TABLE 3.
Oligonucleotide primers and sequences used for C. dubliniensis MLST analysis
| Locus | Amplicon size (bp) in C. dubliniensis | No. of bases analyzed in C. dubliniensis (bp)a | Coordinates ofb:
|
Analyzed segment sequence homology (%)c | Primerd | Analyzed segment start (5′) and end (3′) points in C. dubliniensise | |
|---|---|---|---|---|---|---|---|
| C. albicans amplicon | C. dubliniensis amplicon | ||||||
| CdAAT1a | 480 | 373 | +31-+508 | +35-+497 | 91 | 5′-ATCAAACTACTAAATTTTTGAC-3′ (forward) | 5′-ATTGAAA |
| 5′-CGGCAACATGATTAGCCC-3′ (reverse) | 3′-CGATTT | ||||||
| CdAAT1b | 491 | 341 | +736-+1,226 | +742-+1,233 | 95 | 5′-ATGGCTTATCAAGGTTTTGC-3′ (forward) | 5′-TTAACTAA |
| 5′-GTAGCATAAACTGAATAATCA-3′ (reverse) | 3′-TTGGGATCA | ||||||
| CdACC1 | 519 | 407 | +3,184-+3,702 | +3,190-+3,708 | 93 | 5′-GCCAGAGAAATTTTGATCCAATGT-3′ (forward) | 5′-TTTTGAGAT |
| 5′-TTCATCAACATCATCCAAGTG-3′ (reverse) | 3′-TACAAGA | ||||||
| CdADP1 | 537 | 443 | +868-+1,404 | +868-+1,404 | 90 | 5′-GAGCCAAGTATGAATGACTTG-3′ (forward) | 5′-TACGTTGCAA |
| 5′-TTGATCAACAAACCCGATAAT-3′ (reverse) | 3′-GGAAATCCAA | ||||||
| CdGLN4 | 483 | 404 | +82-+564 | +82-+564 | 100 | 5′-GAGATAGTTAAGAATAAAAAAGTTG-3′ (forward) | 5′-TCTGCTTTA |
| 5′-GTCTCTTTCGTCTTTAGGACCCAATC-3′ (reverse) | 3′-TTCAAACC | ||||||
| CdMPIb | 486 | 375 | +406-+891 | +406-+892 | 90 | 5′-ACCAGAAATGGCC-3′ (forward) | 5′-TTTAAGC |
| 5′-GCAGCCATACATTCAATTAT-3′ (reverse) | 3′-GGGAAGCA | ||||||
| CdRPN2 | 447 | 306 | +1,012-+1,458 | +1,015-+1,461 | 90 | 5′-TTTATGCATGCTGGTACTACTGATG-3′ (forward) | 5′-TTGGTCCAAG |
| 5′-TAACCCCATACTCAAAGCAGCAGCCT-3′ (reverse) | 3′-GTCTTTACGA | ||||||
| CdSYA1 | 543 | 391 | +2,284-+2,826 | +2,284-+2,826 | 90 | 5′-AGAAGAATAGTTGCTCTTACTG-3′ (forward) | 5′-TAAATCCAAG |
| 5′-GTTGCCCTTACCACCAGCTTT-3′ (reverse) | 3′-AGTCTGTATCT | ||||||
| CdVPS13 (exCdVPS13) | 741 | 403 (675) | +4,854-+5,594 | +4,858-+5,598 | 88 | 5′-CGTTGAGAGATATTCGACTT-3′ (forward) | 5′-CCTTGATATG |
| 5′-ACGGATCGATCGCCAATCC-3′l (reverse) | 3′-AAAATCTTGG (5′-AGAGCAAACG) (3′-AAACCTTGG) | ||||||
| CdZWF1b (exCdZWF1b) | 702 | 491 (621) | +787-+1,469 | +766-+1,468 | 93 | 5′-GTTTCATTTGATCCTGAAGC-3′ (forward) | 5′-CAAACCAGG |
| 5′-GCCATTGATAAGTACCTGGAT-3′ (reverse) | 3′-TAGAATTAC (5′-AAAGTTTTAAAA) (3′-GAAAATATTTGAAA) | ||||||
Numbers in parentheses are for extended sequence fragments analyzed for polymorphisms.
Nucleotide coordinates for MLST amplicons are numbered based on the adenine residue of the ATG start codon at the 5′ end of the gene designated +1.
Sequence homology between C. dubliniensis and C. albicans at the sequenced fragments.
Nucleotide bases shown in bold typeface and underlined denote nucleotide bases that vary between C. albicans and C. dubliniensis.
Loci for which additional sequence data were analyzed in both the 5′ and 3′ directions of the original sequence fragment (range, 100 bp to 280 bp) due to the presence of additional polymorphic sites (underlined and bold). Sequences in parentheses are those used with the extended sequence fragments.