title: A comprehensive evaluation of rodent malaria parasite genomes and gene expression.
abstract: BACKGROUND
  Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function.
  
  
  RESULTS
  We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the 'Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family.
  
  
  CONCLUSIONS
  Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.forename: Ulrike
authors.initials: U
authors.lastname: Böhme
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Jackson
authors.forename: Martin
authors.initials: M
authors.lastname: Hunt
authors.forename: Blandine
authors.initials: B
authors.lastname: Franke-Fayard
authors.forename: Wieteke A M
authors.initials: WA
authors.lastname: Hoeijmakers
authors.forename: Agnieszka A
authors.initials: AA
authors.lastname: Religa
authors.forename: Lauren
authors.initials: L
authors.lastname: Robertson
authors.forename: Mandy
authors.initials: M
authors.lastname: Sanders
authors.forename: Solabomi A
authors.initials: SA
authors.lastname: Ogun
authors.forename: Deirdre
authors.initials: D
authors.lastname: Cunningham
authors.forename: Annette
authors.initials: A
authors.lastname: Erhart
authors.forename: Oliver
authors.initials: O
authors.lastname: Billker
authors.forename: Shahid M
authors.initials: SM
authors.lastname: Khan
authors.forename: Hendrik G
authors.initials: HG
authors.lastname: Stunnenberg
authors.forename: Jean
authors.initials: J
authors.lastname: Langhorne
authors.forename: Anthony A
authors.initials: AA
authors.lastname: Holder
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Waters
authors.forename: Chris I
authors.initials: CI
authors.lastname: Newbold
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.forename: Matthew
authors.initials: M
authors.lastname: Berriman
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Janse
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D015870:Gene Expression; D005786:Gene Expression Regulation; D018503:Genome, Protozoan; D005838:Genotype; D008969:Molecular Sequence Data; D005810:Multigene Family; D010961:Plasmodium / Q000145:classification* / Q000235:genetics; D010963:Plasmodium falciparum / Q000145:classification / Q000235:genetics*; D016053:RNA, Protozoan / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D016053:RNA, Protozoan