ArticleBMC genomics2015
Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Major features of parasite adaptation revealed by genomes of Plasmodium falciparum population samples archived for over 50 years.Communications biology · 2026Article
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- Genomic variation during culture adaptation of genetically complexMicrobial genomics · 2023Article
- Performance of SNP barcodes to determine genetic diversity and population structure ofFrontiers in genetics · 2023Article
- Genomic analysis reveals independent evolution of Plasmodium falciparum populations in Ethiopia.Malaria journal · 2021Article
- An open dataset ofWellcome open research · 2021Article
- Genome-Wide Scans for GhanaianFrontiers in cellular and infection microbiology · 2021Article
- Population genetic analysis of the Plasmodium falciparum circumsporozoite protein in two distinct ecological regions in Ghana.Malaria journal · 2020Article
- Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites.Communications biology · 2020Article
- Analysis of Plasmodium falciparum Rh2b deletion polymorphism across different transmission areas.Scientific reports · 2020Article
- Highlights of the 3rd ISCB Africa Student Council Symposium 2019 in Ghana.F1000Research · 2020Article
- Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa.Malaria journal · 2019Review
- Article
- Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp.Genome biology and evolution · 2019Article
- Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development.Scientific reports · 2018Article
- Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia.Scientific reports · 2018Article
- Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections.Nature communications · 2018Article
- Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen.Genome biology and evolution · 2018Article
- Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa.Frontiers in genetics · 2018Review
- Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.PLoS neglected tropical diseases · 2017Article
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10 authors.
Funding
Abstract
backgroundGenome wide sequence analyses of malaria parasites from widely separated areas of the world have identified contrasting population structures and signatures of selection. To compare relatively closely situated but ecologically contrasting regions within an endemic African country, population samples of Plasmodium falciparum clinical isolates were collected in Ghana from Kintampo in the central forest-savannah area, and Navrongo in a drier savannah area ~350 km to the north with more seasonally-restricted transmission. Parasite DNA was sequenced and paired-end reads mapped to the P. falciparum reference genome.
resultsHigh coverage genome wide sequence data for 85 different clinical isolates enabled analysis of 121,712 single nucleotide polymorphisms (SNPs). The local populations had similar proportions of mixed genotype infections, similar SNP allele frequency distributions, and eleven chromosomal regions had elevated integrated haplotype scores (|iHS|) in both. A between-population Rsb metric comparing extended haplotype homozygosity indicated a stronger signal within Kintampo for one of these regions (on chromosome 14) and in Navrongo for two of these regions (on chromosomes 10 and 13). At least one gene in each of these identified regions is a potential target of locally varying selection. The candidates include genes involved in parasite development in mosquitoes, members of variant-expressed multigene families, and a leading vaccine-candidate target of immunity.
conclusionsAgainst a background of very similar population structure and selection signatures in the P. falciparum populations of Ghana, three narrow genomic regions showed evidence indicating local differences in historical timing or intensity of selection. Sampling of closely situated populations across heterogeneous environments has potential to refine the mapping of important loci under temporally or spatially varying selection.
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