Table 1.

Genomic loci enriched in the Cos-Seq screens and isolated for functional validation

DrugCosmid/locus (no. of cosmids)Gene startGene stopGenomic positionCosmid fold resistance§Resistance geneGene productGene fold resistanceFunctional validation
MTXLinJ.06 (1)08400900344645–3840853.3 ± 0.7*LinJ.06.0890DHFR-TSND
LinJ.21 (1)17001780587933–6221381.9 ± 0.4*ND
LinJ.23 (3)0240035081869–117583>10***LinJ.23.0310PTR1Fig. 4CRecomb
LinJ.34 (4)22502340953269–9966932.2 ± 0.5*LinJ.34.2310Phosphatase 2C-like3.5 ± 0.3**Overexp
LinJ.34.2320Phosphatase 2C-like3.7 ± 0.3**Overexp
SbIIILinJ.06a (1)07600810289892–3210831.2 ± 0.4ND
LinJ.07a (1)0070013023843–579401.4 ± 0.1*ND
LinJ.07b (1)0170020068913–762341.4 ± 0.2*ND
LinJ.08a (2)06100640235475–2687451.5 ± 0.3**LinJ.08.0630P299ND
LinJ.12a (1)04700530285805–3207392.1 ± 0.4**ND
LinJ.12b (1)05800640349890–3740942.0 ± 0.2***LinJ.12.0610Ser/Thr phosphatase1.9 ± 0.1**Overexp
LinJ.18b (1)11501220467206–5042531.7 ± 0.2**ND
LinJ.19c (1)06900800301964–3457591.6 ± 0.4*ND
LinJ.23 (2)0240035081869–1175833.3 ± 0.6***LinJ.23.0290MRPAND
LinJ.34a (2)0130023044686–780232.0 ± 0.4**LinJ.34.0220ARM58ND
AMBLinJ.06b (1)09401050399192–4378621.0 ± 0.1ND
LinJ.26b (1)25602670975536–10108251.3 ± 0.1**LinJ.26.2620Hypothetical1.3 ± 0.1 **Recomb and overexp
LinJ.29b (2)22102270921880–9630071.1 ± 0.1ND
LinJ.36b (1)485049501785378–18245751.1 ± 0.2ND
MTFLinJ.06a (1)07600810289892–3210831.2 ± 0.3ND
LinJ.26b (1)25602670975536–10108251.7 ± 0.2*ND
LinJ.29b (2)22102270921880–9630072.6 ± 0.4**LinJ.29.2250C-8 sterol isomerase2.7 ± 0.3***Overexp
LinJ.29c (3)23202400985978–10206682.5 ± 0.3**ND
LinJ.30 (2)22202300816801–8505743.2 ± 0.4***LinJ.30.2270Phospholipid-translocating ATPase2.0 ± 0.2***Overexp
LinJ.33a (2)21002140773766–7998952.0 ± 0.3**ND
LinJ.35c (3)287029701157995–11909652.5 ± 0.3**ND
LinJ.36b (2)485049501785378–18245752.5 ± 0.3*ND
PTDLinJ.06b (6)09401050399192–4378622.2 ± 0.2**LinJ.06.1010Hypothetical1.8 ± 0.1***Overexp
LinJ.06c (6)09901100414996–4522362.7 ± 0.2***LinJ.06.1010Hypothetical1.8 ± 0.1***Overexp
LinJ.26b (1)25602670975536–10108251.2 ± 0.1ND
LinJ.27b (1)22102280961442–9928312.3 ± 0.2***ND
LinJ.29d (1)276028701146381–11813301.6 ± 0.1**ND
LinJ.31b (1)14401470631444–6564713.6 ± 0.3***LinJ.31.1460PRP1Fig. 5CRecomb
PMMLinJ.06b (6)09401050399192–4378622.6 ± 0.2**LinJ.06.1010Hypothetical2.1 ± 0.1***Overexp
LinJ.36b (2)485049501785378–18245751.4 ± 0.2*ND
  • ND, not determined; overexp, gene overexpression; recomb, cosmid recombineering. *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001.

  • A single representative cosmid is reported for each enriched locus. Additional cosmids were often enriched, however, and the total number of distinct cosmids recovered per loci is indicated in parentheses. SI Appendix, Table S1 provides the genomic coordinates of the additional cosmids.

  • Genes found in the cosmid are indicated, including both partial and full ORFs. Previously unidentified resistance genes that were revealed in this study are highlighted in bold type.

  • § The ratio of drug EC50 values for parasites transfected with isolated cosmids compared with cLHYG-transfected parasites. Data are the mean ± SD of three biological replicates unless otherwise indicated. Differences were statistically evaluated by unpaired two-tailed t test.

  • The ratio of drug EC50 for parasites transfected with the target gene cloned into pSP72αHYGα plasmid relative to empty vector-transfected parasites. Data are the mean ± SD of three biological replicates unless otherwise indicated. Differences were statistically evaluated using unpaired two-tailed t test.