Table 1. Determination of the presence or absence of 3D7 var and stevor genes within the E5 genome.
Assay of E5 genomic DNA for the presence or absence of specific genes within the 3D7 var gene repertoire. The presence of all the var genes annotated within the 3D7 genome was assessed by quantitative real-time PCR using a panel of gene specific PCR primers and E5 genomic DNA as template. The left hand column shows the chromosomal location of each var gene, the middle column lists genes that could not be detected, and the right hand column shows genes that amplified as single copy genes. As controls, amplifications using 3D7 gDNA as well as amplifications of single copy housekeeping genes were also performed
| Chromosomal location | “Missing” var genes | Intact var genes | “Missing” stevor genes | Intact stevor genes |
|---|---|---|---|---|
| Chr 1, subtelomeric | PFA0005w, PFA0015c, PFA0765c | PFA0090c, PFA0750w, PFA0705c, PFA0105w | ||
| Chr 2, subtelomeric | PFB0010w | PFB1055c | PFB0050c, PFB0025c | PFB1020w, PFB0955w, PFB0065w |
| Chr 3, subtelomeric | PFC0005w, PFC1120c | PFC0025c, PFC1105w | ||
| Chr 4,subtelomeric | PFD0020c, PFD0005w, PFD1235w, PFD1245c | PFD0035c, PFD1220w | PFD0065w, PFD0125c | |
| Chr 4,internal | PFD0995c, PFD1000c, PFD1005c, PFD1015c | PFD0615c, PFD0625c, PFD0630c, PFD0635c | ||
| Chr 5, subtelomeric | PFE0005w | PFE0030c | ||
| Chr 6, subtelomeric | PFF0010w, PFF0020c, PFF1580c, PF1595c | PFF0850c, PFF1550w | ||
| Chr 6, internal | PFF0845c | |||
| Chr 7, subtelomeric | MAL7P1.187 | MAL7P1.212 | PF07_0130 | MAL7P1.218, MAL7P1.310, MAL7P1.223, MAL7P1.227 |
| Chr 7, internal | MAL7P1.50, MAL7P1.55, MAL7P1.56, PF07_0048, PF07_0049, PF07_0050, PF07_0051 | |||
| Chr 8, subtelomeric | PF08_0140, PF08_0141, PF08_0142 | MAL8P1.217 | ||
| Chr 8, internal | PF08_0103, PF08_0106, PF08_0107 | |||
| Chr 9, subtelomeric | PFI0005w, PFI1820w, PFI1830c | PFI0080w, PFI0045c | ||
| Chr 10, subtelomeric | PF10_0001 | PF10_0406 | PF10_0395 | PF10_0009 |
| Chr 11, subtelomeric | PF11_0007, PF11_0008 | PF11_0521 | PF11_0013 | PF11_0516 |
| Chr 12, subtelomeric | PFL0005w, PFL0020w, PFL0030c, PFL2665c | PFL2610w, PFL2620w, PFL2635w | ||
| Chr 12, internal | PFL0935c, PFL1950w, PFL1955w, PFL1960w | |||
| Chr 13, subtelomeric | PF13_0001, PF13_0003 | MAL13P1.356 | MAL13P1.7, MAL13P1.505 | MAL13P1.490 |
| Chr 14, subtelomeric | PF14_0007 | PF14_0767, PF14_0771 |