Estimating mRNA lengths from Plasmodium falciparum genes by virtual northern RNA-seq analysis. Plasmodium falciparum K1

Accurate gene models are essential for understanding parasite biology. However, transcript structure information is lacking for most parasite genes. Here, we describe “virtual northern” analysis of the malaria parasite Plasmodium falciparum to address this issue. RNA-seq libraries were made from size-fractionated RNA. Transcript sizes for 3052 genes were inferred from the abundance signals in each library. The data show that for almost half of the transcripts, the combined untranslated regions are more than twice the length of the open reading frame. Furthermore, we identified novel polycistronic, or gene overlapping transcripts that suggest revisions to current gene models are needed. Overall design: mRNA profiles of from 8 size-fractions of RNA were compared with unfractionated mRNA; sequence data were obtained from TruSeq stranded RNA-seq libraries sequenced on an Illumina MiSeq instrument