title: Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum.
abstract: BACKGROUND
  It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene models for those expressed in sexual or mosquito stages have not been validated. Antisense transcripts have widely been reported in P. falciparum; however, the extent and pattern of antisense transcripts in different developmental stages remain largely unknown.
  
  
  RESULTS
  We have sequenced seven bidirectional libraries from ring, early and late trophozoite, schizont, gametocyte II, gametocyte V, and ookinete, and four strand-specific libraries from late trophozoite, schizont, gametocyte II, and gametocyte V of the 3D7 parasites. Alignment of the cDNA sequences to the 3D7 reference genome revealed stage-specific antisense transcripts and novel intron-exon splicing junctions. Sequencing of strand-specific cDNA libraries suggested that more genes are expressed in one direction in gametocyte than in schizont. Alternatively spliced genes, antisense transcripts, and stage-specific expressed genes were also characterized.
  
  
  CONCLUSIONS
  It is necessary to continue to sequence cDNA from different developmental stages, particularly those of non-erythrocytic stages. The presence of antisense transcripts in some gametocyte and ookinete genes suggests that these antisense RNA may play an important role in gene expression regulation and parasite development. Future gene expression studies should make use of directional cDNA libraries. Antisense transcripts may partly explain the observed discrepancy between levels of mRNA and protein expression.
authors: Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA.
authors: María J
authors: MJ
authors: López-Barragán
authors: Jacob
authors: J
authors: Lemieux
authors: Mariam
authors: M
authors: Quiñones
authors: Kim C
authors: KC
authors: Williamson
authors: Alvaro
authors: A
authors: Molina-Cruz
authors: Kairong
authors: K
authors: Cui
authors: Carolina
authors: C
authors: Barillas-Mury
authors: Keji
authors: K
authors: Zhao
authors: Xin-zhuan
authors: XZ
authors: Su
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D018076:DNA, Complementary; D005091:Exons; D015870:Gene Expression; D007438:Introns; D010963:Plasmodium falciparum / Q000235:genetics* / Q000502:physiology; D016372:RNA, Antisense / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D016372:RNA, Antisense; D012333:RNA, Messenger