TY - JOUR T1 - Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species <em>Anopheles gambiae</em> and <em>Anopheles coluzzii</em> JF - bioRxiv DO - 10.1101/864314 SP - 864314 AU - The Anopheles gambiae 1000 Genomes Consortium AU - Chris S Clarkson AU - Alistair Miles AU - Nicholas J Harding AU - Eric R Lucas AU - C J Battey AU - Jorge Edouardo Amaya-Romero AU - Jorge Cano AU - Abdoulaye Diabate AU - Edi Constant AU - Davis C Nwakanma AU - Musa Jawara AU - John Essandoh AU - Joao Dinis AU - Gilbert Le Goff AU - Vincent Robert AU - Arlete D Troco AU - Carlo Costantini AU - Kyanne R Rohatgi AU - Nohal Elissa AU - Boubacar Coulibaly AU - Janet Midega AU - Charles Mbogo AU - Henry D Mawejje AU - Jim Stalker AU - Kirk A Rockett AU - Eleanor Drury AU - Daniel Mead AU - Anna E Jeffreys AU - Christina Hubbart AU - Kate Rowlands AU - Alison T Isaacs AU - Dushyanth Jyothi AU - Cinzia Malangone AU - Maryam Kamali AU - Christa Henrichs AU - Victoria Simpson AU - Diego Ayala AU - Nora J Besansky AU - Austin Burt AU - Beniamino Caputo AU - Alessandra della Torre AU - Michael Fontaine AU - H. Charles J Godfray AU - Matthew W Hahn AU - Andrew D Kern AU - Mara K N Lawniczak AU - Samantha O’Loughlin AU - Joao Pinto AU - Michelle M Riehle AU - Igor Sharakhov AU - Daniel R Schrider AU - Kenneth D Vernick AU - Bradley J White AU - Martin J Donnelly AU - Dominic P Kwiatkowski Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/02/19/864314.abstract N2 - 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 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 analysed whole genomes of 1,142 individual mosquitoes sampled from the wild in 13 African countries, and a further 234 individuals comprising parents and progeny of 11 lab 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 used these data to analyse genetic population structure, and characterise genetic diversity within and between populations. We also 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. ER -