Resequencing and de novo Assembly of Leishmania (Viannia) guyanensis from Amazon region: Genome assessment, Aneuploidies, and Phylogenetic insights

The Leishmania genus includes 20 human pathogenic species, 15 occurring in the Americas. In Amazonia, Leishmania guyanensis is frequently associated with therapeutic failure, what is related to genetic plasticity and adaptability during drug exposure. The genomic studies of this species are important to understand different aspects of parasite biology including genetic adaptability to different environments and possible therapeutic alternatives. Taking this into account, we sequenced a L. guyanensis strain (MHOM/BR/75/M4147), performed the quality assessment of the reads (FASTP), and the genome assembly (MEGAHIT). The taxonomic classification was accomplished using BLASTn and Kraken2 software, and the annotation of Leishmania contigs using Augustus v.3.5. The assembled genome showed a size of 31 Mb, N50 = 4.743 bp, genome coverage of 40.85x, and 99,5% of its contigs were related to Leishmania . We confirmed the presence of 36,665 SNPs, 8210 Indels, and aneuploidies. After annotation, we identified 3119 proteins associated with well-known molecular functions in L. guyanensis and 6.371 ortholog genes shared by L. guyanensis , L. major , and L. panamensis . The phylogenetic analysis using the polA1 gene correctly grouped L. guyanensis showing discriminatory potential to identify all Leishmania species, highlighting L. martiniquensis as the more divergent species within the Leishmania genus. The overall results complement the extant genomic data of L. guyanensis and encourage progress in the species-specific diagnostic of Leishmania spp.