UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies

Malaria Journal
Jian LiXin-zhuan Su

Abstract

The rodent malaria parasite Plasmodium yoelii is an important animal model for studying host-parasite interaction and molecular basis of malaria pathogenesis. Although a draft genome of P. yoelii yoelii YM is available, and RNA sequencing (RNA-seq) data for several rodent malaria species (RMP) were reported recently, variations in coding regions and structure of mRNA transcript are likely present between different parasite strains or subspecies. Sequencing of cDNA libraries from additional parasite strains/subspecies will help improve the gene models and genome annotation. Here two directional cDNA libraries from mixed blood stages of a subspecies of P. yoelii (P. y. nigeriensis NSM) with or without mefloquine (MQ) treatment were sequenced, and the sequence reads were compared to the genome and cDNA sequences of P. y. yoelii YM in public databases to investigate single nucleotide polymorphisms (SNPs) in coding regions, variations in intron-exon structure and differential splicing between P. yoelii subspecies, and variations in gene expression under MQ pressure. Approximately 56 million of 100 bp paired-end reads were obtained, providing an average of ~225-fold coverage for the coding regions. Comparison of the sequence reads to...Continue Reading

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Methods Mentioned

BETA
RNA-seq
RNA-seqs
RNA
RNA Assay
Assay
PCR

Software Mentioned

cBot Cluster Generation System
Asprofile
Bowtie
custom
DESeq
Samtools
Tophat2
- tools
Picard
GATK2

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