TABLE 1.
Methods and oligonucleotide sequences used for genotyping transporter loci
| Genea | Position | AA changeb | Methodc | Snapshot oligod | Template oligod |
|---|---|---|---|---|---|
| pfcrt | 72 | C-S | DS | ||
| 74 | M-I | DS | pfcrt-F:GGTGGAGGTTCTTGTCTTGG | ||
| 75 | N-E | DS | pfcrt-R:GAATTTCCCTTTTTATTTCCA | ||
| 76 | K-T | DS | |||
| 220 | A-S | SS | ctgactCATATTTAATCTTGTCTTAATTAGT | ||
| 271 | F-Q | SS | ctgacCTTTCCTAATTAATTCTTACGTT | ||
| 326 | N-D/S | SS | gactgacGGTTATTAAATTATCACAAATGY | ||
| gactgactgTGGTTATTAAATTATCACAAATG | pfcrt2F:TCTTTTGAAACACAAGAAGAAA | ||||
| 356 | I-T/L | SS | gacTGTATACAAGGTCCAGCA | pfcrt-2R:AATTTCACACTTACCAAAGTTAC | |
| actgactTGTATACAAGGTCCAGCA(AT) | |||||
| 371 | R-I | SS | gactgactgactgAATTTTATAGGGTGATGTTGTAA | ||
| pfmdr | 86 | N-Y | SS | gactgactgactgactAGGATTAATATCATCACCTAAAT | pfmdr5′-F TGGGTAAAGAGCAGAAAGAG |
| 184 | Y-F | SS | gactgactgactCATTTTTTAATGACCAAATA | pfmdr5′-R ACGGAAAAACGCAAGTAATA | |
| 1034 | S-C | SS | ATGCAGCTTTATGGGGATTC | pfmdr3′-F TTTCTGTAATTTGATAGAAAAAGC | |
| 1042 | N-D | SS | gactATCCAAACCAATAGGCAAAACTAT | pfmdr3′-R TTGCATCTTCTCTTCCAAAT | |
| gactgactGGGTTCTTGACTAACTATTGAAAATAAGT | |||||
| 1246 | D-Y | SS | TTCTAAGAT | ||
| G2 (PFA0590w) | 191 | Y-H | SS | GTTTTTTGAAGCTCTTTTG | G2-F TAGTGGTAGTGATGATAATGTTTTT |
| 437 | A-S | SS | GACTGAGTAACATAGGAGTTTTTATAAGT | G2-R GATATGGAAGGATCTAAAGATGTAA | |
| G7 (PF13-0271) | 1390 | &1 | MS | G7-F AAACAAATCCAAATATTACGAAAA | |
| G7-R CAAACTACTTTTTCCTGAACCA | |||||
| G25 (PF14-0679) | Intron | G-A | SS | CTTGTAACAGTTTTATGTGTAAGTA | C25-F ATGGGATGCCTTCATCATAG |
| C25-R TTCCAGTTAACACACCATTTG | |||||
| G30 (PF14-0292) | Intron | C-G | SS | GACTGGAAGGCATACTTAAATTACTT | G30-F AAAGGGAAGGAAGGCATAC |
| G30-R GCCATATTCACAACAATTCA | |||||
| G47 (PFE0775c) | 241 | L-V | SS | GTAATTATTCTATATATTATGAGGATAAAAAATTA | G47-F TGCCAAAGAAAAAGAACGAT |
| G47-R TTTTCAAATACACTCGCCATA | |||||
| G49 (PF08-0078) | 146 | Q-E | SS | tATTCATCTTCTTCTAATTCATCTT | G49-1F GGAAGGCATTATAGCGAAACC |
| G49-1R TGTTCATCCAGGTCATCTTCA | |||||
| 1046 | L-I | SS | ctGTTTAAGTTCATGTTTTTAAATATATAT | G49-2F GGTGAAAAATACGGAACAAA | |
| 1116 | L-I | SS | TGGATACAAATTTTTCGAAC | G49-2R TCACCTCCACTTTTGTCTTT | |
| G54 (PF14-0260) | 141 | Y-Y | SS | TAGTGTAAAAAATGATAGTGATTA | G54-F TTTTAAAAGAATCGTTTGTG |
| 144 | T-T | SS | gactATACTCATATCATCTATTAATTTTGT | G54-R TCTTTGTAATTTGTTTGGAT | |
| G55 (PF14-0133) | Intron | &2 | MS | G55-F GAGTTACAGTTTCCCATTG | |
| G55-R TGAACAAAATAAAATGAACA | |||||
| G70 (PFL0620c) | 105 | E-K | SS | gactgactgactGGTATTGGTCATATATGTTGGAAT | G70-F AAAATTGGCTAGTGTTATTG |
| G70-R TTTTAACAACTGGAAACATT |
a
PlasmoDB (version 4) gene identifiers are shown in brackets.
b
Italicized letters indicate nucleotide changes in noncoding regions; &1 and &2 are length variants resulting from indels or microsatellites. AA, amino acid.
c
SS, snapshot; DS, direct sequencing; MS, microsatellite genotyping.
d
Oligo, oligonucleotide. Tails (lowercase) were added to some oligos to adjust length of products and allow multiplexing of multiple SNP assays.