title: A novel protein coding potential of long intergenic non-coding RNAs (lincRNAs) in the kinetoplastid protozoan parasite Leishmania major.
abstract: Cutaneous leishmaniasis (CL) is caused by a kinetoplastid protozoan parasite Leishmania major, as a skin ulcer at the site of the sandfly bite. CL is curable and in most cases ulcers heal spontaneously within three to six months leaving a scar and disfiguration. Complete genome of L. major was reported in 2005 at the very initial phase of kinetoplastid parasite genome sequencing project. Presently, L. major genome is most studied and comprehensively annotated genome and therefore, it is being used as a reference genome for annotating recently sequenced Leishmanial genomes. A recent study reporting global transcriptome of L. major promastigotes, identified 1884 uniquely expressed non-coding RNAs (ncRNA) in L. major. In the current study, an in-depth analysis of the 1884 novel ncRNAs was carried out using a proteogenomic approach to identify their protein coding potential. Our analysis resulted in identification of eight novel protein coding genes based on mass spectrometry data. We have analyzed each of these eight novel CDS and in the process have improved the genome annotation of L. major on the basis of mass spectrometry derived peptide data. Although sequenced a decade ago, the improvement in the L. major genome annotation thus is an ongoing process.
authors.affiliation: Department of Zoology, Savitribai Phule Pune University, Pune 411007, India. Electronic address: harshpawar06@gmail.com.
authors.forename: Harsh
authors.initials: H
authors.lastname: Pawar
authors.affiliation: Department of Zoology, Savitribai Phule Pune University, Pune 411007, India.
authors.forename: Kalpana
authors.initials: K
authors.lastname: Pai
authors.affiliation: National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune 411007, Maharashtra, India. Electronic address: patole@nccs.res.in.
authors.forename: Milind S
authors.initials: MS
authors.lastname: Patole
mesh_terms: D000818:Animals; D001483:Base Sequence; D018503:Genome, Protozoan; D018320:Leishmania major / Q000235:genetics*; D016773:Leishmaniasis, Cutaneous / Q000469:parasitology; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D015800:Protozoan Proteins / Q000235:genetics*; D062085:RNA, Long Noncoding
chemical_list: D015800:Protozoan Proteins; D062085:RNA, Long Noncoding
keywords: Gene annotations and protein coding genes; Leishmania major; Non-coding RNA; Proteogenomics