Table 2.
Genes potentially associated with PMM resistance. Correlation between gene copy number and PMM resistance. Only genes for which the correlation, r, was ≥0.7 or ≤−0.7 and the correlation p-values were lower than 0.05 are reported. GeneID: TriTrypDB L donovani gene ID; Chr: chromosome number; Pos 1: gene initial coordinate; Pos 2: gene final coordinate; Correlation: Gene CN and PMM resistance correlation; p: Correlation p-value; Max: Maximum gene CN in all clone/population; Min: Minimum gene CN in all clone/population; Max–Min: the difference between the Max and Min gene CNV values.
| Gene ID | Chr | Pos1 | Pos2 | Gene Annotation | Correlation | p | Max | Min | Max − Min |
|---|---|---|---|---|---|---|---|---|---|
| LdBPK_020370.1 | chr02 | 171561 | 171713 | hypothetical protein unknown function | 0.73 | 4.96 × 10−3 | 2.09 | 0.88 | 1.21 |
| LdBPK_070160.1 | chr07 | 67067 | 67567 | hypothetical protein conserved | 0.73 | 4.54 × 10−3 | 1.21 | 0.73 | 0.48 |
| LdBPK_070980.1 | chr07 | 404916 | 406232 | hypothetical protein conserved | 0.74 | 3.96 × 10−3 | 1.13 | 0.85 | 0.28 |
| LdBPK_141050.1 | chr14 | 424294 | 425424 | ADP/ATP mitochondrial carrier-like protein | 0.76 | 2.45 × 10−3 | 1.52 | 1.18 | 0.34 |
| LdBPK_180600.1 | chr18 | 242208 | 242483 | hypothetical protein | 0.76 | 2.47 × 10−3 | 1.15 | 0.77 | 0.38 |
| LdBPK_230470.1 | chr23 | 162446 | 163672 | aldose 1-epimerase-like protein | 0.71 | 6.97 × 10−3 | 1.54 | 1.31 | 0.23 |
| LdBPK_250660.1 | chr25 | 217458 | 219455 | predicted zinc finger protein | 0.76 | 2.84 × 10−3 | 1.17 | 0.96 | 0.21 |
| LdBPK_250800.1 | chr25 | 276286 | 277551 | hypothetical protein unknown function | 0.77 | 2.10 × 10−3 | 1.09 | 0.89 | 0.2 |
| LdBPK_270620.1 | chr27 | 239023 | 239625 | ras-related protein RAB1A putative | 0.76 | 2.58 × 10−3 | 1.3 | 0.78 | 0.52 |
| LdBPK_271080.1 | chr27 | 441116 | 442363 | RING-H2 zinc finger putative | 0.76 | 2.47 × 10−3 | 1.13 | 0.88 | 0.25 |
| LdBPK_271370.1 | chr27 | 539921 | 540925 | proteasome regulatory non-ATP-ase subunit 3 putative | 0.70 | 7.57 × 10−3 | 1.26 | 0.84 | 0.42 |
| LdBPK_271520.1 | chr27 | 591692 | 592333 | Eukaryotic translation initiation factor 4E−1 | 0.71 | 6.85 × 10−3 | 1.15 | 0.89 | 0.26 |
| LdBPK_271540.1 | chr27 | 607146 | 609893 | BRO1-like domain/ALIX V-shaped domain binding to HIV putative | 0.75 | 3.40 × 10−3 | 1.19 | 0.96 | 0.23 |
| LdBPK_280530.1 | chr28 | 180433 | 182571 | TPR repeat putative | 0.72 | 5.12 × 10−3 | 1.06 | 0.87 | 0.19 |
| LdBPK_280600.1 | chr28 | 209904 | 211604 | major surface protease gp63 putative | 0.72 | 5.67 × 10−3 | 1.02 | 0.86 | 0.16 |
| LdBPK_280630.1 | chr28 | 222510 | 224015 | hypothetical protein unknown function | 0.75 | 3.31 × 10−3 | 1.06 | 0.9 | 0.16 |
| LdBPK_301200.1 | chr30 | 387893 | 388444 | hypothetical protein conserved | 0.76 | 2.82 × 10−3 | 1.04 | 0.82 | 0.22 |
| LdBPK_302290.1 | chr30 | 855859 | 857973 | tubulin-tyrosine ligase-like protein | 0.81 | 8.65 × 10−4 | 1.08 | 0.88 | 0.2 |
| LdBPK_302310.1 | chr30 | 864017 | 867931 | hypothetical protein conserved | 0.74 | 3.75 × 10−3 | 1.02 | 0.9 | 0.12 |
| LdBPK_302740.1 | chr30 | 1031040 | 1032266 | TPR domain protein conserved | 0.73 | 4.95 × 10−3 | 1 | 0.84 | 0.16 |
| LdBPK_321520.1 | chr32 | 572415 | 582050 | phosphatidylinositol 3-related kinase putative | 0.88 | 7.93 × 10−5 | 1.02 | 0.93 | 0.09 |
| LdBPK_330670.1 | chr33 | 209670 | 210923 | intraflagellar transport protein 57/55 putative | 0.71 | 6.32 × 10−3 | 1.44 | 1.2 | 0.24 |
| LdBPK_330890.1 | chr33 | 292053 | 294803 | hypothetical protein unknown function | 0.76 | 2.47 × 10−3 | 1.45 | 1.25 | 0.2 |
| LdBPK_151060.1 | chr33 | 429431 | 429940 | 60S ribosomal protein L6 putative | 0.71 | 6.78 × 10−3 | 1.36 | 0.98 | 0.38 |
| LdBPK_331560.1 | chr33 | 594808 | 595194 | RNA-binding protein putative | 0.78 | 1.70 × 10−3 | 1.58 | 1.21 | 0.37 |
| LdBPK_332810.1 | chr33 | 1086018 | 1089704 | hypothetical protein conserved | 0.71 | 7.02 × 10−3 | 1.43 | 1.25 | 0.18 |
| LdBPK_332950.1 | chr33 | 1165769 | 1167190 | transcription elongation factor-like protein | 0.71 | 6.23 × 10−3 | 1.49 | 1.24 | 0.25 |
| LdBPK_341840.1 | chr34 | 802817 | 803974 | protein kinase putative | 0.72 | 5.11 × 10−3 | 1.04 | 0.8 | 0.24 |
| LdBPK_343220.1 | chr34 | 1362570 | 1364477 | DNA topoisomerase IB large subunit | 0.78 | 1.48 × 10−3 | 1.02 | 0.84 | 0.18 |
| LdBPK_343390.1 | chr34 | 1417106 | 1417627 | Complex 1 protein (LYR family) putative | 0.74 | 4.04 × 10−3 | 1.09 | 0.81 | 0.28 |
| LdBPK_361330.1 | chr36 | 475562 | 475984 | hypothetical protein (fragment) | 0.86 | 1.79 × 10−4 | 0.52 | 0.27 | 0.25 |
| LdBPK_361780.1 | chr36 | 673858 | 675498 | hypothetical protein conserved | 0.88 | 8.22 × 10−5 | 1.12 | 0.89 | 0.23 |
| LdBPK_362310.1 | chr36 | 878592 | 880163 | protein-tyrosine phosphatase 1-like protein | 0.73 | 4.69 × 10−3 | 1.02 | 0.9 | 0.12 |
| LdBPK_241390.1 | chr24 | 496214 | 498880 | hypothetical protein conserved | −0.80 | 1.13 × 10−3 | 1.27 | 0.94 | 0.33 |
| LdBPK_261490.1 | chr26 | 541997 | 546778 | hypothetical protein unknown function | −0.72 | 5.61 × 10−3 | 1.65 | 1.37 | 0.28 |
| LdBPK_261660.1 | chr26 | 599794 | 600579 | hypothetical protein conserved | −0.79 | 1.19 × 10−3 | 1.61 | 1.25 | 0.36 |
| LdBPK_291180.1 | chr29 | 429699 | 429965 | ribosomal protein L1aputative (fragment) | −0.81 | 7.78 × 10−4 | 1.25 | 0.89 | 0.36 |
| LdBPK_300440.1 | chr30 | 142693 | 144375 | quiescin sulfhydryl oxidase putative | −0.72 | 5.96 × 10−3 | 1 | 0.81 | 0.19 |
| LdBPK_363720.1 | chr36 | 1394227 | 1395405 | phytoene synthase putative | −0.79 | 1.33 × 10−3 | 1.06 | 0.79 | 0.27 |