Chromosome level genome assembly of the World Health standards Leishmania (Viannia) guyanensis M4147 and L. (V.) shawi M8408 using a hybrid sequencing approachFIRST REVIEW ROUND - REVIEWERS' COMMENTSREVIEWERS' COMMENTS.

Abstract

Background: The Leishmania (Viannia) subgenus contains important pathogens that cause a variety of different clinical forms of cutaneous leishmaniasis in the Americas. Their response to antimonial chemotherapy differs according to species. Having high-quality genomic resources of these species is a significant step towards investigating and understanding these factors.

Objectives: This study aims to characterise the main genomic features of L. (V.) guyanensis strain MHOM/BR/75/M4147 and L. (V.) shawi strain MCEB/BR/84/M8408.

Methods: Genomes were sequenced combining short- and long-read sequencing platforms and assembled, scaffolded, and polished using Flye2, Ragtag, and Pilon, respectively. Annotations were performed using mainly similarity and profile search methods, and phylogenetic analyses were performed using the maximum likelihood (ML) and Bayesian inference approaches, using IQ-TREE and MrBayes, respectively.

Findings: De novo assembly produced genome sizes of 32.27 Mb for L. guyanensis and 32.41 Mb for L. shawi, and predicted 8,505 and 8,592 protein-coding genes, respectively. Phylogenetic analysis based on these assemblies confidently places L. guyanensis and L. shawi as the closest known relatives to L. panamensis within the Viannia clade.

Main conclusions: These genomes will increase the knowledge about the subgenus L. (Viannia) in the Americas and also represent valuable information for future comparative studies with other human pathogenic Leishmania spp.