TABLE 2.
Molecular polymorphisms discriminating D. yakuba and D. santomea
| Marker | Cytological location | Primer sequence (5′-3′) | Type | PCR TA (°) | Restriction endonuclease |
|---|---|---|---|---|---|
| y | 1A5 | CGCTGCGTGTTTGTTTATTT | S | 55 | AvaII |
| GCGAATGTTCAAAGAATAATTTC | |||||
| per | 3B1–2 | TTCCAGTTCTCCGAATCAGC | S | 55 | BbvI |
| CCTTAGGGCTGAGCCACTCT | |||||
| sog | 13E1 | GCTGGCGTACAACATTGAAA | S | 57 | XhoI |
| CTCGGTGGCCACATTCAC | |||||
| v | 9F11 | AGACTCCCTTCCTGCCTTTC | S | 55 | SspI |
| TGAGAGCTCCAGTTCCGACT | |||||
| rux | 5D2 | CATTTGCTCATCCGTTTCCT | S | 55 | HpyCH4IV |
| GTGCTTGTAGCGCGTTGTC | |||||
| f | 15F4–7 | CTCGCCGAATGGCAGCAT | S | 55 | HpaII |
| AATGTACGTCCGCCTGGAT | |||||
| bnb | 17D6 | TTCCTTCTCCTGCTCCTTGA | S | 55 | PvuII |
| CCGAGAAGAAGTCCATCGAG | |||||
| Hex-A | 8E10 | GGTACCCAGCTCTTCGATCA | S | 57 | HhaI |
| GGCAATGGCATCCTTTAGAA | |||||
| AnnX | 19C1 | AAACCAGAGAGCTGCCTTCA | S | 55 | Taq1α |
| ATTCTCCTTGCGACGTCTTG | |||||
| su(f) | 20E | TGGTGGGCAAAAGTCAAAAT | ID | 57 | NcoI |
| AAAATCTTAGCCGCCTGGAC | |||||
| l(2)gl | 21A5 | TGACGTCGCTGAAGTTCTTG | S | 54 | MseI |
| GATGGGCCAGCTTATATTGC | |||||
| Rad1 | 23A1 | ATGAATGTGCTGTCCGAGTG | S | 55 | HpyCH4IV |
| GTTCGTGGAACACCTTCGAT | |||||
| RpL27A | 24F3 | ATCAAGCGGAAGAAGACCAG | S | 55 | NcoI |
| GACCTTGCCGAAGTAACCAG | |||||
| salr | 32E4–F1 | AGCTGACTGATCCCAACCAG | S | 60 | ScrF1 |
| GATGATGCCGTTGGAGAACT | |||||
| Rep4 | 34B4 | TCACGGAGTACGAACACCAA | S | 57 | Taq1α |
| TACGGGTCAGTTCCTCCTTG | |||||
| His3 | 39D3–E1 | TTTCAGGACCACAAACCACA | ID | 57 | MfeI |
| CCGTTTGCCCCTTATAAACA | |||||
| barr | 38B1–2 | GCAGTGCAGGATGAAGATCA | S | 53 | HaeIII |
| TTGGAGTCCACCTCCAGAAC | |||||
| Sara | 57E6 | CGACCACAAACCCTGAATTT | S | 55 | HphI |
| CATGTTATCCGGCACCCATA | |||||
| Kr | 60F5 | ACCAGCCATGAGTGGAGATT | S | 56 | MlyI |
| CTACAGAGCTGGCTCCATCC | |||||
| Lsp1γ | 61A6 | CAAAACCCACCACAAGCAG | S | 52 | AluI |
| CCTTGTACTCCTTCTCGTACATGAT | |||||
| dib | 64A5 | AGTCCTTTTCTCCCCAGGAA | S | 52 | NruI |
| ATTGGGCCTGGCTGAGTT | |||||
| sfl | 65B3–4 | GGGTAATCCCTGTGACGATG | S | 52 | NsiI |
| TTCCGATGGAAAGAAGTCCA | |||||
| Est-6 | 69A1 | TCCTGCCTACGCTTTTGTCT | ID | 52 | MseI |
| AAAAGTAGTCGTCGCCATGC | |||||
| Ssl1 | 80B2 | GGTGCCCAGTAGTGGTGAGT | S | 52 | BsrI |
| GACGCACATTTTCGAGATCA | |||||
| ry | 87D9 | CGCTTTGAGCAAAAATCCA | S | 52 | SacI |
| GAAGAACAAGCTCACCACCA | |||||
| Rpn5 | 83C4 | TACCGAGGGCAAGATTTACG | S | 57 | MseI |
| TGCTGATCTTCTTGGCAATG | |||||
| AP-50 | 94A15–16 | AGTGCAAGTTCGGCATCAA | S | 57 | HaeIII |
| GAATGGCAGCGAAATGTCTT | |||||
| Mlc1 | 98A14–15 | TGCAAACAGAGTTCGTCCAG | S | 52 | Tsp5091 |
| AACGGGCATTATCAGCATGT | |||||
| ymp | 96E | CCTCGAGACCCGCAGTAGT | S | 53 | HaeIII |
| CACCTCGCACTTCTGATTGA | |||||
| janB | 99D3 | CATGGCTTCACGAAATACGG | S | 57 | SalI |
| CTTACCCTGGAGGTGCCATA | |||||
| krz | 100E3 | CGCATGTTGTCAAATAAAATCG | S | 55 | MseI |
| TTTTTGGGATAACCCATTATTCA | |||||
| ci | 102A1–3 | AGCCCTTGCAGTGAAGACTC | S | 50 | HpaI |
| TGGTAGGTCTGCTACGTCC |
Cytological locations are given on the basis of D. melanogaster cytology (Lemeunier and Ashburner 1976). The order of the markers in the first column reflects their relative positions in D. yakuba/D. santomea chromosomes inferred from the D. yakuba genome project (http://www.genome.wustl.edu/projects/yakuba/). Marker types: S, SNP; ID, insertion/deletion. The PCR protocol for all markers is 1 cycle at 94° for 2 min; 35 cycles at 94° for 30 sec, annealing temperature (TA) for 30 sec, and 72° for 30 sec; and 1 cycle at 72° for 4 min, where the TA is listed. PCR products were digested with a restriction endonuclease, run on a 3% agarose gel stained with ethidium bromide, imaged with the Bio-Rad Chemi Doc System PC RS-170 using Quantity One (version 4.2.1) software, and manually genotyped.