A bioinformatics approach to reanalyze the genome annotation of kinetoplastid protozoan parasite Leishmania donovani

• Mass spectrometry derived peptide data was used to correct existing gene models.
• Extended the C-terminal boundary of 241 genes in Leishmania donovani
• Identified 51 tandemly repeated paralogs with non-overlapping gene models
• Identified 15 gene models with wrong chromosomal assignment
• Identified one case of joining of two genes thus improving gene annotations

Leishmania donovani is a kinetoplastid protozoan parasite which causes the fatal disease visceral leishmaniasis in humans. Genome sequencing of L. donovani revealed information about the arrangement of genes and genome architecture. After curation of the genome sequence, many genes in L. donovani were assigned as truncated or “partial” genes by the genome sequencing group. In the present study, we have carried out an extensive analysis and attempted to improve the gene models of these partial genes. Our analysis resulted in the identification of 308 partial genes in L. donovani, which were further categorized as C-terminal extensions, joining of genes, tandemly repeated paralogs and wrong chromosomal assignments. We have analyzed each of these genes from these categories and have improved the annotation of existing gene models in L. donovani. Some of these corrections have been confirmed by mass spectrometry derived peptide data from our previous comparative proteogenomics study in L. donovani.

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