Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development

Abstract Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 c...

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Autores principales:	Craig W. Duffy, Alfred Amambua-Ngwa, Ambroise D. Ahouidi, Mahamadou Diakite, Gordon A. Awandare, Hampate Ba, Sarah J. Tarr, Lee Murray, Lindsay B. Stewart, Umberto D’Alessandro, Thomas D. Otto, Dominic P. Kwiatkowski, David J. Conway
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Gametocytes Falciparum Gambiae Long-read Sequencing Data Recent Directional Selection Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5832f85adf7a48e2933c54d172a4d56c
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spelling	oai:doaj.org-article:5832f85adf7a48e2933c54d172a4d56c2021-12-02T15:08:49ZMulti-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development10.1038/s41598-018-34078-32045-2322https://doaj.org/article/5832f85adf7a48e2933c54d172a4d56c2018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-34078-3https://doaj.org/toc/2045-2322Abstract Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3′-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.Craig W. DuffyAlfred Amambua-NgwaAmbroise D. AhouidiMahamadou DiakiteGordon A. AwandareHampate BaSarah J. TarrLee MurrayLindsay B. StewartUmberto D’AlessandroThomas D. OttoDominic P. KwiatkowskiDavid J. ConwayNature PortfolioarticleGametocytesFalciparumGambiaeLong-read Sequencing DataRecent Directional SelectionMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-12 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Gametocytes Falciparum Gambiae Long-read Sequencing Data Recent Directional Selection Medicine R Science Q
spellingShingle	Gametocytes Falciparum Gambiae Long-read Sequencing Data Recent Directional Selection Medicine R Science Q Craig W. Duffy Alfred Amambua-Ngwa Ambroise D. Ahouidi Mahamadou Diakite Gordon A. Awandare Hampate Ba Sarah J. Tarr Lee Murray Lindsay B. Stewart Umberto D’Alessandro Thomas D. Otto Dominic P. Kwiatkowski David J. Conway Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
description	Abstract Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3′-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.
format	article
author	Craig W. Duffy Alfred Amambua-Ngwa Ambroise D. Ahouidi Mahamadou Diakite Gordon A. Awandare Hampate Ba Sarah J. Tarr Lee Murray Lindsay B. Stewart Umberto D’Alessandro Thomas D. Otto Dominic P. Kwiatkowski David J. Conway
author_facet	Craig W. Duffy Alfred Amambua-Ngwa Ambroise D. Ahouidi Mahamadou Diakite Gordon A. Awandare Hampate Ba Sarah J. Tarr Lee Murray Lindsay B. Stewart Umberto D’Alessandro Thomas D. Otto Dominic P. Kwiatkowski David J. Conway
author_sort	Craig W. Duffy
title	Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
title_short	Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
title_full	Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
title_fullStr	Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
title_full_unstemmed	Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
title_sort	multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/5832f85adf7a48e2933c54d172a4d56c
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Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development

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