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.

Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii / Clarkson, C. S.; Miles, A.; Harding, N. J.; Lucas, E. R.; Battey, C. J.; Amaya-Romero, J. E.; Kern, A. D.; Fontaine, M. C.; Donnelly, M. J.; Lawniczak, M. K. N.; Kwiatkowski, D. P.; Donnelly, M. J.; Ayala, D.; Besansky, N. J.; Burt, A.; Caputo, B.; Della Torre, A.; Fontaine, M. C.; Godfray, H. Charles J.; Hahn, M. W.; Kern, A. D.; Kwiatkowski, D. P.; Lawniczak, M. K. N.; Midega, J.; O'Loughlin, S.; Pinto, J.; Riehle, M. M.; Sharakhov, I.; Schrider, D. R.; Vernick, K. D.; Weetman, D.; Wilding, C. S.; White, B. J.. - In: GENOME RESEARCH. - ISSN 1088-9051. - 30:10(2020), pp. 1533-1546. [10.1101/GR.262790.120]

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

Caputo B.;Della Torre A.;
2020

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.
2020
mosquito; anopheles; genome
01 Pubblicazione su rivista::01a Articolo in rivista
Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii / Clarkson, C. S.; Miles, A.; Harding, N. J.; Lucas, E. R.; Battey, C. J.; Amaya-Romero, J. E.; Kern, A. D.; Fontaine, M. C.; Donnelly, M. J.; Lawniczak, M. K. N.; Kwiatkowski, D. P.; Donnelly, M. J.; Ayala, D.; Besansky, N. J.; Burt, A.; Caputo, B.; Della Torre, A.; Fontaine, M. C.; Godfray, H. Charles J.; Hahn, M. W.; Kern, A. D.; Kwiatkowski, D. P.; Lawniczak, M. K. N.; Midega, J.; O'Loughlin, S.; Pinto, J.; Riehle, M. M.; Sharakhov, I.; Schrider, D. R.; Vernick, K. D.; Weetman, D.; Wilding, C. S.; White, B. J.. - In: GENOME RESEARCH. - ISSN 1088-9051. - 30:10(2020), pp. 1533-1546. [10.1101/GR.262790.120]
File allegati a questo prodotto
File Dimensione Formato  
Clarkson_Genome_2020.pdf

accesso aperto

Tipologia: Versione editoriale (versione pubblicata con il layout dell'editore)
Licenza: Creative commons
Dimensione 2.85 MB
Formato Adobe PDF
2.85 MB Adobe PDF
Clarkson_supplemento_Genome_2020.pdf

accesso aperto

Tipologia: Versione editoriale (versione pubblicata con il layout dell'editore)
Licenza: Creative commons
Dimensione 8.28 MB
Formato Adobe PDF
8.28 MB Adobe PDF

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1466130
Citazioni
  • ???jsp.display-item.citation.pmc??? 40
  • Scopus 59
  • ???jsp.display-item.citation.isi??? 55
social impact