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Volume 29, Number 5—May 2023
Research Letter

Genome Analysis of Triploid Hybrid Leishmania Parasite from the Neotropics

Frederik Van den BroeckComments to Author , Senne Heeren, Ilse Maes, Mandy Sanders, James A. Cotton1, Elisa Cupolillo, Eugenia Alvarez, Lineth Garcia, Maureen Tasia, Alice Marneffe, Jean-Claude Dujardin, and Gert Van der AuweraComments to Author 
Author affiliations: Katholieke Universiteit Leuven, Leuven, Belgium (F. Van den Broeck, S. Heeren); Institute of Tropical Medicine, Antwerp, Belgium (F. Van den Broeck, S. Heeren, I. Maes, J.-C. Dujardin, G. Van der Auwera); Wellcome Sanger Institute, Hinxton, UK (M. Sanders, J.A. Cotton); Instituto Oswaldo Cruz–Fiocruz, Rio de Janeiro, Brazil (E. Cupolillo); Cayetano Heredia University, Lima, Peru (E. Alvarez); Universidad Mayor de San Simon, Cochabamba, Bolivia (L. Garcia); Centre Hospitalier Universitaire St. Pierre, Brussels, Belgium (M. Tasia, A. Marneffe)

Main Article

Figure

Midpoint rooted maximum-likelihood phylogenetic trees based on single-nucleotide polymorphisms called in chromosome 1 and the first 140kb of the telomeric region of chromosome 20 of a hybrid Leishmania parasite from Costa Rica. For each strain, sequences were composed based on concatenated single-nucleotide polymorphisms that were each coded by 2 base pairs, after which invariant sites were removed, resulting in 2,382 bp sequences for chromosome 1 and 3,015 bp sequences for chromosome 20. Consensus phylogenetic trees were generated from 1,000 bootstrap trees using IQ-TREE (http://www.iqtree.org) with 37 taxa (excluding L. naiffi and L. lainsoni strains) under the  transversion with empirical base frequencies, ascertainment bias correction, and discrete gamma with 4 rate categories substitution model, which was the best-fit model revealed by ModelFinder as implemented in IQTREE. Branch support values are presented near each node following 1,000 bootstrap replicates; bootstrap values within the clade containing L. panamensis strains were omitted for clarity reasons. Scale bar indicates number of substitutions per site. Appendix 2) includes a description of the L. braziliensis 1–4 lineages.

Figure. Midpoint rooted maximum-likelihood phylogenetic trees based on single-nucleotide polymorphisms called in chromosome 1 and the first 140kb of the telomeric region of chromosome 20 of a hybrid Leishmania parasite from Costa Rica. For each strain, sequences were composed based on concatenated single-nucleotide polymorphisms that were each coded by 2 base pairs, after which invariant sites were removed, resulting in 2,382 bp sequences for chromosome 1 and 3,015 bp sequences for chromosome 20. Consensus phylogenetic trees were generated from 1,000 bootstrap trees using IQ-TREE (http://www.iqtree.org) with 37 taxa (excluding L. naiffi and L. lainsoni strains) under the  transversion with empirical base frequencies, ascertainment bias correction, and discrete gamma with 4 rate categories substitution model, which was the best-fit model revealed by ModelFinder as implemented in IQTREE. Branch support values are presented near each node following 1,000 bootstrap replicates; bootstrap values within the clade containing L. panamensis strains were omitted for clarity reasons. Scale bar indicates number of substitutions per site. Appendix 2) includes a description of the L. braziliensis 1–4 lineages.

Main Article

1Current affiliation: Wellcome Center for Integrative Parasitology, University of Glasgow, Glasgow, Scotland, UK.

Page created: March 22, 2023
Page updated: April 19, 2023
Page reviewed: April 19, 2023
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