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. 2020 Mar 25;9:e51243. doi: 10.7554/eLife.51243

Figure 9. Copy number variation of putative drug resistance genes.

(A) Copy numbers (CNs) for all four genes on the H-locus are shown for all 151 samples across all 10 different (sub-)groups. (B) Genome coverage in the genomic regions surrounding the MSL in all six samples showing a deletion and one sample with no CN reduction. Genome coverage for 50 bp windows is normalised by the haploid chromosome coverage and colours indicate the somy equivalent coverage of the respective window. The genes, LinJ.31.2370, LinJ.31.2380, LinJ.31.2390 and LinJ.31.2400, are marked as black horizontal lines. Colours of the sample names indicate group colours used throughout this study.

Figure 9.

Figure 9—figure supplement 1. Copy number increase at the H-locus.

Figure 9—figure supplement 1.

Shown are coverage plots across isolates for the H-locus on chromosome 23 highlighting the four genes (YIP1, MRPA, argininosuccinate synthase, PTR1) present at this locus by black, horizontal bars. Isolate names are coloured by the group colours used throughout this study. (A) Copy number variation is shown for all 37% of isolates that have a copy number increase of at least three genes at the H-locus. Coverages of each isolate are coloured by the somy of chromosome 23 in the respective isolate. For comparison for each group, the coverage of one isolate with no copy number increase is also plotted (dark grey headers). (B) Copy number variation of all isolates that show a copy number increase in only two of the associated genes. Window-specific coverages are coloured by its somy equivalent. Somies of chromosome 23 for each isolate are indicated in the respective row.
Figure 9—figure supplement 2. Copy number variation of putative drug resistance genes.

Figure 9—figure supplement 2.

Gene copy number for all four genes and all 151 samples is shown across 10 different groups for three different loci putatively involved in drug resistance. (A) MAPK1 (LinJ.36.6760) and (B) AQP1 (LinJ.31.0030) genes are putatively involved antimony drug resistance. (C) The Miltefosine transporter (LinJ.13.1590), the adjacent gene (LinJ.13.1600) and the Ros3 (LinJ.32.1040) gene are putatively involved in Miltefosine resistance.
Figure 9—figure supplement 3. Measures of adaptive evolution.

Figure 9—figure supplement 3.

Species species-specific evolution is measured for (A) L. donovani and (B) L. infantum. Each point represents the neutrality index (NI) and the associated p-value of the McDonald-Kreitman test for each of 8234 genes. The horizontal line represents the. -log10 value equivalent to a p-value of 0.05. None of the shown values passes multiple testing correction.
Figure 9—figure supplement 4. Gene ontology enrichment of marker genes with putative biological impact.

Figure 9—figure supplement 4.

For each group our species-specific GO enrichment, biological process results are shown for genes with at least one moderate or high effect variant according to SNPeff annotation (Supplementary file 3). Plots show enrichment for the lenient cut-off of a p-value<0.05 using the weighted Fisher test statistic (weightFish, topGO, Alexa et al., 2006) using Revigo (Supek et al., 2011). Sizes of rectangles are normalised by absolute log10 p-value. Plot titles indicate the group marker sets or the species comparison, respectively. Stars in the group names indicate that samples that have previously been identified as mixtures of clones have been removed (Table 1 B3 and B4). Additionally, hybrids between the major groups (Table 1 B2) were removed from this analysis. Group sample sizes are indicated at the end of each name.