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SRX27153455: Bulk Sequencing of Pf DSM1Treated DD2
1 ILLUMINA (Illumina MiSeq) run: 40.7M spots, 11.9G bases, 5.4Gb downloads

Design: Bulk sequencing from DSM1 Treated DD2
Submitted by: University of Virginia
Study: Low-Input Genomic Sequencing of the malaria Parasite, Plasmodium falciparum
show Abstracthide Abstract
Changes in the copy number of large genomic regions, termed copy number variations (CNVs), contribute to important phenotypes in many organisms. CNVs are readily identified using conventional approaches when present in a large fraction of the cell population. However, CNVs that are present in only a few genomes across a population are often overlooked but important; if beneficial under specific conditions, a de novo CNV that arises in a single genome can expand during selection to create a larger population of cells with novel characteristics. While the reach of single cell methods to study de novo CNVs is increasing, we continue to lack information about CNV dynamics in rapidly evolving microbial populations. Here, we investigated de novo CNVs in the genome of the Plasmodium parasite that causes human malaria. The highly AT-rich P. falciparum genome readily accumulates CNVs that facilitate rapid adaptation to new drugs and host environments. We employed a low-input genomics approach optimized for this unique genome as well as specialized computational tools to evaluate the de novo CNV rate both before and after the application of stress. We observed a significant increase in genome-wide de novo CNVs following treatment with a replication inhibitor. These stress-induced de novo CNVs encompassed genes that contribute to various cellular pathways and tended to be altered in clinical parasite genomes. This snapshot of CNV dynamics emphasizes the connection between replication stress, DNA repair, and CNV generation in this important microbial pathogen.
Sample:
SAMN45925815 • SRS23607919 • All experiments • All runs
Library:
Name: Bulk2
Instrument: Illumina MiSeq
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED
Runs: 1 run, 40.7M spots, 11.9G bases, 5.4Gb
Run# of Spots# of BasesSizePublished
SRR3179225540,743,25711.9G5.4Gb2024-12-20

ID:
36639891

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