Table 2.
Key genomic regions characterized in AT, GOUNDRY, and Tengrela A. coluzzii.
| Locus | Description | Chromosome | Position | Allele | AT Frequency | GOUNDRY Frequency | Tengrela Anopheles coluzzii Frequency |
|---|---|---|---|---|---|---|---|
| 2La | 22 Mb inversion | 2L | 20000000–42000000 | 2L+a (haplotype) | 48% | 70% | 3% |
| 2La2L+a (heterozygous genotype) | 73% (expect 50%; χ2 = 10.5; P = 0.001) | 31% (expect 42%; χ2 = 36.2; P < 0.0001) | 5% (expect 5%) | ||||
| Y-linked | Y-chromosome sequence in PEST, excluding sex-determining gene | Y | 50000–230000 | Y sequence present | 94% | 100% | 3% |
| Rdl | Insecticide resistance | 2L | 25429235 | SER (resistant) | 32% | 58% | 68% in 2011–2012; 38% in 2015–2016 |
| Kdr | Insecticide resistance | 2L | 2422652 | PHE (resistant) | 51% | 46% | 78% |
| CYP9K1 | Insecticide resistance | X | 15242000 | cyp-II (resistant?) | 100% | 67% | 11% |
| TEP1 | Plasmodium resistance | 3L | 11205000 | R (protective) | 0% | 12% | 98% |
| APL1A | Plasmodium resistance | 2L | 41271000 | APL1A2 (protective) | 15% | 17% | 80% |
| Xh | 1.5 Mb inversion | X | 8470000–10100000 (example SNP at 9361641) | Non-reference | 100% | 100% | 0% |
| Sweep region | Unknown phenotypic effect | 3R | 8900000–13300000 (example SNP at 13081325) | T (non-reference) | 100% | 88% | 0% |
| rDNA IGS | Intergenic region of ribosomal DNA (multiple copies) | UNK (sequence from Scott et al., 1993) | 580–581 | HhaI cut site (S-form specific; Fanello et al., 2002) | 0% | 8% | 0% |
| M/S diagnostic SNPs | Divergence island SNPs (Lee et al., 2013) | 2L | 209536, 1274353, 2430786, 2430915, 2431005 | M-form | 46–51% | 54–58% | 22–28% |
| 3L | 296897, 387877, 413944 | M-form | 99–100% | 100% | 100% | ||
| X | 20015634, 22105429, 22105860, 22497157,22750432, 22750572, 22944682 | M-form | 99–100% | 96% | 100% | ||
| S200 X6.1 | 230bp diagnostic indel | X | 22951000 | M-form insertion present | 100% | 100% | 100% |
| SNP within insertion | X | 22951586 | T (non-reference) | 100% | 100% | 1% |