Resequencing and De Novo Assembly of Leishmania (Viannia) guyanensis from Amazon Region: Genome Assessment, Phylogenetic Insights and Therapeutic Targets

TL;DR

This paper presents a genomic analysis of Leishmania guyanensis, identifying genetic variations and potential drug targets to improve treatment outcomes.

Contribution

The study provides a new genome assembly and identifies novel candidate genes for therapeutic development in L. guyanensis.

Findings

The assembled genome of L. guyanensis is 31 Mb with an N50 of 4743 bp and 40.85× coverage.

Ten candidate genes, including calpain and GSK3 family members, were identified as potential therapeutic targets.

Phylogenetic analysis using polA1 gene showed L. guyanensis clusters closely, with L. martiniquensis being the most divergent.

Abstract

Leishmania guyanensis is one of 15 American human-pathogenic species, frequently linked to therapeutic failure due to its marked genetic plasticity and adaptability under drug pressure. To broaden the genomic understanding of this species, its biological traits, and potential therapeutic alternatives, we sequenced the L. guyanensis strain MHOM/BR/75/M4147. Raw reads underwent quality-filtering and assembly. Taxonomic classification utilized BLASTn and Kraken2, confirming that 99.95% of contigs matched Leishmania. The assembled genome size was 31 Mb, with an N50 of 4743 bp and 40.85× coverage. Variant calling subsequently identified 36,665 SNPs, 8210 indels, and chromosomal aneuploidies. Genomic annotation identified 3119 proteins with known molecular functions in L. guyanensis, alongside 6371 orthologous genes shared with L. major and L. panamensis. The search for pharmacological relevance yielded ten candidate genes, including one calpain and nine GSK3 family members. Phylogenetic reconstruction using the polA1 gene consistently grouped L. guyanensis, demonstrating strong discriminatory capacity, with L. martiniquensis emerging as the most divergent species. Overall, these findings expand the available genomic framework for L. guyanensis and support advances in species-specific diagnostic approaches.

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