Identification of new protein-coding potential in Leishmania donovani using a proteogenomics approach

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

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.

Application of Proteogenomic Approaches for Refinement of the Entamoeba histolytica Reference Genome Using High Resolution Mass-Spectrometry Data

Defining the ESKAPE pathogen prophage repertoire with PHORAGER

PHORAGER (Prophage Hunting, vOtu Retrieval, Annotation and Genomic ExploRation), a scalable Nextflow pipeline for the standardised identification and quality assessment of prophages from bacterial genomes, validated using 30,824 publicly available ESKAPE pathogen genomes.

Comparative De Novo Transcriptomic Analysis of Leishmania tropica Provides Insights into Translation, Metabolism, and Virulence-Related Pathways Potentially Associated with Leishmania RNA Virus 2 Status.

Leishmania tropica is an intracellular parasite belonging to the phylum Euglenozoa; it exhibits significant clinical heterogeneity and is spread by sandfly vectors through anthroponotic or zoonotic transmission. Leishmania RNA virus, a viral endosymbiont belonging to the Totiviridae family, has been reported in Old and New World isolates. In this study, we conducted a comparative de novo RNA-Seq analysis of LRV2 negative (LRV2-) and LRV2 positive (LRV2+) L. tropica isolates. Raw sequencing reads were quality-filtered, assembled, and clustered to generate unigenes, which were functionally annotated against seven comprehensive functional and taxonomic databases. In addition, differential expression and functional enrichment analyses were performed. A validation study was conducted using qRT-PCR with a 32-gene target panel across 26 strains for which LRV2 status had previously been determined. In total, approximately 10.53 Gb of sequence data were generated using the BGISEQ-500 platform. Our comparative analysis points toward a significant transcriptomic modulation that may be associated with LRV2 status, encompassing 6,774 differentially expressed genes. Functional enrichment analyses suggested alterations in the expression of genes associated with central dogma processes, the endomembrane system, cell cycle regulation, and fundamental metabolic responses. Multiple Leishmania strain sets used in qRT-PCR validation confirmed the expression patterns of key signature components potentially associated with LRV2 in the parasite system. The identified profile encompasses stress adaptation and virulence factors, as well as distinct gene modules. Overall, these findings provide a comprehensive transcriptomic resource that may guide further functional investigations into the mechanisms governing virus-parasite interactions in Old World leishmaniasis.

[Construction and analysis of a deep-coverage proteomic map of Mycobacterium avium based on high-resolution mass spectrometry].

The modular origin and evolutionary expansion of the enigmatic DGF-1 protein family in trypanosomatids

These findings reconstruct the evolutionary emergence of the DGF-1 architecture from pre-existing structural modules and provide a framework for one of the largest and most enigmatic gene families in trypanosomatids.