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Parasite Metagenome

ABSTRACT: Parasite Metagenome

PROVIDER: PRJNA445845 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6903290.fastq.gz	Fastqsanger.gz
	SRR6903291.fastq.gz	Fastqsanger.gz
	SRR6903292.fastq.gz	Fastqsanger.gz
	SRR6903293.fastq.gz	Fastqsanger.gz
	SRR6903294.fastq.gz	Fastqsanger.gz

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Project description:We compared transcript levels at several points along the asexual blood cycle between 21 P. falciparum lines. These 21 parasite lines are organized in 4 sets of parasite lines, with all parasite lines within a set sharing a clonal origin. We compared transcript levels within each set. We also performed comparative genome hybridization (CGH) for all 21 parasite lines.

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Project description:Purpose: this study is to analyze the change of overal transcriptome after disruption of DNA methyltransferase (DNMT) in Plasmodium falciparum. Methods: In this study, the transcriptomes of a PfDNMT gene knockout (KO) parasite line with its wildtype control, its complementation (adding back the DNMT expression by episomal expression of DNMT in the DNMT KO parasite), and overexpression (episomal expression of DNMT in the wildtype parasite) were analyzed by RNAseq. Total RNA were harvested from the asexual parasites at three developmental stages (ring, trophozoite, and schizont) using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2. Results: Using an optimized data analysis workflow, we mapped about 5 million sequence reads per sample to the malaria parasite genome (pf3D7_V3.0.) and identified 5712 transcripts with high mapping rate at the range between 80% and 95. PfDNMT KO profoundly disturbed the global transcription pattern,especially at trophozoite stage, causing 1732 (30.3%) genes to be differentially expressed at trophozoite.Complementation restored the expression pattern and overexpression of PfDNMT caused nearly 2000 gene ro be differentially expressed at schizont stage. Conclusions: Collectively, transcriptomic analysis of DNMT KO, complemetation and overexpression shows PfDNMT plays important role in gene regulation.

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