Single-cell sequencing of the small and AT-skewed genome of malaria parasites
| Autor: | Audrey C. Brown, Adam C Huckaby, Shiwei Liu, Ian E. Burbulis, Jennifer L. Guler, Christopher C. Moore, Michael J. McConnell |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Plasmodium
Erythrocytes DNA Copy Number Variations Plasmodium falciparum MALBAC Method Genomics Computational biology Biology QH426-470 Genome Polymorphism Single Nucleotide Genetics Humans Copy-number variation Whole-genome amplification Molecular Biology Genetics (clinical) Whole Genome Amplification Single-nucleotide polymorphism Base Composition Copy number variation Intracellular parasite Computational Biology High-Throughput Nucleotide Sequencing Sequence Analysis DNA AT-skewed genome biology.organism_classification Malaria Single cell sequencing Single-cell sequencing Molecular Medicine Medicine Single-Cell Analysis Genome Protozoan |
| Zdroj: | Genome Medicine, Vol 13, Iss 1, Pp 1-23 (2021) Genome Medicine |
| Popis: | 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. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00889-9. |
| Databáze: | OpenAIRE |
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