ArticleGenome research2016
Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers.
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Who cites it
156 citing papers in PubMed, 266 citations in OpenAlex.
- Dual plasmepsin IX and X inhibitors are refractory to development of resistance.PLoS pathogens · 2026Article
- Emergence and spread of Plasmodium falciparum PX1 polymorphisms associated with decreased susceptibility to antimalarials in Uganda.Nature medicine · 2026Article
- Identification of genetic markers of quinine partial resistance in Plasmodium falciparum.Nature microbiology · 2026Article
- Unpacking boxes: identification of novel inhibitors of malaria parasite invasion.International journal for parasitology. Drugs and drug resistance · 2026Article
- Single-cell analysis ofbioRxiv : the preprint server for biology · 2026Article
- Impact of intensive control on malaria population genomics under elimination settings in Southeast Asia.Nature microbiology · 2026Article
- Comprehensive computational insights into Plasmodium retrocopies reveals potential roles in virulence-associated functions.Genetica · 2026Article
- hmmibd-rs: an enhanced hmmIBD implementation for parallelizable identity-by-descent detection from large-scale Plasmodium genomic data.Malaria journal · 2026Article
- A previously low prevalence Plasmodium falciparum clone expands in an outbreak in the Pacific Coast of South America.BMC infectious diseases · 2026Article
- Replication stress increases de novo CNVs across the malaria parasite genome.Nucleic acids research · 2026Article
- Towards an evolutionary baseline model ofbioRxiv : the preprint server for biology · 2025Article
- Target gene mutation discovery and amplicon sequencing for evaluating maduramicin resistance in Eimeria tenella.Communications biology · 2025Article
- Deconvolution of the On-Target Activity of Plasmepsin V Peptidomimetics inACS infectious diseases · 2025Article
- Heterogeneous constraint and adaptation across the malaria parasite life cycle.Proceedings. Biological sciences · 2025Article
- Replication stress increases de novo CNVs across the malaria parasite genome.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking and optimization of methods for the detection of identity-by-descent in high-recombiningeLife · 2025Article
- Direct long-read visualization reveals hidden variation in GCH1 gene copy number and precise expansion steps.BMC genomics · 2025Article
- Tracking Plasmodium falciparum antimalarial resistance markers during a malaria pre-elimination period in the Pacific coast of South America.Scientific reports · 2025Article
- Genomic investigation of a non-travel Plasmodium falciparum case linked to imported malaria in China's post-elimination era.Malaria journal · 2025Article
- Article
96 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors at 9 institutions in 4 countries.
Funding
Abstract
The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.