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Recombination Hotspots and Population Structure in Plasmodium falciparum

Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-...

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Autores principales: Mu, Jianbing, Awadalla, Philip, Duan, Junhui, McGee, Kate M, Joy, Deirdre A, McVean, Gilean A. T, Su, Xin-zhuan
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201364/
https://www.ncbi.nlm.nih.gov/pubmed/16144426
http://dx.doi.org/10.1371/journal.pbio.0030335
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author Mu, Jianbing
Awadalla, Philip
Duan, Junhui
McGee, Kate M
Joy, Deirdre A
McVean, Gilean A. T
Su, Xin-zhuan
author_facet Mu, Jianbing
Awadalla, Philip
Duan, Junhui
McGee, Kate M
Joy, Deirdre A
McVean, Gilean A. T
Su, Xin-zhuan
author_sort Mu, Jianbing
collection PubMed
description Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously. The parasites are clustered according to continental origin, but alternative groupings were obtained using SNPs at 37 putative transporter genes that are potentially under selection. Geographic isolation and highly variable multiple infection rates are the major factors affecting haplotype structure. Variation in effective recombination rates is high, both among populations and along the chromosome, with recombination hotspots conserved among populations at chromosome ends. This study supports the feasibility of genome-wide association studies in some parasite populations.
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spelling pubmed-12013642005-10-13 Recombination Hotspots and Population Structure in Plasmodium falciparum Mu, Jianbing Awadalla, Philip Duan, Junhui McGee, Kate M Joy, Deirdre A McVean, Gilean A. T Su, Xin-zhuan PLoS Biol Research Article Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously. The parasites are clustered according to continental origin, but alternative groupings were obtained using SNPs at 37 putative transporter genes that are potentially under selection. Geographic isolation and highly variable multiple infection rates are the major factors affecting haplotype structure. Variation in effective recombination rates is high, both among populations and along the chromosome, with recombination hotspots conserved among populations at chromosome ends. This study supports the feasibility of genome-wide association studies in some parasite populations. Public Library of Science 2005-10 2005-09-13 /pmc/articles/PMC1201364/ /pubmed/16144426 http://dx.doi.org/10.1371/journal.pbio.0030335 Text en Copyright: © 2005 Mu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Mu, Jianbing
Awadalla, Philip
Duan, Junhui
McGee, Kate M
Joy, Deirdre A
McVean, Gilean A. T
Su, Xin-zhuan
Recombination Hotspots and Population Structure in Plasmodium falciparum
title Recombination Hotspots and Population Structure in Plasmodium falciparum
title_full Recombination Hotspots and Population Structure in Plasmodium falciparum
title_fullStr Recombination Hotspots and Population Structure in Plasmodium falciparum
title_full_unstemmed Recombination Hotspots and Population Structure in Plasmodium falciparum
title_short Recombination Hotspots and Population Structure in Plasmodium falciparum
title_sort recombination hotspots and population structure in plasmodium falciparum
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201364/
https://www.ncbi.nlm.nih.gov/pubmed/16144426
http://dx.doi.org/10.1371/journal.pbio.0030335
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