title: UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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 the YM genome revealed introns in 5' and 3' untranslated regions (UTRs), altered intron/exon boundaries, alternative splicing, overlapping sense-antisense reads, and potentially new transcripts. Interestingly, comparison of the NSM RNA-seq reads obtained here with those of YM discovered differentially spliced introns; e.g., spliced introns in one subspecies but not the other. Alignment of the NSM cDNA sequences to the YM genome sequence also identified ~84,000 SNPs between the two parasites.
  
  
  CONCLUSIONS
  The discoveries of UTR introns and differentially spliced introns between P. yoelii subspecies raise interesting questions on the potential role of these introns in regulating gene expression and evolution of malaria parasites.
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. jianli_204@xmu.edu.cn.
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. bcai@houstonmethodist.org.
authors.forename: Baowei
authors.initials: B
authors.lastname: Cai
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. qiyanwei1987@163.com.|Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, 20892, USA. qiyanwei1987@163.com.
authors.forename: Yanwei
authors.initials: Y
authors.lastname: Qi
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. ai_wt0205@126.com.
authors.forename: Wenting
authors.initials: W
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. liujianwenyihui@163.com.
authors.forename: Jianwen
authors.initials: J
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. xujiaxuezi@163.com.
authors.forename: Ruixue
authors.initials: R
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. 18059238161@163.com.
authors.forename: Qin
authors.initials: Q
authors.lastname: Pang
authors.affiliation: Department of Parasitology, Bengbu Medical College, 2600 Donghai Dadao Road, Bengbu, 233030, People's Republic of China. bengbucity@163.com.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Tao
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. honglx@xmu.edu.cn.
authors.forename: Lingxian
authors.initials: L
authors.lastname: Hong
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. liuxie@xmu.edu.cn.
authors.forename: Shengfa
authors.initials: S
authors.lastname: Liu
authors.affiliation: Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. maarten.leerkes@nih.gov.
authors.forename: Maarten
authors.initials: M
authors.lastname: Leerkes
authors.affiliation: Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. quinonesm@niaid.nih.gov.
authors.forename: Mariam
authors.initials: M
authors.lastname: Quiñones
authors.affiliation: State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. xsu@niaid.nih.gov.|Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, 20892, USA. xsu@niaid.nih.gov.
authors.forename: Xin-zhuan
authors.initials: XZ
authors.lastname: Su
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D018503:Genome, Protozoan / Q000235:genetics; D007438:Introns / Q000235:genetics*; D008288:Malaria / Q000469:parasitology; D010967:Plasmodium yoelii / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D016372:RNA, Antisense / Q000235:genetics*
chemical_list: D016372:RNA, Antisense