Single-cell sequencing of the small and AT-skewed genome of malaria parasites

Genome Medicine

Michael J. McConnell¹  Ian Burbulis²  Audrey C. Brown³  Adam C. Huckaby³  Shiwei Liu³  Jennifer L. Güler⁴  Christopher C. Moore⁵ 

[1] Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA;Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA;Current address: Lieber Institute for Brain Development, Baltimore, MD, USA;Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA;Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile;Department of Biology, University of Virginia, Charlottesville, VA, USA;Department of Biology, University of Virginia, Charlottesville, VA, USA;Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA;Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA;

关键词: Whole-genome amplification;    AT-skewed genome;    Malaria;    Single-cell sequencing;    MALBAC;    Copy number variation;    Single-nucleotide polymorphism;   

DOI  :  10.1186/s13073-021-00889-9

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY