Genome and transcriptome analyses of Leishmania spp.: opening Pandora’s box

A summary of the primary conditions and stages thoroughly analyzed by genomics and transcriptomics approaches. Leishmania main life cycle stages are represented as procyclic promastigotes; the sand fly proliferative stage (PRO), metacyclic promastigotes, the sand fly infective stage (META), and amastigotes, the mammalian intracellular proliferative stage (AMA). All of the represented stages are amenable to axenic culture growth (for many species), and these conditions are presented on the mid-row (Axenic). The lower row represents the natural conditions, in which each stage occurs (‘True’). [Display omitted] •Genomes and transcriptomes: illuminating possible phenotype/genotype correlation.•Genome-wide studies of clinical isolates reveal diversity in the field and lab lines.•Genome-wide studies reveal differences on field isolates intra and interspecies.•Comparative transcriptomes of life-cycle stages intra and interspecies.•Host and parasite transcriptomes are concomitantly analyzed. In the last 30 years, significant advances in genetic manipulation tools along with complete genome and transcriptome sequencing have advanced our understanding of the biology of Leishmania parasites and their interplay with the sand fly and mammalian hosts. High-throughput sequencing in association with CRISPR/Cas9 have prepared the ground for significant advances. Given the richness of the progress made over the last decade, in this article, we focused on the most recent contributions of genome-wide and transcriptome analyses of Leishmania spp., which permit the comparison of life cycle stages, the evaluation of different strains and species in their natural niches and in the field and the simultaneously comparison of the gene expression profiles of parasites and hosts.