title: A bioinformatics approach to reanalyze the genome annotation of kinetoplastid protozoan parasite Leishmania donovani.
abstract: 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.
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Rajiv Gandhi University for Health Sciences, Bangalore 560 041, India.
authors.forename: Harsh
authors.initials: H
authors.lastname: Pawar
authors.affiliation: National Centre for Cell Sciences, Pune 411007, India.
authors.forename: Aditi
authors.initials: A
authors.lastname: Kulkarni
authors.affiliation: National Centre for Cell Sciences, Pune 411007, India.
authors.forename: Tanwi
authors.initials: T
authors.lastname: Dixit
authors.affiliation: National Centre for Cell Sciences, Pune 411007, India.
authors.forename: Deepa
authors.initials: D
authors.lastname: Chaphekar
authors.affiliation: National Centre for Cell Sciences, Pune 411007, India. Electronic address: patole@nccs.res.in.
authors.forename: Milind S
authors.initials: MS
authors.lastname: Patole
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D018105:DNA, Kinetoplast / Q000737:chemistry* / Q000235:genetics; D018503:Genome, Protozoan; D007893:Leishmania donovani / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D018105:DNA, Kinetoplast; D015800:Protozoan Proteins
keywords: Gene annotation; Genome components; Genomics; Proteomics; Visceral leishmaniasis