Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium1
- 2Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- 3MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK
- 4Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- 5Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- 6Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229), Centre IRD de Montpellier, 34395 Montpellier Cedex 5, France
- 7Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9700 Groningen, The Netherlands
- 8Unit d'Ecologie des Systèmes Vectoriels, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- 9Eck Institute for Global Health, Department of Biological Sciences and University of Notre Dame, IN 46556, USA
- 10Department of Life Sciences, Imperial College, Berkshire SL5 7PY, UK
- 11Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Dipartimento di Sanita Pubblica e Malattie Infettive, Università di Roma SAPIENZA, Rome, Italy
- 12Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
- 13Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
- 14KEMRI-Wellcome Trust Research Programme, 80108 Kilifi, Kenya
- 15Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
- 16Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- 17Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA
- 18Department of Cytology and Genetics, Tomsk State University, Tomsk 634050, Russia
- 19Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
- 20Unit for Genetics and Genomics of Insect Vectors, Institut Pasteur, 75015 Paris, France
- 21School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
- 22Verily Life Sciences, South San Francisco, CA 94080, USA
- 23Programa Nacional de Controle da Malária, Direcção Nacional de Saúde Pública, Ministério da Saúde, Luanda, Angola
- 24London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
- 25Institut de Recherche en Sciences de la Santé (IRSS), Bobo Dioulasso, B.P. 7192 Burkina Faso
- 26Laboratoire de Recherche sur le Paludisme, Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), B.P. 288 Yaoundé, Cameroon
- 27Centre Suisse de Recherches Scientifiques. Yopougon, Abidjan - 01 BP 1303 Abidjan, Côte d'Ivoire
- 28Institut Pasteur de Madagascar, Avaradoha, BP 1274, 101 Antananarivo, Madagascar
- 29Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine (MRCG at LSHTM), Banjul, The Gambia
- 30Department of Wildlife and Entomology, University of Cape Coast, Cape Coast, Ghana
- 31Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, BP: E 423 Bamako-Mali
- 32Instituto Nacional de Saaúde Paública, Ministaério da Saaúde Paública, Bissau, Guinaé-Bissau
- 33Infectious Diseases Research Collaboration, Kampala, Uganda
- 34Microbiotica Limited, Biodata, Innovation Centre, Wellcome Genome Campus, Cambridge CB10 1DR, UK
- 35European Bioinformatics Institute, Hinxton, Cambridge CB10 1SA, UK
- 36Department of Medical Entomology and Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
Abstract
Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with a high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high-quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii. We analyzed whole genomes of 1142 individual mosquitoes sampled from the wild in 13 African countries, as well as a further 234 individuals comprising parents and progeny of 11 laboratory crosses. The data resource includes high-confidence single-nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We use these data to analyze genetic population structure and characterize genetic diversity within and between populations. We illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance and for accelerating research and development of new vector control tools. It also provides a unique resource for the study of population genomics and evolutionary biology in eukaryotic species with high levels of genetic diversity under strong anthropogenic evolutionary pressures.
Footnotes
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↵1 A complete list of Consortium authors and affiliations appears at the end of this article.
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.262790.120.
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Freely available online through the Genome Research Open Access option.
- Received March 11, 2020.
- Accepted August 27, 2020.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.