Abstract
BackgroundAlthough the genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome was incomplete, both regarding the real number of genes and their primary structure.ResultsHere, we describe the first comprehensive transcriptome analysis of a parasite from the genus Leishmania. Using high-throughput RNA sequencing (RNA-seq), a total of 10285 transcripts were identified, of which 1884 were considered novel, as they did not match previously annotated genes. In addition, our data indicate that current annotations should be modified for many of the genes. The detailed analysis of the transcript processing sites revealed extensive heterogeneity in the spliced leader (SL) and polyadenylation addition sites. As a result, around 50% of the genes presented multiple transcripts differing in the length of the UTRs, sometimes in the order of hundreds of nucleotides. This transcript heterogeneity could provide an additional source for regulation as the different sizes of UTRs could modify RNA stability and/or influence the efficiency of RNA translation. In addition, for the first time for the Leishmania major promastigote stage, we are providing relative expression transcript levels.ConclusionsThis study provides a concise 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.
Highlights
The genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome was incomplete, both regarding the real number of genes and their primary structure
RNA sequencing (RNA-seq) data and delineation of transcripts RNA isolated from an axenic culture of L. major promastigotes (Friedlin strain, clone V1) was sequenced, after poly(A) + selection, on an Illumina GAII platform generating a total of 14 656 121 sequence reads (75-nt long)
It was possible to define a total of 6937 transcripts; a number lower than the 8272 protein-coding genes previously predicted to exist in the L. major genome [13]
Summary
The genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome was incomplete, both regarding the real number of genes and their primary structure. Species of the genus Leishmania are protozoan parasites and aetiological agents of a spectrum of clinical diseases, known as leishmaniases, ranging from disfiguring skin lesions to life-threatening visceral infection. In 1999, the complete sequence of chromosome 1 of Leishmania major was published and showed a remarkable feature of the gene organization in Leishmania, i.e. genes are grouped in large clusters sharing the same transcriptional direction. When transcriptional activity was examined by nuclear run-on analyses using single-stranded DNA probes, the protein-coding strand was found to be more strongly transcribed than the non-coding strand in the majority of the chromosome 1
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