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Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestr... Full description

Journal Title: PLoS Genetics Sep 2017, Vol.13(9)
Main Author: Moon, Robert
Other Authors: Holder, Anthony , Blackman, Michael , Roper, Cally , Drakeley, Christopher , Pain, Arnab , Sutherland, Colin , Hibberd, Martin , Campino, Susana , Clark, Taane
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 15537404 ; DOI: 10.1371/journal.pgen.1007008
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title: Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations
format: Article
creator:
  • Moon, Robert
  • Holder, Anthony
  • Blackman, Michael
  • Roper, Cally
  • Drakeley, Christopher
  • Pain, Arnab
  • Sutherland, Colin
  • Hibberd, Martin
  • Campino, Susana
  • Clark, Taane
subjects:
  • Plasmodium Falciparum
  • Malaysia
  • Macaca Nemestrina
  • Macaca Fascicularis
  • Crick, Francis
  • Plasmodium Ovale
  • Singapore
  • Plasmodium
  • Plasmodium Knowlesi
  • Infections
  • Supervision
  • Population
  • Phylogenetics
  • Evolution
  • Bioinformatics
  • Epidemiology
  • Genomes
  • Funding
  • Dimorphism
  • Genetics
  • Genomes
  • Deforestation
  • Genotypes
  • Parasites
  • Population Structure
  • Deforestation
  • Malaria
  • Chromosome 8
  • Mosaics
  • Proteins
  • Dimorphism
  • Medicine
  • Councils
  • Hygiene
  • Historical Structures
  • Parasites
  • Medical Research
  • Subpopulations
  • Manganese
  • Genomes
  • Recombination
  • Mosaics
  • Tropical Diseases
  • Parameter Estimation
  • Macaque
  • Plasmodium
  • DNA-Binding Proteins
  • Phylogenetic Analysis
  • Mammalian Genomics
  • Malarial Parasites
  • Haplotypes
  • Mitochondria
ispartof: PLoS Genetics, Sep 2017, Vol.13(9)
description: The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.
language: eng
source:
identifier: E-ISSN: 15537404 ; DOI: 10.1371/journal.pgen.1007008
fulltext: fulltext_linktorsrc
issn:
  • 15537404
  • 1553-7404
url: Link


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titleAnalysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations
creatorMoon, Robert ; Holder, Anthony ; Blackman, Michael ; Roper, Cally ; Drakeley, Christopher ; Pain, Arnab ; Sutherland, Colin ; Hibberd, Martin ; Campino, Susana ; Clark, Taane
ispartofPLoS Genetics, Sep 2017, Vol.13(9)
identifierE-ISSN: 15537404 ; DOI: 10.1371/journal.pgen.1007008
subjectPlasmodium Falciparum ; Malaysia ; Macaca Nemestrina ; Macaca Fascicularis ; Crick, Francis ; Plasmodium Ovale ; Singapore ; Plasmodium ; Plasmodium Knowlesi ; Infections ; Supervision ; Population ; Phylogenetics ; Evolution ; Bioinformatics ; Epidemiology ; Genomes ; Funding ; Dimorphism ; Genetics ; Genomes ; Deforestation ; Genotypes ; Parasites ; Population Structure ; Deforestation ; Malaria ; Chromosome 8 ; Mosaics ; Proteins ; Dimorphism ; Medicine ; Councils ; Hygiene ; Historical Structures ; Parasites ; Medical Research ; Subpopulations ; Manganese ; Genomes ; Recombination ; Mosaics ; Tropical Diseases ; Parameter Estimation ; Macaque ; Plasmodium ; DNA-Binding Proteins ; Phylogenetic Analysis ; Mammalian Genomics ; Malarial Parasites ; Haplotypes ; Mitochondria
descriptionThe macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.
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titleAnalysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations
descriptionThe macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.
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titleAnalysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations
authorMoon, Robert ; Holder, Anthony ; Blackman, Michael ; Roper, Cally ; Drakeley, Christopher ; Pain, Arnab ; Sutherland, Colin ; Hibberd, Martin ; Campino, Susana ; Clark, Taane
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3Macaca Fascicularis
4Crick, Francis
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8Plasmodium Knowlesi
9Infections
10Supervision
11Population
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13Evolution
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16Genomes
17Funding
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19Genetics
20Deforestation
21Genotypes
22Parasites
23Population Structure
24Malaria
25Chromosome 8
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30Hygiene
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35Recombination
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abstractThe macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.
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