title: Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis.
abstract: BACKGROUND
  The sequencing of the Plasmodium yoelii genome, a model rodent malaria parasite, has greatly facilitated research for the development of new drug and vaccine candidates against malaria. Unfortunately, only preliminary gene models were annotated on the partially sequenced genome, mostly by in silico gene prediction, and there has been no major improvement of the annotation since 2002.
  
  
  RESULTS
  Here we report on a systematic assessment of the accuracy of the genome annotation based on a detailed analysis of a comprehensive set of cDNA sequences and proteomics data. We found that the coverage of the current annotation tends to be biased toward genes expressed in the blood stages of the parasite life cycle. Based on our proteomic analysis, we estimate that about 15% of the liver stage proteome data we have generated is absent from the current annotation. Through comparative analysis we identified and manually curated a further 510 P. yoelii genes which have clear orthologs in the P. falciparum genome, but were not present or incorrectly annotated in the current annotation. This study suggests that improvements of the current P. yoelii genome annotation should focus on genes expressed in stages other than blood stages. Comparative analysis will be critically helpful for this re-annotation. The addition of newly annotated genes will facilitate the use of P. yoelii as a model system for studying human malaria.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Seattle Biomedical Research Institute, Seattle, WA 98109, USA.
authors.forename: Ashley
authors.initials: A
authors.lastname: Vaughan
authors.forename: Sum-Ying
authors.initials: SY
authors.lastname: Chiu
authors.forename: Gowthaman
authors.initials: G
authors.lastname: Ramasamy
authors.forename: Ling
authors.initials: L
authors.lastname: Li
authors.forename: Malcolm J
authors.initials: MJ
authors.lastname: Gardner
authors.forename: Alice S
authors.initials: AS
authors.lastname: Tarun
authors.forename: Stefan H I
authors.initials: SH
authors.lastname: Kappe
authors.forename: Xinxia
authors.initials: X
authors.lastname: Peng
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D018503:Genome, Protozoan / Q000235:genetics*; D010967:Plasmodium yoelii / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*