title: The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania.
abstract: Control of pathogens arising from humans, livestock and wild animals can be enhanced by genome-based investigation. Phylogenetically classifying and optimal construction of these genomes using short sequence reads are key to this process. 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 comparison with other Sauroleishmania species. Chromosome-level scaffolding was achieved by combining reference-guided with de novo assembly followed by extensive improvement steps to produce a final draft genome with contiguity comparable with other references. L. tarentolae and L. major genome annotation was transferred and these gene models were manually verified and improved. This first high-quality draft Leishmania adleri reference genome is also the first Sauroleishmania genome from a non-reptilian host. 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 fission of chromosomes 30 and 36. There was little genetic differentiation between L. adleri extracted from mammals and reptiles, highlighting challenges for leishmaniasis surveillance.
authors.affiliation: School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway, Ireland.
authors.forename: Simone
authors.initials: S
authors.lastname: Coughlan
authors.affiliation: School of Biotechnology, Dublin City University, Dublin, Ireland.
authors.forename: Peter
authors.initials: P
authors.lastname: Mulhair
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Mandy
authors.initials: M
authors.lastname: Sanders
authors.affiliation: Charite University Medicine, Berlin, Germany.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Schonian
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: James A
authors.initials: JA
authors.lastname: Cotton
authors.affiliation: School of Mathematics, Applied Mathematics and Statistics, National University of Ireland, Galway, Ireland.|School of Biotechnology, Dublin City University, Dublin, Ireland.
authors.forename: Tim
authors.initials: T
authors.lastname: Downing
mesh_terms: D000818:Animals; D002875:Chromosomes; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D005838:Genotype; D054884:Host-Pathogen Interactions; D006801:Humans; D007891:Leishmania / Q000145:classification / Q000235:genetics*; D007896:Leishmaniasis / Q000662:veterinary*; D008116:Lizards / Q000235:genetics* / Q000382:microbiology*; D008322:Mammals / Q000382:microbiology*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide