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Ag1000G

Started 2014

Mosquito
 

Introduction

Ag1000G is an international collaboration using whole genome deep sequencing to provide a high-resolution view of genetic variation in natural populations of Anopheles gambiae, the principal vector of Plasmodium falciparum malaria in Africa.

Objectives & Coordination

We have three core objectives:

  • Discovering natural genetic variation – We’re using high-throughput sequencing of a large number of wild-caught mosquitoes sampled from across Africa to build a comprehensive catalogue of genetic variation in natural vector populations. Our primary focus is on A. gambiae sensu strictu and A. coluzzii, but we will be expanding to include A. arabiensis in the future.
  • Describing the structure and history of vector populations – We’re analysing genetic variation data to characterise key features of natural vector populations, such as patterns of diversity, linkage disequilibrium and recombination, population structure and gene flow, signals of recent selection, and demographic history.
  • Connecting genetic variation and population biology with ecology and malaria epidemiology – We aim to study associations between genotype and broad phenotypes such as ecological specialisation and differences in local malaria epidemiology.

Our work is coordinated by two working groups:

  • Partner Working Group (led by Martin Donnelly) is comprised of the investigators contributing samples or other significant resources and/or strategic guidance
  • Data Analysis Group (led by Dominic Kwiatkowski) is undertaking core project analyses

Locations

To date, we’ve collected and sequenced mosquitoes from 13 countries:

Sampling locations

Angola, Bioko Island, Equatorial Guinea, Burkina Faso, Cameroon, Central African Republic, Congo, Equatorial Guinea, Gabon, The Gambia, Ivory Coast, Kenya, Malawi, Mali, Mayotte Island, Mozambique, Tanzania, Uganda.

Data

Ag1000G samples are sequenced by the Wellcome Trust Sanger Institute Parasites and Microbes Programme using Illumina high-throughput technology. The sequence data are then used to discover genetic variation between samples and to make genotype calls. Raw sequence reads are deposited into the European Nucleotide Archive (ENA). The variant call data generated by the project is publicly released on a regular basis.

Any use of Ag1000G data is subject to the Terms of Use.

Current

4 Nov 2021 Ag3.0 (Ag1000G phase 3) haplotypes data release
Species: A. gambiae sensu lato

Phased haplotypes for 2,784 wild-caught mosquitoes collected from 19 countries in sub-Saharan Africa.

This data is subject to
Ag1000G Terms of Use

9 Jul 2021 Ag3.0 (Ag1000G phase 3) CNV data release
Species: A. gambiae sensu lato

Sample set: 2,784 wild-caught specimens from 19 countries and 297 specimens comprising parents and progeny of 15 crosses.

This data is subject to
Ag1000G Terms of Use

11 Feb 2021 Ag3.0 (Ag1000G phase 3) SNP data release
Species: A. gambiae sensu lato

Sample set: 2,784 wild-caught specimens from 19 countries and 297 specimens comprising parents and progeny of 15 crosses.

This data is subject to
Ag1000G Terms of Use

6 Nov 2017 Ag1000G phase 2 AR1 data release
Species: A. gambiae sensu lato

Sample set: 1,142 wild-caught specimens from 13 countries and 234 specimens comprising parents and progeny of 11 crosses.

This data is subject to
Open access

21 Dec 2016 Ag1000G phase 1 AR3.1 data release
Species: A. gambiae sensu lato

Sample set: 765 wild-caught specimens from 8 countries and 80 specimens comprising parents and progeny of four crosses.

This data is subject to
Open access

Archived

22 Jul 2015 Ag1000G phase 1 AR3 data release
Species: A. gambiae sensu lato

Sample set: 765 wild-caught specimens from 8 countries and 80 specimens comprising parents and progeny of four crosses

This data is subject to
Open access

Archived

8 Dec 2014 Ag1000G phase 1 AR2 data release
Species: A. gambiae sensu lato

Sample set: 765 wild-caught specimens from 8 countries

This data is subject to
Open access

Archived

21 May 2014 Ag1000G phase 1 preview data release
Species: A. gambiae sensu lato

Sample set: 103 wild-caught specimens from Uganda

This data is subject to
Open access

Archived

For partners

Resources for partners working on mosquitoes

Partner studies

The Ag1000G project is coordinated by a consortium of partners from a range of different research institutions and countries. This includes consortium members who are carrying out independent research studies in malaria endemic regions, and who have contributed mosquito specimens or mosquito DNA samples collected in the course of their own research. The pages below describe the studies that have contributed samples to the Ag1000G project, which includes wild-caught samples from 19 African countries. They also provide information about the collection locations and methods, the people involved in the studies, and references to any published articles providing further information about the studies.

We use species nomenclature following (1). Unless otherwise stated, the DNA extraction method used for the collections described below was Qiagen DNeasy Blood and Tissue Kit (Qiagen Science, MD, USA).

1. Maureen Coetzee, Richard H. Hunt, Richard Wilkerson, Alessandra Della Torre, Mamadou B. Coulibaly, and Nora J. Besansky. Anopheles coluzzii and anopheles amharicus, new members of the anopheles gambiae complex. Zootaxa, 3619(3):246–274, February 2013. doi:10.11646/zootaxa.3619.3.2.

24 Mar 2022 Ag1000G - ANGOLA (AG1000G-AO)

Partner study description Adult mosquitoes were obtained by rearing larvae collected from breeding sites along the main roads connecting the municipalities of Kilamba-Kiaxi and Viana, Luanda province (-8.821, 13.291), in April/May 2009. These…

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24 Mar 2022 Ag1000G - BURKINA FASO (AG1000G-BF-1)

Partner study description The Target Malaria project contributed samples from collections made in three villages separated by at most 30km: Bana (11.233, -4.472), Souroukoudinga (11.235, -4.535) and Pala (11.150, -4.235). These collections were…

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31 Mar 2022 Ag1000G - BURKINA FASO (AG1000G-BF-2)

Partner study description Samples were contributed from collections of indoor resting adults made by spray catch from Monomtenga in central Burkina Faso (12.06, -1.17). These specimens were sorted morphologically to An. gambiae s.l..…

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31 Mar 2022 Ag1000G - CAMEROON (AG1000G-CM-1)

Partner study description Pyrethrum spray collections were conducted in three villages in Cameroon during September and October 2009. These villages comprise a transect from forest (village of Mayos: 4.341, 13.558) to forest/savanna transition…

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31 Mar 2022 Ag1000G - CAMEROON (AG1000G-CM-2)

Partner study description These samples were collected as part of a study which took place in Cameroon in Central Africa. The country is commonly referred to as “miniature Africa”, owing to the diversity…

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31 Mar 2022 Ag1000G - CAMEROON (AG1000G-CM-3)

Partner study description Samples were contributed from pyrethrum spray collections, larval sampling and human landing catches conducted in twenty locations during October 2013. These villages are scattered throughout the country and reflect a…

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5 Apr 2022 Ag1000G - CENTRAL AFRICAN REPUBLIC (AG1000G-CF)

Partner study description Collections were carried out in Bangui (4.367, 18.583), during December 1993, by indoor resting aspiration or pyrethrum spray catch. Contributors Alessandra della Torre (alessandra.dellatorre@uniroma1.it) Istituto Pasteur Italia–Fondazione Cenci Bolognetti, Dipartimento…

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6 Apr 2022 Ag1000G - COLONY CROSSES (AG1000G-X)

Partner study description 15 crosses were contributed to Ag1000G phase 3, 11 of which were previously released in Ag1000G phase 2. Crosses were generated using parents from eight different colonies: G3 (MRA-112); Kisumu…

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5 Apr 2022 Ag1000G - CÔTE D'IVOIRE (AG1000G-CI)

Partner study description Samples were collected in Tiassale (5.898, -4.823), located in the evergreen forest zone of southern Côte d’Ivoire. The primary agricultural activity is rice cultivation in irrigated fields. High malaria transmission…

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5 Apr 2022 Ag1000G - DEMOCRATIC REPUBLIC OF THE CONGO (AG1000G-CD)

Partner study description Samples were collected from Gbadolite (4.283, 21.017), a town located in the far north of the Democratic Republic of Congo (DRC) near the border with the Central African Republic, surrounded…

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24 Mar 2022 Ag1000G - EQUATORIAL GUINEA - BIOKO ISLAND (AG1000G-GQ)

Partner study description Collections were performed during the rainy season in September 2002 by overnight CDC light traps in Sacriba of Bioko island (3.7, 8.7). Specimens were stored dry on silica gel before…

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5 Apr 2022 Ag1000G - GABON (AG1000G-GA-1)

Partner study description Mosquitoes were collected by landing catches in the capital city Libreville (0.384, 9.455) in December 2000 (1), an urban and polluted site. Malaria is endemic throughout the year. Specimens were…

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5 Apr 2022 Ag1000G - GHANA (AG1000G-GH)

Partner study description Samples were collected in Twifo Praso (5.609, -1.549), a peri-urban community located in semi-deciduous forest in the Central Region of Ghana. It is an extensive agricultural area characterised by small-scale…

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5 Apr 2022 Ag1000G - GUINEA AND MALI (AG1000G-GN-ML)

Partner study description Collections were made from four different study sites around the border between Guinea and Mali. From Mali; Takan (11.47, -8.33) and Toumani Oulena (10.83, -7.81) are both small villages in…

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5 Apr 2022 Ag1000G - GUINEA BISSAU (AG1000G-GW)

Partner study description Guinea Bissau samples were collected from three sites in October 2010 by indoor CDC light traps. Safim (11.957, -15.649) and Antula (11.891, -15.582), from a south-western coastal region, characterised mainly…

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5 Apr 2022 Ag1000G - KENYA (AG1000G-KE)

Partner study desrcription Kenyan specimens were obtained from villages located in Kilifi County near the Kenyan coast between 2000 and 2014. All Anopheles mosquito sampling was conducted indoors using CDC light traps which…

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5 Apr 2022 Ag1000G - MALAWI (AG1000G-MW)

Partner study description Specimens were obtained from villages within the catchment of the Majete Malaria Project, Chikhwawa District, Malawi (-15.933, 34.755) (1). Mosquitoes were collected indoors and outdoors by Suna light trap from…

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5 Apr 2022 Ag1000G - MALI (AG1000G-ML-1)

Partner study description Collections were made in four villages in the Koulikoro region; Tieneguebougou (12.810, -8.080) approximately 20km north of Bamako, and Kababougou (12.890, -8.150), Ouassorola (12.900, -8.160), Sogolombougou (12.880, -8.140), approximately 30km…

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5 Apr 2022 Ag1000G - MALI (AG1000G-ML-2)

Partner study description Collections of indoor resting adults were made by spray catch from seven villages in the southern part of Mali in August-September 2004: Banambani (12.800, -8.050), Bancoumana (12.200, -8.200), Douna (13.210,…

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5 Apr 2022 Ag1000G - MAYOTTE (AG1000G-FR)

Partner study description Collections were taken from multiple sites on the island of Mayotte. Samples were collected as larvae during March-April 2011 in temporary pools by dipping. Sites included Mtsanga Charifou (-12.991, 45.156)…

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5 Apr 2022 Ag1000G - MOZAMBIQUE (AG1000G-MZ)

Partner study description Mosquito samples were collected in Furvela (-23.716, 35.299), Mozambique, by CDC light traps between December 2003 and April 2004. Specimens were stored on silica gel and DNA was extracted according…

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5 Apr 2022 Ag1000G - TANZANIA (AG1000G-TZ)

Partner study description Tanzanian samples were collected from four distinct locations. Moshi samples came from lower Mabogini (-3.400, 37.350), rice fields near lower Moshi on the southern slope of Mount Kilimanjaro, a region…

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5 Apr 2022 Ag1000G - THE GAMBIA (AG1000G-GM-1)

Partner study description Indoor resting female mosquitoes were collected by pyrethrum spray catch from four hamlets around Njabakunda (13.55, -15.90), North Bank Region, The Gambia between August and October 2011. The four hamlets…

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5 Apr 2022 Ag1000G - THE GAMBIA (AG1000G-GM-2)

Partner study description Specimens were collected along the Gambia River from the western coastal region of The Gambia (1), in August 2006. An. gambiae and An. coluzzii specimens were identified to species following…

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5 Apr 2022 Ag1000G - THE GAMBIA (AG1000G-GM-3)

Partner study description Adult mosquitoes were collected at Wali Kunda in the rural, central river region of The Gambia (13.567, -14.917). The area is 180km from the sea, on the south bank of…

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5 Apr 2022 Ag1000G - UGANDA (AG1000G-UG)

Partner study description Specimens were obtained from two locations in Uganda: Nagongera, 30km to the North of Lake Victoria near the border with Kenya, and Kihihi, in the very South-West of the country.…

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Publications

User guide

765 mosquitoes

from

8 countries

Project contact

People

The Ag1000G Consortium involves researchers from several institutions around the world, including experts in Anopheles genomics, population genetics, epidemiology, and vector biology. The Ag1000G Consortium comprises members of two working groups, as well as affiliates involved in data production and analysis.

Partner Working Group

The Partner Working Group (PWG) is comprised of the investigators contributing samples or other significant resources / strategic guidance to the Project.

Data Analysis Working Group

The Data Analysis Group (DAG) is undertaking core project analyses and includes members of both the PWG and PMG, alongside additional members of the Ag1000G Consortium.

Updates

6 Oct 2015

This data is subject to