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. 2024 Nov 28;7:1587. doi: 10.1038/s42003-024-07278-z

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Coverages across the accessible genomes of all 257 isolates. Isolates contained a median of 17.8 k accessible genomic regions, altogether spanning a median of 29.96 Mb (i.e. 91.5% of the haploid genome). Three isolates (55_AVSA1, ELIZETE, and NMT_LTCP_14417_PA1) were removed because of aberrantly low coverage of accessible regions (10.2-10.8 Mb) compared to the other isolates; in silico multi-locus sequencing analysis (MLSA) revealed that these isolates were Leishmania amazonensis (55_AVSA1, ELIZETE) and Leishmania infantum (NMT_LTCP_14417_PA1) (results not shown). Three other isolates identified as L. braziliensis (4450A1, GC08A1, and ORO13A1) were also removed because of low median coverages (9×–14×) and fragmented callable genomes. b Number of homozygous and heterozygous SNPs in the remaining 244 L. (Viannia) isolates. c Phylogenetic network of the 244 L. (Viannia) isolates based on 834,178 bi-allelic SNPs. Note: the bold legend labels in panels (a, b) represent the same isolates, all of the L. braziliensis clade.