, While the reads were aligned against full assemblies, including unsorted contigs, just the canonical 36 chromosomes were considered for downstream analyses of ploidy estimation and copy number alterations. This filter was necessary because of the high content of repetitive elements and the absence of comparable and high-quality annotations in the contigs. Given that the L. tropica reference genome is still unfinished, the sample Ltr_16 was aligned against the L. major Friedlin genome. Overall, starting from a total of 1,011,803,806 short reads, 952,093,114 were successfully aligned to the respective reference genomes (see Table S3 at GitLab, To determine reproducibility of in vitro genome evolution, duplicate EP 3 samples (EP 3.1 and EP 3.2) were generated for the Linf_ZK27, Lmj_1948, Lmj_A445, Ldo_BPK26, and Ltr_16 strains (Fig. S1). Culture conditions and time in culture for the 25 samples are detailed in Table S2 at GitLab, 2017.

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