The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq.
Background: Although the genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome is incomplete, both regarding the real number of genes and their primary structure.  Results: Here, we described the first comprehensive transcriptome analysis of a parasite of the genus Leishmania. Using high-throughput RNA sequencing (RNA-seq), a total of 10287 transcripts were defined, of which 1929 correspond to previously non-annotated genes. In addition, our data indicate that current annotation for many genes should be corrected. Analysis of the transcript processing sites revealed extensive heterogeneity in trans-splicing and polyadenylation events; for about 50% of the genes, several transcripts were detected differing in the length of UTRs, sometimes in the order of hundreds of nucleotides. Thus, this transcript heterogeneity would provide an additional source for regulation as the different sizes of UTRs could modify RNA stability and/or influence the efficiency of RNA translation. Finally, the relative expression levels for the transcripts present in the promastigote stage were determined. Conclusions: This study provides a complete view of the global transcriptome of the L. major promastigote stage, providing the basis for future comparative analysis with other development stages or other Leishmania species.