Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates
Date
2023
Authors
Journal Title
Journal ISSN
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Publisher
Microbial Genomics
Abstract
Experimental studies on the biology of malaria parasites have mostly been based on laboratory-adapted lines, but there is
limited understanding of how these may differ from parasites in natural infections. Loss-of-function mutants have previously
been shown to emerge during culture of some Plasmodium falciparum clinical isolates in analyses focusing on single-genotype
infections. The present study included a broader array of isolates, mostly representing multiple-genotype infections, which are
more typical in areas where malaria is highly endemic. Genome sequence data from multiple time points over several months
of culture adaptation of 28 West African isolates were analysed, including previously available sequences along with new
genome sequences from additional isolates and time points. Some genetically complex isolates eventually became fixed over
time to single surviving genotypes in culture, whereas others retained diversity, although proportions of genotypes varied over
time. Drug resistance allele frequencies did not show overall directional changes, suggesting that resistance-associated costs
are not the main causes of fitness differences among parasites in culture. Loss-of-function mutants emerged during culture
in several of the multiple-genotype isolates, affecting genes (including AP2-HS, EPAC and SRPK1) for which loss-of-function
mutants were previously seen to emerge in single-genotype isolates. Parasite clones were derived by limiting dilution from
six of the isolates, and sequencing identified de novo variants not detected in the bulk isolate sequences. Interestingly, several
of these were nonsense mutants and frameshifts disrupting the coding sequence of EPAC, the gene with the largest number
of independent nonsense mutants previously identified in laboratory-adapted lines. Analysis of genomic identity by descent
to explore relatedness among clones revealed co-occurring non-identical sibling parasites, illustrative of the natural genetic
structure within endemic populations.
Description
Research Article
Keywords
culture, loss-of-function mutants, mixed genotypes, genomic, relatedness, adaptation