Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

Autor: Matthew W. Hahn, Alison T. Isaacs, Edi Constant, Jim Stalker, Boubacar Coulibaly, Michelle M. Riehle, Alistair Miles, Austin Burt, Chris S Clarkson, Charles Mbogo, Alessandra della Torre, Michael C Fontaine, Nora J. Besansky, Eric R. Lucas, Victoria Simpson, Daniel R. Schrider, Samantha M. O’Loughlin, Kirk A. Rockett, Henry D. Mawejje, Bradley J. White, Arlete D. Troco, Andrew D. Kern, Jorge Edouardo Amaya-Romero, Abdoulaye Diabaté, Jorge Cano, Beniamino Caputo, H. Charles J. Godfray, Nicholas J. Harding, Kyanne R. Rohatgi, Igor V. Sharakhov, Christa Henrichs, Martin J. Donnelly, C. J. Battey, Cinzia Malangone, Anna E. Jeffreys, João Pinto, Nohal Elissa, Kate Rowlands, Maryam Kamali, Davis Nwakanma, Kenneth D. Vernick, Carlo Costantini, Janet Midega, John Essandoh, Diego Ayala, Musa Jawara, Eleanor Drury, Daniel Mead, Vincent Robert, Mara K. N. Lawniczak, Dushyanth Jyothi, Joao Dinis, Gilbert Le Goff, Christina Hubbart, Dominic P. Kwiatkowski
Přispěvatelé: Van Doorn group, Fontaine lab, Centre Muraz [Bobo-Dioulasso, Burkina Faso], Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité d'Entomologie Médicale [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), The Wellcome Trust Sanger Institute [Cambridge], The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford [Oxford], Laboratorio Pasteur [Istituto Pasteur-Fondazione Cenci Bolognetti, Rome], Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Computer Science Departement [Indiana], Indiana University [Bloomington], Indiana University System-Indiana University System, Virginia Tech [Blacksburg], University of Oxford
Jazyk: angličtina
Předmět:
Insecticides
[SDV]Life Sciences [q-bio]
Anopheles gambiae
Genome
Insect
[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics
Phylogenetics and taxonomy
Population genomics
0302 clinical medicine
CRISPR-Associated Protein 9
Pyrethrins
Copy-number variation
Genetics (clinical)
0303 health sciences
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
INTROGRESSION
KDR MUTATION
3. Good health
Mosquito control
Resource
mosquito
anopheles
genome
MOLECULAR-FORMS
DNA Copy Number Variations
030231 tropical medicine
Mosquito Vectors
Biology
Polymorphism
Single Nucleotide
MECHANISMS
03 medical and health sciences
QH301
Genetic variation
Anopheles
parasitic diseases
Genetics
medicine
Animals
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
GENE DRIVE
QH426
030304 developmental biology
Isolation by distance
Genetic diversity
COMPLEX
IDENTIFICATION
Whole Genome Sequencing
QH
Genetic Variation
AMPLIFICATION
Gene drive
15. Life on land
medicine.disease
biology.organism_classification
EVOLUTION
Haplotypes
Evolutionary biology
INSECTICIDE RESISTANCE
030217 neurology & neurosurgery
Malaria
Zdroj: Genome Res
Genome Research, 30(12), 1533-1546. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
Genome Research
Genome Research, Cold Spring Harbor Laboratory Press, 2020, 30 (10), pp.1533-1546. ⟨10.1101/gr.262790.120⟩
Genome Research, 2020, 30 (10), pp.1533-1546. ⟨10.1101/gr.262790.120⟩
ISSN: 1088-9051
1549-5469
Popis: 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.
Databáze: OpenAIRE
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