Applying a proteogenomic approach for improving genome annotation in Leishmania panamensis using high-resolution mass spectrometry data.

Abstract

Leishmania panamensis, a protozoan parasite of the Viannia subgenus, causes American tegumentary leishmaniasis (ATL) throughout Central and South America, with clinical manifestations ranging from cutaneous lesions to mucosal involvement. Despite the availability of a reference genome for L. panamensis MHOM/COL/81/L13 strain, comprising 30.69 megabases across 35 chromosomes and 8,665 predicted protein-coding genes, comprehensive proteogenomic analyses to refine these annotations have remained limited. This study utilised a proteogenomic approach to enhance the genome annotation of the L. panamensis MHOM/COL/81/L13 strain by integrating publicly available liquid chromatography-tandem mass spectrometry data with a custom six-frame translated genome database. Through systematic peptide mapping and validation, we identified 50 novel protein-coding genes previously absent from the reference annotation and corrected 50 existing genes. The newly identified genes encode proteins containing functional domains, including thioredoxin, glucosyltransferases, and myotubularin, which likely contribute to parasite metabolism, host-pathogen interactions, and intracellular survival mechanisms. These findings substantially refine the genomic resource available for L. panamensis research and provide potential targets for diagnostic and therapeutic development. Future studies will incorporate orthogonal validation methods such as RNA-seq and Ribosome profiling to distinguish between functional genes and translational noise. The refined annotation enables more accurate functional genomic studies and enhances our understanding of the molecular basis underlying L. panamensis pathogenicity and immune evasion strategies. Moreover, the peptide-supported novel and corrected protein-coding genes identified in this study represent a valuable resource for the future exploration of candidate biomarkers and may be provide the molecular targets for improved diagnosis, prognosis, and therapeutic intervention in American tegumentary leishmaniasis.