Genetic diversity and comparative genomics across Leishmania (Viannia) species.

Leishmaniasis is an important public health problem worldwide, with a broad spectrum of clinical and epidemiological features partly associated with the diversity and complex life cycle of the Leishmania parasites. This study analyzes genomic data from 205 Leishmania (Viannia) samples, including 65 newly sequenced clinical isolates. It also provides chromosome-level genome assemblies for 10 isolates representing different species and populations. The observed distribution of Leishmania genomic diversity across the sampling locations suggests rapid adaptation to different ecosystems. The phylogenomic analysis provides new hypotheses challenging the current delimitation of species. Pangenomic analysis of high-quality assemblies shows consistent copy number variation between species for different gene families. Larger and more diverse amastin gene families were observed in the assembled genomes compared to previous reports based on the analysis of short-read data. This work provides genomic resources and helpful information regarding central problems in the biology of Leishmania spp, including species diversification, transmission dynamics, and the evolution of virulence mechanisms.