The_genome_of_Leishmania_adleri_from_a_mammalian_host_highlights_chromosome_fission_in_Sauroleishmania. The_genome_of_Leishmania_adleri_from_a_mammalian_host_highlights_chromosome_fission_in_Sauroleishmania

Monitoring and control of pathogens arising from human, domestic and sylvatic sources that threaten public health can be enhanced by genome-based investigation. Phylogenetically classifying such samples and identifying optimal protocols for constructing their genomes using short sequence reads are key to this. Here, we examined the mammal-infecting unicellular parasite Leishmania adleri belonging to the lizard-infecting Sauroleishmania subgenus. L. adleri has been associated with cutaneous disease in humans, but can be asymptomatic in wild animals. We sequenced, assembled and investigated the L. adleri genome isolated from an asymptomatic Ethiopian rodent (MARV/ET/75/HO174) and verified it as L. adleri by compared with other Sauroleishmania species: L. hoogstraali, L. gymnodactyli and L. tarentolae. Chromosome-level scaffolding was achieved using a hybrid approach combining reference-guided and de novo assembly followed by extensive improvement steps to close gaps, merge contigs into scaffolds, break scaffolds at misassemblies, and maximise nucleotide-level accuracy. The final draft genome of L. adleri had contiguity comparable with other high-quality genomes. L. tarentolae and L. major annotation was transferred to the L. adleri genome and the gene models were manually verified and improved. Comparison of the L. adleri HO174 genome with those of L. tarentolae Parrot-TarII and lizard-infecting L. adleri RLAT/KE/1957/SKINK-7 showed extensive gene amplifications, pervasive aneuploidy, and two fission events of chromosomes 30 and 36 shared by HO174 and SKINK-7. There was no substantive genetic differentiation between L. adleri extracted from mammals and reptiles, highlighting key challenges for leishmaniasis surveillance and eradication. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/