Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations
AuthorsDiez Benavente, Ernest
Florez de Sessions, Paola
Moon, Robert W.
Holder, Anthony A.
Blackman, Michael J.
Drakeley, Christopher J.
Sutherland, Colin J.
Hibberd, Martin L.
Clark, Taane G.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/625486
MetadataShow full item record
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.
CitationDiez Benavente E, Florez de Sessions P, Moon RW, Holder AA, Blackman MJ, et al. (2017) Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations. PLOS Genetics 13: e1007008. Available: http://dx.doi.org/10.1371/journal.pgen.1007008.
SponsorsTGC is funded by the Medical Research Council UK (Grant no. MR/K000551/1, MR/M01360X/1, MR/N010469/1, MC_PC_15103). SC and CR are funded by the Medical Research Council UK (Grant no. MR/M01360X/1). RWM is supported by an MRC Career Development Award jointly funded by the UK MRC and UK Department for International Development. This work was supported in part by the Francis Crick Institute that receives its core funding from Cancer Research UK (FC001097, FC001043), the UK Medical Research Council (FC001097, FC001043), and the Wellcome Trust (FC001097, FC001043). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
PublisherPublic Library of Science (PLoS)
Except where otherwise noted, this item's license is described as 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 credited.
- Admixture in Humans of Two Divergent Plasmodium knowlesi Populations Associated with Different Macaque Host Species.
- Authors: Divis PC, Singh B, Anderios F, Hisam S, Matusop A, Kocken CH, Assefa SA, Duffy CW, Conway DJ
- Issue date: 2015 May
- Three Divergent Subpopulations of the Malaria Parasite Plasmodium knowlesi.
- Authors: Divis PC, Lin LC, Rovie-Ryan JJ, Kadir KA, Anderios F, Hisam S, Sharma RS, Singh B, Conway DJ
- Issue date: 2017 Apr
- Plasmodium knowlesi: reservoir hosts and tracking the emergence in humans and macaques.
- Authors: Lee KS, Divis PC, Zakaria SK, Matusop A, Julin RA, Conway DJ, Cox-Singh J, Singh B
- Issue date: 2011 Apr
- Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations.
- Authors: Benavente ED, Gomes AR, De Silva JR, Grigg M, Walker H, Barber BE, William T, Yeo TW, de Sessions PF, Ramaprasad A, Ibrahim A, Charleston J, Hibberd ML, Pain A, Moon RW, Auburn S, Ling LY, Anstey NM, Clark TG, Campino S
- Issue date: 2019 Jul 8
- Phylogenetic analysis of simian Plasmodium spp. infecting Anopheles balabacensis Baisas in Sabah, Malaysia.
- Authors: Chua TH, Manin BO, Daim S, Vythilingam I, Drakeley C
- Issue date: 2017 Oct