biostudies-literatureLiu SNational Institute of Allergy and Infectious DiseasesMcDonnell FellowshipUniversity of VirginiaNIAID NIH HHSUniversity of Virginia Global Infectious Disease InstituteNIGMS NIH HHS75https://www.ebi.ac.uk/biostudies/studies/S-EPMC8094492biostudies-literatureUnknown13(1)Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.Genome medicineSingle-cell sequencing of the small and AT-skewed genome of malaria parasites.PMC8094492NIH 7R21AI111072R01 AI150856R21 AI111072iGrant3Cavaliers GrantT32 GM139787R35 GM122471FONDECYT Regular #1191737Brown ACBurbulis IMcConnell MJLiu SMoore CCGuler JLHuckaby ACfalseSingle-cell sequencing of the small and AT-skewed genome of malaria parasites.Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.2021-01-01T00:00:00Z2021 May2025-04-26T17:13:17.175Z2025-04-06T15:23:24.034ZS-EPMC80944923394744910.1186/s13073-021-00889-9