CY3) allows tobacco-adapted races of M. persicae to efficiently detoxify nicotine and has preadapted them to resist neonicotinoid insecticides. CYP6CY3, is highly overexpressed in M. persicae nicotianae clones from three continents compared with M. persicae s.s. and expression level is significantly correlated with tolerance to nicotine. CYP6CY3 is highly efficient (compared with the primary human nicotine-metabolizing P450) at metabolizing nicotine and neonicotinoids to less toxic metabolites in vitro and generation of transgenic Drosophila expressing CYP6CY3 demonstrate that it confers resistance to both compounds in vivo. Overexpression of CYP6CY3 results from the expansion of a dinucleotide microsatellite in the promoter region and a recent gene amplification, with some aphid clones carrying up to 100 copies. We conclude that the mutations leading to overexpression of CYP6CY3 were a prerequisite for the host shift of M. persicae to tobacco and that gene amplification and microsatellite polymorphism are evolutionary drivers in insect host adaptation.
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Affiliation(s)
- Chris Bass
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Christoph T. Zimmer
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
- Pest Control Biology, Bayer CropScience AG, D40789 Monheim, Germany; and
| | - Jacob M. Riveron
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Craig S. Wilding
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Charles S. Wondji
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Martin Kaussmann
- Pest Control Biology, Bayer CropScience AG, D40789 Monheim, Germany; and
| | - Linda M. Field
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Martin S. Williamson
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Ralf Nauen
- Pest Control Biology, Bayer CropScience AG, D40789 Monheim, Germany; and
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Mawejje HD, Wilding CS, Rippon EJ, Hughes A, Weetman D, Donnelly MJ. Insecticide resistance monitoring of field-collected Anopheles gambiae s.l. populations from Jinja, eastern Uganda, identifies high levels of pyrethroid resistance. Med Vet Entomol 2013; 27:276-283. [PMID: 23046446 PMCID: PMC3543752 DOI: 10.1111/j.1365-2915.2012.01055.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Insecticide resistance in the malaria vector Anopheles gambiae s.l. (Diptera: Culicidae) threatens insecticide-based control efforts, necessitating regular monitoring. We assessed resistance in field-collected An. gambiae s.l. from Jinja, Uganda using World Health Organization (WHO) bioassays. Only An. gambiae s.s. and An. arabiensis (≈70%) were present. Female An. gambiae exhibited extremely high pyrethroid resistance (permethrin LT50 > 2 h; deltamethrin LT50 > 5 h). Female An. arabiensis were resistant to permethrin and exhibited reduced susceptibility to deltamethrin. However, while An. gambiae were DDT resistant, An. arabiensis were fully susceptible. Both species were fully susceptible to bendiocarb and fenitrothion. Kdr 1014S has increased rapidly in the Jinja population of An. gambiae s.s. and now approaches fixation (≈95%), consistent with insecticide-mediated selection, but is currently at a low frequency in An. arabiensis (0.07%). Kdr 1014F was also at a low frequency in An. gambiae. These frequencies preclude adequately-powered tests for an association with phenotypic resistance. PBO synergist bioassays resulted in near complete recovery of pyrethroid susceptibility suggesting involvement of CYP450s in resistance. A small number (0.22%) of An. gambiae s.s. ×An. arabiensis hybrids were found, suggesting the possibility of introgression of resistance alleles between species. The high levels of pyrethroid resistance encountered in Jinja threaten to reduce the efficacy of vector control programmes which rely on pyrethroid-impregnated bednets or indoor spraying of pyrethroids.
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Affiliation(s)
| | - Craig S. Wilding
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Emily J. Rippon
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Angela Hughes
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - David Weetman
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Martin J. Donnelly
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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Wilding CS, Smith I, Lynd A, Yawson AE, Weetman D, Paine MJI, Donnelly MJ. A cis-regulatory sequence driving metabolic insecticide resistance in mosquitoes: functional characterisation and signatures of selection. Insect Biochem Mol Biol 2012; 42:699-707. [PMID: 22732326 DOI: 10.1016/j.ibmb.2012.06.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 06/01/2023]
Abstract
Although cytochrome P450 (CYP450) enzymes are frequently up-regulated in mosquitoes resistant to insecticides, no regulatory motifs driving these expression differences with relevance to wild populations have been identified. Transposable elements (TEs) are often enriched upstream of those CYP450s involved in insecticide resistance, leading to the assumption that they contribute regulatory motifs that directly underlie the resistance phenotype. A partial CuRE1 (Culex Repetitive Element 1) transposable element is found directly upstream of CYP9M10, a cytochrome P450 implicated previously in larval resistance to permethrin in the ISOP450 strain of Culex quinquefasciatus, but is absent from the equivalent genomic region of a susceptible strain. Via expression of CYP9M10 in Escherichia coli we have now demonstrated time- and NADPH-dependant permethrin metabolism, prerequisites for confirmation of a role in metabolic resistance, and through qPCR shown that CYP9M10 is >20-fold over-expressed in ISOP450 compared to a susceptible strain. In a fluorescent reporter assay the region upstream of CYP9M10 from ISOP450 drove 10× expression compared to the equivalent region (lacking CuRE1) from the susceptible strain. Close correspondence with the gene expression fold-change implicates the upstream region including CuRE1 as a cis-regulatory element involved in resistance. Only a single CuRE1 bearing allele, identical to the CuRE1 bearing allele in the resistant strain, is found throughout Sub-Saharan Africa, in contrast to the diversity encountered in non-CuRE1 alleles. This suggests a single origin and subsequent spread due to selective advantage. CuRE1 is detectable using a simple diagnostic. When applied to C. quinquefasciatus larvae from Ghana we have demonstrated a significant association with permethrin resistance in multiple field sites (mean Odds Ratio = 3.86) suggesting this marker has relevance to natural populations of vector mosquitoes. However, when CuRE1 was excised from the allele used in the reporter assay through fusion PCR, expression was unaffected, indicating that the TE has no direct role in resistance and hence that CuRE1 is acting only as a marker of an as yet unidentified regulatory motif in the association analysis. This suggests that a re-evaluation of the assumption that TEs contribute regulatory motifs involved in gene expression may be necessary.
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Affiliation(s)
- Craig S Wilding
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
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17
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Ayres CFJ, Müller P, Dyer N, Wilding CS, Rigden DJ, Donnelly MJ. Comparative genomics of the anopheline glutathione S-transferase epsilon cluster. PLoS One 2011; 6:e29237. [PMID: 22206003 PMCID: PMC3242777 DOI: 10.1371/journal.pone.0029237] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 11/23/2011] [Indexed: 02/04/2023] Open
Abstract
Enzymes of the glutathione S-transferase (GST) family play critical roles in detoxification of xenobiotics across many taxa. While GSTs are ubiquitous both in animals and plants, the GST epsilon class (GSTE) is insect-specific and has been associated with resistance to chemical insecticides. While both Aedes aegypti and Anopheles gambiae GSTE clusters consist of eight members, only four putative orthologs are identifiable between the species, suggesting independent expansions of the class in each lineage. We used a primer walking approach, sequencing almost the entire cluster from three Anopheles species (An. stephensi, An. funestus (both Cellia subgenus) and An. plumbeus (Anopheles subgenus)) and compared the sequences to putative orthologs in An. gambiae (Cellia) in an attempt to trace the evolution of the cluster within the subfamily Anophelinae. Furthermore, we measured transcript levels from the identified GSTE loci by real time reverse transcription PCR to determine if all genes were similarly transcribed at different life stages. Among the species investigated, gene order and orientation were similar with three exceptions: (i) GSTE1 was absent in An. plumbeus; (ii) GSTE2 is duplicated in An. plumbeus and (iii) an additional transcriptionally active pseudogene (ψAsGSTE2) was found in An. stephensi. Further statistical analysis and protein modelling gave evidence for positive selection on codons of the catalytic site in GSTE5 albeit its origin seems to predate the introduction of chemical insecticides. Gene expression profiles revealed differences in expression pattern among genes at different life stages. With the exception of GSTE1, ψAsGSTE2 and GSTE2b, all Anopheles species studied share orthologs and hence we assume that GSTE expansion generally predates radiation into subgenera, though the presence of GSTE1 may also suggest a recent duplication event in the Old World Cellia subgenus, instead of a secondary loss. The modifications of the catalytic site within GSTE5 may represent adaptations to new habitats.
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18
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Weetman D, Wilding CS, Steen K, Pinto J, Donnelly MJ. Gene flow-dependent genomic divergence between Anopheles gambiae M and S forms. Mol Biol Evol 2011; 29:279-91. [PMID: 21836185 DOI: 10.1093/molbev/msr199] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anopheles gambiae sensu stricto exists as two often-sympatric races termed the M and S molecular forms, characterized by fixed differences at an X-linked marker. Extreme divergence between M and S forms at pericentromeric "genomic islands" suggested that selection on variants therein could be driving interform divergence in the presence of ongoing gene flow, but recent work has detected much more widespread genomic differentiation. Whether such genomic islands are important in reproductive isolation or represent ancestral differentiation preserved by low recombination is currently unclear. A critical test of these competing hypotheses could be provided by comparing genomic divergence when rates of recent introgression vary. We genotyped 871 single nucleotide polymorphisms (SNPs) in A. gambiae sensu stricto from locations of M and S sympatry and allopatry, encompassing the full range of observed hybridization rates (0-25%). M and S forms were readily partitioned based on genomewide SNP variation in spite of evidence for ongoing introgression that qualitatively reflects hybridization rates. Yet both the level and the heterogeneity of genomic divergence varied markedly in line with levels of introgression. A few genomic regions of differentiation between M and S were common to each sampling location, the most pronounced being two centromere-proximal speciation islands identified previously but with at least one additional region outside of areas expected to exhibit reduced recombination. Our results demonstrate that extreme divergence at genomic islands does not simply represent segregating ancestral polymorphism in regions of low recombination and can be resilient to substantial gene flow. This highlights the potential for islands comprising a relatively small fraction of the genome to play an important role in early-stage speciation when reproductive isolation is limited.
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Affiliation(s)
- David Weetman
- Vector Group, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
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19
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Abilio AP, Kleinschmidt I, Rehman AM, Cuamba N, Ramdeen V, Mthembu DS, Coetzer S, Maharaj R, Wilding CS, Steven A, Coleman M, Hemingway J, Coleman M. The emergence of insecticide resistance in central Mozambique and potential threat to the successful indoor residual spraying malaria control programme. Malar J 2011; 10:110. [PMID: 21535872 PMCID: PMC3096596 DOI: 10.1186/1475-2875-10-110] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [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: 11/30/2010] [Accepted: 05/02/2011] [Indexed: 12/02/2022] Open
Abstract
Background Malaria vector control by indoor residual spraying was reinitiated in 2006 with DDT in Zambézia province, Mozambique. In 2007, these efforts were strengthened by the President's Malaria Initiative. This manuscript reports on the monitoring and evaluation of this programme as carried out by the Malaria Decision Support Project. Methods Mosquitoes were captured daily through a series of 114 window exit traps located at 19 sentinel sites, identified to species and analysed for sporozoites. Anopheles mosquitoes were collected resting indoors and tested for insecticide resistance following the standard WHO protocol. Annual cross sectional household parasite surveys were carried out to monitor the impact of the control programme on prevalence of Plasmodium falciparum in children aged 1 to 15 years. Results A total of 3,769 and 2,853 Anopheles gambiae s.l. and Anopheles funestus, respectively, were captured from window exit traps throughout the period. In 2010 resistance to the pyrethroids lambda-cyhalothrin and permethrin and the carbamate, bendiocarb was detected in An. funestus. In 2006, the sporozoite rate in An. gambiae s.s. was 4% and this reduced to 1% over 4 rounds of spraying. The sporozoite rate for An. funestus was also reduced from 2% to 0 by 2008. Of the 437 Anopheles arabiensis identified, none were infectious. Overall prevalence of P. falciparum in the sentinel sites fell from 60% to 32% between October 2006 and October 2008. Conclusion Both An. gambiae s.s. and An. funestus were controlled effectively with the DDT-based IRS programme in Zambézia, reducing disease transmission and burden. However, the discovery of pyrethroid resistance in the province and Mozambique's policy change away from DDT to pyrethroids for IRS threatens the gains made here.
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Affiliation(s)
- Ana P Abilio
- 1National Institute of Health, Av. Eduardo Mondlane/Salvador Allende, PO Box 264, Maputo, Mozambique
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20
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Weetman D, Wilding CS, Steen K, Morgan JC, Simard F, Donnelly MJ. Association mapping of insecticide resistance in wild Anopheles gambiae populations: major variants identified in a low-linkage disequilbrium genome. PLoS One 2010; 5:e13140. [PMID: 20976111 PMCID: PMC2956759 DOI: 10.1371/journal.pone.0013140] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [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] [Received: 07/15/2010] [Accepted: 09/03/2010] [Indexed: 11/18/2022] Open
Abstract
Background Association studies are a promising way to uncover the genetic basis of complex traits in wild populations. Data on population stratification, linkage disequilibrium and distribution of variant effect-sizes for different trait-types are required to predict study success but are lacking for most taxa. We quantified and investigated the impacts of these key variables in a large-scale association study of a strongly selected trait of medical importance: pyrethroid resistance in the African malaria vector Anopheles gambiae. Methodology/Principal Findings We genotyped ≈1500 resistance-phenotyped wild mosquitoes from Ghana and Cameroon using a 1536-SNP array enriched for candidate insecticide resistance gene SNPs. Three factors greatly impacted study power. (1) Population stratification, which was attributable to co-occurrence of molecular forms (M and S), and cryptic within-form stratification necessitating both a partitioned analysis and genomic control. (2) All SNPs of substantial effect (odds ratio, OR>2) were rare (minor allele frequency, MAF<0.05). (3) Linkage disequilibrium (LD) was very low throughout most of the genome. Nevertheless, locally high LD, consistent with a recent selective sweep, and uniformly high ORs in each subsample facilitated significant direct and indirect detection of the known insecticide target site mutation kdr L1014F (OR≈6; P<10−6), but with resistance level modified by local haplotypic background. Conclusion Primarily as a result of very low LD in wild A. Gambiae, LD-based association mapping is challenging, but is feasible at least for major effect variants, especially where LD is enhanced by selective sweeps. Such variants will be of greatest importance for predictive diagnostic screening.
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Affiliation(s)
- David Weetman
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom.
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Donnelly MJ, Corbel V, Weetman D, Wilding CS, Williamson MS, Black WC. Does kdr genotype predict insecticide-resistance phenotype in mosquitoes? Trends Parasitol 2009; 25:213-9. [PMID: 19369117 DOI: 10.1016/j.pt.2009.02.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 02/06/2009] [Accepted: 02/12/2009] [Indexed: 10/20/2022]
Abstract
Several groups are developing and applying DNA-based technologies to monitor insecticide-based disease control programmes. However, several recent papers have concluded that the knockdown resistance (kdr) genotype-phenotype correlation that is observed in a wide variety of taxa might not hold in all mosquitoes. In this article, we review the evidence to support this putative breakdown and argue that the conclusion follows from unreliable data or the unparsimonious interpretation of data. We assert that the link between kdr genotype and DDT- and pyrethroid-susceptibility phenotype is clear. However, we emphasize that kdr genotype might explain only a portion of heritable variation in resistance and that diagnostic assays to test the importance of other resistance mechanisms in field populations are required.
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Affiliation(s)
- Martin J Donnelly
- Vector Group, Liverpool School of Tropical Medicine, Liverpool L35QA, UK.
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22
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Wilding CS, Weetman D, Steen K, Donnelly MJ. High, clustered, nucleotide diversity in the genome of Anopheles gambiae revealed through pooled-template sequencing: implications for high-throughput genotyping protocols. BMC Genomics 2009; 10:320. [PMID: 19607710 PMCID: PMC2723138 DOI: 10.1186/1471-2164-10-320] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [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: 12/23/2008] [Accepted: 07/16/2009] [Indexed: 02/04/2023] Open
Abstract
Background Association mapping approaches are dependent upon discovery and validation of single nucleotide polymorphisms (SNPs). To further association studies in Anopheles gambiae we conducted a major resequencing programme, primarily targeting regions within or close to candidate genes for insecticide resistance. Results Using two pools of mosquito template DNA we sequenced over 300 kbp across 660 distinct amplicons of the An. gambiae genome. Comparison of SNPs identified from pooled templates with those from individual sequences revealed a very low false positive rate. False negative rates were much higher and mostly resulted from SNPs with a low minor allele frequency. Pooled-template sequencing also provided good estimates of SNP allele frequencies. Allele frequency estimation success, along with false positive and negative call rates, improved significantly when using a qualitative measure of SNP call quality. We identified a total of 7062 polymorphic features comprising 6995 SNPs and 67 indels, with, on average, a SNP every 34 bp; a high rate of polymorphism that is comparable to other studies of mosquitoes. SNPs were significantly more frequent in members of the cytochrome p450 mono-oxygenases and carboxy/cholinesterase gene-families than in glutathione-S-transferases, other detoxification genes, and control genomic regions. Polymorphic sites showed a significantly clustered distribution, but the degree of SNP clustering (independent of SNP frequency) did not vary among gene families, suggesting that clustering of polymorphisms is a general property of the An. gambiae genome. Conclusion The high frequency and clustering of SNPs has important ramifications for the design of high-throughput genotyping assays based on allele specific primer extension or probe hybridisation. We illustrate these issues in the context of the design of Illumina GoldenGate assays.
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Affiliation(s)
- Craig S Wilding
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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Mzilahowa T, Ball AJ, Bass C, Morgan JC, Nyoni B, Steen K, Donnelly MJ, Wilding CS. Reduced susceptibility to DDT in field populations of Anopheles quadriannulatus and Anopheles arabiensis in Malawi: evidence for larval selection. Med Vet Entomol 2008; 22:258-263. [PMID: 18816274 DOI: 10.1111/j.1365-2915.2008.00736.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bioassays for insecticide resistance in adult mosquitoes were conducted on samples of Anopheles gambiae Giles s.l. (Diptera: Culicidae) species collected as larvae from breeding sites in the lower Shire Valley, Malawi. The results indicate full susceptibility to permethrin, deltamethrin and malathion, but reduced susceptibility to DDT in one sample from Thom (LT(50) of 8.39 min for females and 25.09 min for males). Polymerase chain reaction-based species identification of the mosquitoes assayed revealed a mixture of Anopheles arabiensis Patton and Anopheles quadriannulatus (Theobold). The LT(50) did not differ significantly between species. Genotyping of the L1014F and L1014S kdr alleles showed all mosquito specimens to be homozygous wild type; thus the reduced susceptibility detected is not attributable to target site insensitivity and instead is likely to be metabolic in nature. Anopheles quadriannulatus is characteristically zoophagic and exophilic. Indeed, of 82 Anopheles collected through knockdown collections within dwellings, only one was An. quadriannulatus and the rest were An. arabiensis. They are unlikely, therefore, to have been exposed to selection pressure arising from insecticide-treated net usage or to DDT indoor residual spraying. Therefore, it is suggested that this example of reduced susceptibility to DDT in An. quadriannulatus reflects selection in the larval stages.
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Affiliation(s)
- T Mzilahowa
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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Bass C, Williamson MS, Wilding CS, Donnelly MJ, Field LM. Identification of the main malaria vectors in the Anopheles gambiae species complex using a TaqMan real-time PCR assay. Malar J 2007; 6:155. [PMID: 18034887 PMCID: PMC2213665 DOI: 10.1186/1475-2875-6-155] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [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: 07/27/2007] [Accepted: 11/22/2007] [Indexed: 12/02/2022] Open
Abstract
Background The Anopheles gambiae sensu lato species complex comprises seven sibling species of mosquitoes that are morphologically indistinguishable. Rapid identification of the two main species which vector malaria, Anopheles arabiensis and An. gambiae sensu stricto, from the non-vector species Anopheles quadriannulatus is often required as part of vector control programmes. Currently the most widely used method for species identification is a multiplex PCR protocol that targets species specific differences in ribosomal DNA sequences. While this assay has proved to be reasonably robust in many studies, additional steps are required post-PCR making it time consuming. Recently, a high-throughput assay based on TaqMan single nucleotide polymorphism genotyping that detects and discriminates An. gambiae s.s and An. arabiensis has been reported. Methods A new TaqMan assay was developed that distinguishes between the main malaria vectors (An. arabiensis and An. gambiae s.s.) and the non-vector An. quadriannulatus after it was found that the existing TaqMan assay incorrectly identified An. quadriannulatus, An. merus and An. melas as An. gambiae s.s. The performance of this new TaqMan assay was compared against the existing TaqMan assay and the standard PCR method in a blind species identification trial of over 450 samples using field collected specimens from a total of 13 countries in Sub-Saharan Africa. Results The standard PCR method was found to be specific with a low number of incorrect scores (<1%), however when compared to the TaqMan assays it showed a significantly higher number of failed reactions (15%). Both the new vector-specific TaqMan assay and the exisiting TaqMan showed a very low number of incorrectly identified samples (0 and 0.54%) and failed reactions (1.25% and 2.96%). In tests of analytical sensitivity the new TaqMan assay showed a very low detection threshold and can consequently be used on a single leg from a fresh or silica-dried mosquito without the need to first extract DNA. Conclusion This study describes a rapid and sensitive assay that very effectively identifies the two main malaria vectors of the An. gambiae species complex from the non-vector sibling species. The method is based on TaqMan SNP genotyping and can be used to screen single legs from dried specimens. In regions where An. merus/melas/bwambae, vectors with restricted distributions, are not present it can be used alone to discriminate vector from non-vector or in combination with the Walker TaqMan assay to distinguish An. arabiensis and An. gambiae s.s.
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Affiliation(s)
- Chris Bass
- Department of Biological Chemistry, Rothamsted Research, Harpenden, AL5 2JQ, UK.
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Wilding CS, Curwen GB, Tawn EJ, Sheng X, Winther JF, Chakraborty R, Boice JD. Influence of polymorphisms at loci encoding DNA repair proteins on cancer susceptibility and G2 chromosomal radiosensitivity. Environ Mol Mutagen 2007; 48:48-57. [PMID: 17177211 PMCID: PMC2730149 DOI: 10.1002/em.20274] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Sixteen candidate polymorphisms (13 SNPs and 3 microsatellites) in nine genes from four DNA repair pathways were examined in 83 subjects, comprising 23 survivors of childhood cancer, their 23 partners, and 37 offspring, all of whom had previously been studied for G(2) chromosomal radiosensitivity. Genotype at the Asp148Glu SNP site in the APEX gene of the base excision repair (BER) pathway was associated with childhood cancer in survivors (P = 0.001, significant even after multiple test adjustment), due to the enhanced frequency of the APEX Asp148 allele among survivors in comparison to that of their partners. Analysis of variance (ANOVA) of G(2) radiosensitivity in the pooled sample, as well as family-based association test (FBAT) of the family-wise data, showed sporadic suggestions of associations between G(2) radiosensitivity and polymorphisms at two sites (the Thr241Met SNP site in the XRCC3 gene of the homologous recombinational pathway by ANOVA, and the Ser326Cys site in the hOGG1 gene of the BER pathway by FBAT analysis), but neither of these remained significant after multiple-test adjustment. This pilot study provides an intriguing indication that DNA repair gene polymorphisms may underlie cancer susceptibility and variation in radiosensitivity.
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Affiliation(s)
- Craig S. Wilding
- Genetics Department, Westlakes Research Institute, Westlakes Science and Technology Park, Moor Row, Cumbria, United Kingdom
| | - Gillian B. Curwen
- Genetics Department, Westlakes Research Institute, Westlakes Science and Technology Park, Moor Row, Cumbria, United Kingdom
| | - E. Janet Tawn
- Genetics Department, Westlakes Research Institute, Westlakes Science and Technology Park, Moor Row, Cumbria, United Kingdom
- Correspondence to: Dr. E. J. Tawn, Genetics Department, Westlakes Research Institute, Westlakes Science and Technology Park, Moor Row, Cumbria CA24 3JY, UK. E-mail:
| | - Xiaohua Sheng
- Center for Genome Information, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jeanette F. Winther
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Ranajit Chakraborty
- Center for Genome Information, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - John D. Boice
- International Epidemiology Institute, Rockville, Maryland
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
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Wilding CS, Rees GS, Relton CL, Tawn EJ. Genotype profiles of loci encoding DNA repair enzymes in newborn and elderly populations: no evidence of association with longevity. Biogerontology 2006; 7:35-41. [PMID: 16518718 DOI: 10.1007/s10522-005-6042-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Accepted: 11/21/2005] [Indexed: 10/25/2022]
Abstract
The comparison of genotype frequencies between neonates and elderly populations can aid in the identification of loci, and polymorphisms within those loci, that affect longevity. Here we have compared genotype frequencies of seven polymorphisms at four loci involved in DNA repair between a cohort of newborns (n = 290) and a retired population (average age at sampling 70.02 years; n = 430) who have suffered a lifetime of DNA damage from normal, metabolic processes, and on whom selection on DNA repair gene variants may be expected to have acted. No differences in genotype frequencies at the four SNP loci were seen, indicating that there is no evidence of association with longevity in this population. Significant differences in frequency of certain repeat sizes at three microsatellite loci were detected. However, since there is no known functional consequence of these repeat lengths, the action of selection cannot yet be ascribed.
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Affiliation(s)
- C S Wilding
- Genetics Department, Westlakes Research Institute, Westlakes Science and Technology Park, CA24 3JY, Moor Row, Cumbria, UK.
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Wilding CS, Cadwell K, Tawn EJ, Relton CL, Taylor GA, Chinnery PF, Turnbull DM. Mitochondrial DNA mutations in individuals occupationally exposed to ionizing radiation. Radiat Res 2006; 165:202-7. [PMID: 16435918 DOI: 10.1667/rr3494.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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: 11/03/2022]
Abstract
Mutations in a 443-bp amplicon of the hypervariable region HVR1 of the D-loop of mitochondrial DNA (mtDNA) were quantified in DNA extracted from peripheral blood samples of 10 retired radiation workers who had accumulated external radiation doses of >0.9 Sv over the course of their working life and were compared to the levels of mutations in 10 control individuals matched for age and smoking status. The mutation rate in the 10 exposed individuals was 9.92 x 10(-5) mutations/ nucleotide, and for the controls it was 8.65 x 10(-5) mutations/ nucleotide, with a procedural error rate of 2.65 x 10(-5) mutations/nucleotide. No increase in mtDNA mutations due to radiation exposure was detectable (P = 0.640). In contrast, chromosomal translocation frequencies, a validated radiobiological technique for retrospective dosimetric purposes, were significantly elevated in the exposed individuals. This suggests that mutations identified through sequencing of mtDNA in peripheral blood lymphocytes do not represent a promising genetic marker of DNA damage after low-dose or low-dose-rate exposures to ionizing radiation. There was an increase in singleton mutations above that attributable to procedural error in both exposed and control groups that is likely to reflect age-related somatic mutation.
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Affiliation(s)
- Craig S Wilding
- Genetics Department, Westlakes Research Institute, Moor Row, Cumbria, CA24 3JY, United Kingdom.
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Grahame JW, Wilding CS, Butlin RK. ADAPTATION TO A STEEP ENVIRONMENTAL GRADIENT AND AN ASSOCIATED BARRIER TO GENE EXCHANGE IN LITTORINA SAXATILIS. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb01105.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Grahame JW, Wilding CS, Butlin RK. Adaptation to a steep environmental gradient and an associated barrier to gene exchange in Littorina saxatilis. Evolution 2006; 60:268-78. [PMID: 16610319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Steep environmental gradients offer important opportunities to study the interaction between natural selection and gene flow. Allele frequency clines are expected to form at loci under selection, but unlinked neutral alleles may pass easily across these clines unless a generalized barrier evolves. Here we consider the distribution of forms of the intertidal gastropod Littorina saxatilis, analyzing shell shape and amplified fragment length polymorphism (AFLP) loci on two rocky shores in Britain. On the basis of previous work, the AFLP loci were divided into differentiated and undifferentiated groups. On both shores, we have shown a sharp cline in allele frequencies between the two morphs for differentiated AFLP loci. This is coincident with a habitat transition on the shore where the two habitats (cliff and boulder field) are immediately contiguous. The allele frequency clines coincide with a cline in shell morphology. In the middle of the cline, linkage disequilibrium for the differentiated loci rises in accordance with expectation. The clines are extremely narrow relative to dispersal, probably as a result of both strong selection and habitat choice. An increase in F(ST) for undifferentiated AFLPs between morphs, relative to within-morph comparisons, is consistent with there being a general barrier to gene flow across the contact zone. These features are consistent either with an episode of allopatric divergence followed by secondary contact or with primary, nonallopatric divergence. Further data will be needed to distinguish between these alternatives.
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Affiliation(s)
- John W Grahame
- Faculty of Biological Sciences, Institute of Integrative and Comparative Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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Wilding CS, Trikic MZ, Hingston JL, Copplestone D, Janet Tawn E. Mitochondrial DNA mutation frequencies in experimentally irradiated compost worms, Eisenia fetida. Mutat Res 2006; 603:56-63. [PMID: 16378751 DOI: 10.1016/j.mrgentox.2005.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 10/21/2005] [Accepted: 10/27/2005] [Indexed: 05/05/2023]
Abstract
The compost worm Eisenia fetida is routinely used in ecotoxicological studies. A standard assay to assess genetic damage in this species would be extremely valuable. Since mitochondrial DNA (mtDNA) is known to exhibit an increased mutation rate following exposure to ionising radiation we assessed the validity of a mtDNA-based assay for measuring increases in mutation rate in laboratory-irradiated compost worms. To this end the mutation frequency in the mtDNA of the compost worm E. fetida was quantified following in vivo gamma-irradiation of adult worms in three dose groups. Five adult worms exposed to 1.4 mGy/h for 55 days (total dose 1.85 Gy), five adult worms exposed to 8.5 mGy/h for 55 days (total dose 11.22 Gy) and five adult control worms were used to assess the effect of irradiation on mtDNA mutation induction. DNA samples extracted from irradiated adult worms were used in high-fidelity PCR of a 486 bp region of mtDNA spanning the ATPase 8 gene, chosen for its high spontaneous mutation rate. PCR products were cloned and sequenced to identify mutations, with 89-102 clones successfully sequenced per individual. A significant elevation in mtDNA mutation frequency (p=0.032) was seen in worms exposed at the higher dose rate (8.5 mGy/h, total dose 11.22 Gy; mutation frequency 27.98+/-4.85 x 10(-5)mutations/bp) in comparison to controls (mutation frequency 12.68+/-3.06 x 10(-5)mutations/bp), but no elevation in mutation frequency (p=0.764) was seen for the lower dose rate (1.4 mGy/h, total dose 1.85 Gy; mutation frequency 13.74+/-1.29 x 10(-5)mutations/bp) compared with controls. This indicates that although the technique has the potential to detect an elevation in mutation frequency, it does not have sufficient sensitivity at the doses likely to be encountered in environmental monitoring scenarios.
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Affiliation(s)
- Craig S Wilding
- Genetics Department, Westlakes Research Institute, Moor Row, Cumbria CA24 3JY, UK.
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Grahame JW, Wilding CS, Butlin RK. ADAPTATION TO A STEEP ENVIRONMENTAL GRADIENT AND AN ASSOCIATED BARRIER TO GENE EXCHANGE IN LITTORINA SAXATILIS. Evolution 2006. [DOI: 10.1554/05-592.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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De Ruyck K, Wilding CS, Van Eijkeren M, Morthier R, Tawn EJ, Thierens H. Microsatellite polymorphisms in DNA repair genes XRCC1, XRCC3 and XRCC5 in patients with gynecological tumors: association with late clinical radiosensitivity and cancer incidence. Radiat Res 2005; 164:237-44. [PMID: 16137195 DOI: 10.1667/rr3417.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study investigates the association of microsatellite polymorphisms in XRCC1, XRCC3 and XRCC5 with the development of late radiation-induced radiotherapy reactions and examines the correlation between these microsatellites and cancer incidence. Sixty-two women with cervical or endometrial cancer treated with radiotherapy were included in the study. According to the CTCAEv3.0 scale, 22 patients showed late adverse radiotherapy reactions (grade 2 or more). PCR on lymphocyte DNA followed by automated fragment analysis was performed to examine the number of tandem repeat units at each locus. No significant association was found between the repeat length at any of the microsatellites in XRCC1, XRCC3 or XRCC5 and the incidence of late radiotherapy complications. Since higher odds ratios (ORs) were found for the rare XRCC1 [AC]11 and [AC]21 repeats (OR = 2.65, P = 0.325 and OR = 8.67, P = 0.093, respectively), the possible involvement of these small and large repeats in clinical radiosensitivity cannot be completely ruled out. When specific numbers of repeats were examined, no significant correlation was found between the microsatellite repeat length in XRCC1 and XRCC5 and cancer incidence. A weak correlation between XRCC3 [AC]16 homozygotes and cancer incidence was found (OR = 2.56, P = 0.055). A large-scale multicenter study of cancer patients with a high number of radiosensitive individuals is needed to clarify the value of rare polymorphic microsatellite repeats in XRCC1 and XRCC3 as a biomarker of clinical radiosensitivity or increased cancer risk.
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Affiliation(s)
- K De Ruyck
- Department of Anatomy, Embryology, Histology and Medical Physics, Ghent University, Gent, Belgium.
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Abstract
Intron 3 and the flanking exons of the calmodulin gene have been amplified, cloned, and sequenced from 18 members of the gastropod genus Littorina. From the 48 sequences, at least five different gene copies have been identified and their functionality characterized using a strategy based upon the potential protein product predicted from flanking exon data. The functionality analyses suggest that four of the genes code for functional copies of calmodulin. All five copies have been identified across a wide range of littorinid species although not ubiquitously. Using this novel approach based on intron sequences, we have identified an unprecedented number of potential calmodulin copies in Littorina, exceeding that reported for any other invertebrate. This suggests a higher number of, and more ancient, gene duplications than previously detected in a single genus.
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Affiliation(s)
- R J Simpson
- School of Biology, The University of Leeds, Leeds, LS2 9JT, UK.
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Wilding CS, Relton CL, Rees GS, Tarone RE, Whitehouse CA, Tawn EJ. DNA repair gene polymorphisms in relation to chromosome aberration frequencies in retired radiation workers. Mutat Res 2005; 570:137-45. [PMID: 15680411 DOI: 10.1016/j.mrfmmm.2004.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Revised: 10/18/2004] [Accepted: 11/10/2004] [Indexed: 05/01/2023]
Abstract
Polymorphic variation in DNA repair genes was examined in a group of retired workers from the British Nuclear Fuels plc facility at Sellafield in relation to previously determined translocation frequencies in peripheral blood lymphocytes. Variation at seven polymorphisms in four genes involved in the base excision repair (XRCC1 R194W, R399Q and a [AC]n microsatellite in the 3' UTR) and double strand break repair (XRCC3 T241M and a [AC]n microsatellite in intron 3 of XRCC3, XRCC4 I134T, and a GACTAn microsatellite located 120 kb 5' of XRCC5) pathways was determined for 291 retired radiation workers who had received cumulative occupational external radiation doses of between 0 and 1873 mSv. When the interaction between radiation dose and each DNA repair gene polymorphism was examined in relation to translocation frequency there was no evidence for any of the polymorphisms studied influencing the response to occupational exposure. A positive interaction observed between genotype (individuals with at least one allele > or =20 repeat units) at a microsatellite locus in the XRCC3 gene and smoking status should be interpreted cautiously because interactions were investigated for seven polymorphisms and two exposures. Nonetheless, further research is warranted to examine whether this DNA repair gene variant might be associated with a sub-optimal repair response to smoking-induced DNA damage and hence an increased frequency of translocations.
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Affiliation(s)
- Craig S Wilding
- Genetics Department, Westlakes Research Institute, Westlakes Science and Technology Park, Moor Row, Cumbria CA24 3JY, UK.
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Wilding CS, Relton CL, Sutton MJ, Jonas PA, Lynch SA, Tawn EJ, Burn J. Thymidylate synthase repeat polymorphisms and risk of neural tube defects in a population from the northern United Kingdom. ACTA ACUST UNITED AC 2004; 70:483-5. [PMID: 15259039 DOI: 10.1002/bdra.20038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND A 28-bp repeat polymorphism in the 5'UTR of the thymidylate synthase (TYMS) gene represents a candidate risk factor for neural tube defects (NTDs) due to involvement in folate-dependent homocysteine metabolism. Non-Hispanic, white, U.S. citizens carrying at least one 2x 28-bp repeat allele have recently been shown to be at a four-fold increased risk of spina bifida (SB). We investigated the association between this polymorphism and risk of NTD in families affected by NTDs and controls from the northern United Kingdom (UK). METHODS PCR was performed on genomic DNA extracted from blood or mouth swabs of family members affected by NTDs (mothers, fathers, and cases), and unaffected controls (mothers and infants) to determine the number of 28-bp repeat units within the promoter region of TYMS. Case-control and TDT analyses of the influence of TYMS genotype on risk of NTD, or NTD pregnancy, were conducted. RESULTS Odds ratio (OR) analysis indicated that individuals carrying the 2x 28-bp repeat allele either in homozygous or heterozygous form, are not at increased risk of NTDs, or of having an NTD affected pregnancy. Control population allele frequencies are seen to be markedly different between the U.S. controls and those in this study. CONCLUSIONS TYMS polymorphism appears to be not universally associated with NTD risk across Caucasian samples. The elevated risk of spina bifida in U.S. samples appears to be driven by an unusually low risk allele (2x 28 bp) frequency in control samples. Family based (TDT) testing of U.S. samples is therefore advocated.
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Affiliation(s)
- Craig S Wilding
- Genetics Department, Westlakes Research Institute, Cumbria, United Kingdom.
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Abstract
Neural tube defects (NTDs) have a well-established genetic basis, although no single genetic factor has been identified as a major risk factor in NTD susceptibility. A large number of association studies have been conducted to investigate the possibility that NTD susceptibility is linked to polymorphic variation in genes involved in early embryonic development or in the absorption or metabolism of folate, a nutrient that has been clearly associated with a reduction in the risk of NTD pregnancy. A study of three candidate gene polymorphisms at loci implicated in folate absorption and metabolism has been conducted on a population of 211 mothers of a heterogeneous mix of NTD phenotypes: 59% spina bifida aperta (SBA), 20.3% spina bifida occulta (SBO), 17% anencephaly, and 3.7% other NTD. Allele and genotype frequencies were stratified according to offspring NTD phenotype, and variation in the level of NTD risk was associated with different phenotypes. All the three variants (MTHFR 677C > T, GCPII 1561C > T, and RFC-1 80G > A) were shown to significantly influence the risk of anencephalic pregnancy. In addition, the MTHFR 677C > T variant conferred a modest protective effect in SBO mothers and the total NTD mother group, but not in SBA mothers. The RFC-1 80G > A variant elevated the risk of SBO and anencephalic pregnancy. The findings of this study suggest that NTD phenotypic heterogeneity may help explain the mixed findings of previous association studies and that different polymorphisms may hold differing degrees of significance for the various NTD phenotypes.
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Affiliation(s)
- C L Relton
- Genetics Department, Westlakes Research Institute, Westlakes Science and Technology Park, Cumbria, UK; West Cumberland Hospital, Whitehaven, Cumbria, UK.
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Relton CL, Wilding CS, Pearce MS, Laffling AJ, Jonas PA, Lynch SA, Tawn EJ, Burn J. Gene-gene interaction in folate-related genes and risk of neural tube defects in a UK population. J Med Genet 2004; 41:256-60. [PMID: 15060097 PMCID: PMC1735724 DOI: 10.1136/jmg.2003.010694] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To investigate the contribution of polymorphic variation in genes involved in the folate-dependent homocysteine pathway in the aetiology of neural tube defects (NTD). DESIGN Case-control association study. SUBJECTS A total of 530 individuals from families affected by NTD, 645 maternal controls, and 602 healthy newborn controls from the northern UK. MAIN OUTCOME MEASURES Seven polymorphisms in six genes coding for proteins in the folate-dependent homocysteine pathway (MTHFR 677C-->T, MTHFR 1298A-->C, MTRR 66A-->G, SHMT 1420C-->T, CbetaS 844ins68, GCPII 1561C-->T, RFC-1 80G-->A). The impact of each polymorphism and the effect of gene-gene interactions (epistasis) upon risk of NTD were assessed using logistic regression analysis. RESULTS The MTHFR 677C-->T polymorphism was shown to represent a risk factor in NTD cases (CC v CT+TT odds ratio (OR) 2.03 [95% confidence interval (CI) 1.09, 3.79] p = 0.025) and the MTRR 66A-->G polymorphism was shown to exert a protective effect in NTD cases (AA v AG+GG OR 0.31 [95% CI 0.10, 0.94] p = 0.04). When statistical tests for interaction were conducted, three genotype combinations in cases (MTRR/GCPII; MTHFR 677/CbetaS; MTHFR 677/MTRR) and one combination in case mothers (CbetaS/RFC-1) were shown to elevate NTD risk. Maternal-fetal interaction was also detected when offspring carried the MTHFR 677C-->T variant and mothers carried the MTRR 66A-->G variant, resulting in a significantly elevated risk of NTD. CONCLUSION Both independent genetic effects and gene-gene interaction were observed in relation to NTD risk. Multi-locus rather than single locus analysis might be preferable to gain an accurate assessment of genetic susceptibility to NTD.
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Affiliation(s)
- C L Relton
- Paediatric and Lifecourse Epidemiology Research Group, School of Clinical Medical Sciences, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK.
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Relton CL, Wilding CS, Laffling AJ, Jonas PA, Burgess T, Binks K, Tawn EJ, Burn J. Low erythrocyte folate status and polymorphic variation in folate-related genes are associated with risk of neural tube defect pregnancy. Mol Genet Metab 2004; 81:273-81. [PMID: 15059614 DOI: 10.1016/j.ymgme.2003.12.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 12/22/2003] [Indexed: 11/30/2022]
Abstract
Previous studies have shown conflicting findings in linking polymorphic variation in folate-related genes to the risk of neural tube defect pregnancy. Recent evidence points to maternal genotype being important in determining NTD risk. A case-control study was undertaken in 97 mothers of NTD cases from the northern region of the UK. Pregnant controls (n = 190) from a regional DNA bank and non-pregnant controls (n = 100) from the same geographical area were recruited. MTHFR 677C >T, MTHFR 1298A >C, MTRR 66A >G, SHMT 1420C >T, CbetaS 844ins68, and RFC-1 80G >A allele and genotype frequencies were determined and odds ratios (OR) calculated. Erythrocyte folate levels for cases and controls were also measured and a comparison made of median erythrocyte folate levels stratified according to genotype. The MTHFR 677C >T variant was not shown to be an independent NTD risk factor in mothers of NTD-affected pregnancy. A second polymorphism in MTHFR, 1298A >C, was less frequently observed in mothers of NTD cases (OR [95% CI]=0.57 [0.33, 0.97]). Possession of compound 1298A >C and 677C >T variants elevated risk of NTD pregnancy considerably (TT/AC+TT/CC vs CC/AA OR [95% CI]=6.56 [1.10, 39.33]). Erythrocyte folate levels were persistently lower in NTD mothers (p = 0.001) despite assays being conducted many years after the index pregnancy (17.6+/-12.6 years). Erythrocyte folate levels were depressed in the presence of the MTHFR 677C >T variant.
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Affiliation(s)
- Caroline L Relton
- Paediatric and Lifecourse Epidemiology Research Group, School of Clinical Medical Sciences (Child Health), Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary, Newcastle upon Tyne NE2 4LP, UK.
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Wilding CS, Grahame J, Mill PJ. Nuclear DNA restriction site polymorphisms and the phylogeny and population structure of an intertidal snail species complex (Littorina). Hereditas 2001; 133:9-18. [PMID: 11206859 DOI: 10.1111/j.1601-5223.2000.00009.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Primers for amplification of four novel, unlinked nuclear DNA loci, the first reported for the rough periwinkles of the genus Littorina, are described. Patterns of restriction site polymorphism for these loci are detailed within the rough periwinkles. RFLPs are not found to be diagnostic for any of the currently accepted species within this group, nor for any of the contentious subspecies, or forms, whose taxonomic status is uncertain. However, there are important differences in allele frequencies between these taxa and certain of these mirror differences detected in a previous study of the mitochondrial DNA. These allele frequency data are used to construct a phylogeny in which groupings of the three recognised species are obvious when either Nei's genetic distances or Reynold's distances are clustered. Contentious forms (L. neglecta, L. saxatilis 'b' and L. tenebrosa) do not cluster as distinct taxa, although populations of L. neglecta have important allele frequency differences from L. saxatilis. These four loci have confirmed the consensus view of Littorina phylogeny and provided important information on population structure-however four loci is insufficient for reaching definitive conclusions. Since analysis of nuclear DNA polymorphisms such as these is invaluable for analysis of phylogeny, population structure and phylogeography, identification of additional loci is considered imperative.
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Affiliation(s)
- C S Wilding
- The School of Biology, University of Leeds, UK.
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Abstract
Three sibling species of rough periwinkles are currently recognized: Littorina arcana, L. compressa and L. saxatilis. Certain forms of L. saxatilis are also argued by some to deserve species status, such as the barnacle-dwelling 'L. neglecta' and the lagoonal 'L. tenebrosa'. Relationships between these taxa, and between and within representative populations, are investigated using sequence analysis and restriction fragment length polymorphism of a mitochondrial DNA fragment spanning the cytochrome oxidase I and cytochrome oxidase II gene boundary. These data show that there is some sharing of haplotypes between species, with L. arcana haplotypes paraphyletic with respect to L. saxatilis haplotypes, and L. compressa haplotypes paraphyletic to both L. arcana and L. saxatilis haplotypes. Such sharing of mtDNA haplotypes could be a consequence of either persistent hybridization or episodes of hybridization, or incomplete lineage sorting of ancestral polymorphisms. On the balance of evidence it is suggested that the latter, rather than hybridization events, is the more likely causal agent of the observed distribution. Intraspecific variation is extensive and it is suggested that the patterns of intraspecific polymorphism are explainable by a combination of historical factors (the impact of the Pleistocene ice-age) and contemporary restrictions to gene flow. It is argued that Littorina haplotypes evolved in at least two separate glacial refugia and became scattered by the subsequent range expansion around most of the coastline. Recent factors such as restricted gene flow and bottlenecks would then be capable of affecting the haplotype distribution, resulting in the pattern observed.
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Affiliation(s)
- C S Wilding
- School of Biology, The University of Leeds, Leeds LS2 9JT, UK
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Abstract
A 8022 base pair fragment from the mitochondrial DNA of the prosobranch gastropod Littorina saxatilis has been sequenced and shown to contain the complete genes for 12 transfer RNAs and five protein genes (CoII, ATPase 6, ATPase 8, ND1, ND6), two partial protein genes (CoI and cyt b), and two ribosomal RNAs (small and large subunits). The order of these constituent genes differs from those of other molluscan mitochondrial gene arrangements. Only a single rearrangement involving a block of protein coding genes and three tRNA translocations are necessary to produce identical gene orders between L. saxatilis and K. tunicata. However, only one gene boundary is shared between the L. saxatilis gene order and that of the pulmonate gastropod Cepaea nemoralis. This extends the observation that there is little conservation of mitochrondrial gene order amongst the Mollusca and suggests that radical mitochondrial DNA gene rearrangement has occurred on the branch leading to the pulmonates.
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Wilding CS, Beaumont AR, Latchford JW. Mitochondrial DNA variation in the scallop Pecten maximus (L.) assessed by a PCR-RFLP method. Heredity (Edinb) 1997; 79 ( Pt 2):178-89. [PMID: 9279012 DOI: 10.1038/hdy.1997.141] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Two PCR-RFLP mitochondrial DNA (mtDNA) markers were developed through the cloning and sequencing of mtDNA from the scallop Pecten maximus, and were used to study genetic differentiation off UK and Atlantic coast populations of this species. Although no distinct pattern of mtDNA haplotype frequencies was apparent and no diagnostic haplotypes were identified for any population, sequence divergence data provided convincing evidence that a P. maximus sample taken from Mulroy Bay, Eire, a semi-enclosed sea lough, was genetically differentiated form all other samples. However, this could not be unequivocally attributed to a restriction in gene flow, as the sample consisted of an ongrown single spatfall, which may not have been representative of the wild population. Despite the inability to separate populations on the basis of haplotype frequency, it was noteworthy that the frequency pattern of the commonest haplotype varied between sampling sites in a manner similar to that of allozyme allele frequencies in Aequipecten opercularis, a scallop species with a similar distribution and life history, for which there is evidence of population subdivision. Pecten maximus from St. Brieuc Bay, reasoned to be a self-recruiting population from reproductive and physiological evidence, could not be separated from other populations using mtDNA markers. Further investigation of this population with alternative markers is warranted.
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Affiliation(s)
- C S Wilding
- School of Ocean Sciences, University of Wales (Bangor), Gwynedd, U.K.
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