TABLE 2.
Manual alignments of the ITS2 pyrosequencing signature sequencesa
| Organism | Pyrosequencing profile | Similarity (no. of nucleotides) | Total no. of isolates tested (no. of reference isolates/no. of clinical isolates) | No. of isolates tested previously (reference) |
|---|---|---|---|---|
| Candida albicans | GTCAAA----GTTTGAAGATATACG-TGG-TAGACGTTACC | 35 | 21 (1/20) | 21 (3) |
| Lodderomyces elongisporus | GTCgAA----GTTTGAA-ATATAga-TtG-gAGcttTTAtt | 24 | 2 (0/2) | 2 (3) |
| Candida dubliniensis | GTCAAA----GTTTGAAGAataAaa-TGG-gcGACGccaga | 23 | 14 (0/14) | |
| Candida tropicalis | GTCAAA----GTTatgAaATAaAttgTGG-TgGcCacTAgC | 23 | 34 (0/34) | |
| Saccharomyces cerevisiae* | GTCAAA----cTTTaAgaAcATtgttcGccTAGACGcTctC | 22 | 16 (0/16) | |
| Candida metapsilosis | GTCgAA-----TTTGgAagaATgtt-TGG--AGtttgTACC | 21 | 4 (2/2) | 3 (3) |
| Candida pelliculosa | GTCAAA----cTTTtAgttTATt-GtTGt-TAagCcgagCC | 21 | 10 (1/9) | |
| Candida parapsilosis | GTCgAA-----TTTGgAagaAgttt-TGG--AGtttgTACC | 20 | 69 (1/68) | 69 (3) |
| Candida orthopsilosis | GTCgAA-----TTTGgAagaA-ttt-TGG--AGtttgTACC | 20 | 11 (10/1) | 11 (3) |
| Filobasidiella uniguttulatus | GTCAgA----tgTcaAAG-TATACacaGG-aAGcaacacCa | 20 | 1 (1/0) | |
| Pichia membranifaciens | GTCgA-----GcTcaAtGATATAtttTcGcTcGgCGgcAaa | 20 | 3 (1/2) | |
| Candida palmioleophila | GTCAAActt-GTTTGttGtTtTttaagGcaaAGcCtaacaC | 19 | 2 (1/1) | |
| Candida glaebosa | GTCAAActt-GTTTGt-GtTtTAtaagGcaaAGcCtaatga | 19 | 1 (1/0) | |
| Zygosaccharomyces bailii | GTCAAA----cTTTGAgagTATtgttTGc-ccaAgGcgcgC | 19 | 1 (1/0) | |
| Candida kefyr | GTCAAA----cTTTGAgagTtTtgGtTaa-agcggtaTgCC | 19 | 16 (1/15) | 1 (4) |
| Candida bracarensis | GTCAAA----cTTaaAgGtTtctgt-TtG-ccGtgGTcACa | 18 | 1 (1/0) | |
| Candida eremophila | GTCgAgcttaGTTaaAAGtTcggCG--GccaAagCGTgcta | 18 | 1 (1/0) | |
| Candida blankii | GTCAAA----tTTTGgAGcggTtgttacGcctGtCtcgAaC | 18 | 1 (1/0) | |
| Kazachstania sp.* | GTCAAA----cTTaaAAGAacactGtTcG--ccACGgctgt | 18 | 3 (1/2) | |
| Candida nivariensis | GTCAAA----cTTaaAgGtTcctgt-TtGccAGcaGacttC | 17 | 26 (12/14) | 16 (4) |
| Candida utilis | GTCAAg----cTTaGAAaggtgtta-aGccgAG-CtcTgCC | 17 | 1 (0/1) | |
| Cryptococcus neoformans* | GTCAAA-----caaaAAGAgATggt-TGttatcAgcaagCC | 17 | 17 (5/12) | |
| Sporopachydermia sp. | GTCAAA---gaTTTAgAtcTtTgtcaaGc-aAGACaaacta | 17 | 2 (0/2) | |
| Sporobolomyces salmonicolor | aTCtAA----tcTaaAAGgTAgACttTaGggAttaGaagCt | 17 | 2 (2/0) | |
| Candida fabianii* | GTCAAA----cTTatgAagaAattGtTaGgccGAgcccAaa | 16 | 9 (0/9) | |
| Candida glabrata | GTCAAA----cTTaaAGacgtctgtcTGccTcagCGacgCa | 16 | 47 (1/46) | 13 (4) |
| Candida inconspicua | GTCgAg----cTT-GAttAaAagTt-cGGcggGgaGaacgC | 16 | 11 (1/10) | 1 (4) |
| Candida lusitaniae | GgCgAA----aTgTcgtGcTgTAacaaGctTAactGTTtta | 16 | 59 (35/24) | |
| Candida zeylanoides | GTCAAA----cTTTGtttgTtgttGtaaGgccGAgccTgtg | 16 | 1 (1/0) | 1 (4) |
| Candida famata* | GTCAAA----cTTgtttGtTATAttgTaaggccgaGcctag | 15 | 4 (0/4) | |
| Candida guilliermondii* | GTCAAA----cTTgtttGgTtgttG-TaaggccggGccAaC | 15 | 27 (0/27) | |
| Candida norvegensis | GTCgAg----cTTaGAtttaAaAaaaaaGtTcGgCGggcca | 15 | 4 (1/3) | 1 (4) |
| Pseudozyma sp.* | GcCgAt---gaaTTGAAatTAaAtcccttcctctCcTTcCg | 15 | 1 (1/0) | |
| Rhodotorula mucilaginosa | aTCtAA----tcTTaAA-ATgTAgacattcTgattagaAgC | 15 | 7 (3/4) | |
| Cryptococcus saitoi | GcCAgA----tgTTatgaATATtaa-TccgaAGAtcaatgg | 14 | 1 (0/1) | |
| Cryptococcus terreus* | GcCAgA----taaTaAA-AaAgtca-TGtccAcgaGgTgga | 14 | 1 (1/0) | |
| Candida pseudointermedia* | GgCgAA--aaGaaTaAAGtTgaAgtaacG-TAttgcaacaa | 14 | 2 (2/0) | |
| Malassezia pachydermatis | acCAgA----aaTgaAAaAggaAtG-TactTttcaGTTcgt | 14 | 2 (2/0) | |
| Candida krusei* | GTCgAg----cTTTttgttgtctCGcaacactcgCtcTcgg | 11 | 28 (1/27) | 1 (4) |
| Candida rugosa | aatAAc----GTcaaAgGgTccgtaacaagcttAacTgttt | 9 | 6 (3/3) | |
| Total | 469 (40 species) | |||
| Candida lambica | Successful PCR; no pyrosequence generated | 2 (2/0) | ||
| Candida lipolytica | Successful PCR; no pyrosequence generated | 2 (1/1) | ||
| Candida pararugosa | Successful PCR; no pyrosequence generated | 4 (0/4) |
a
The sequences are aligned and nucleotide conservation (similarity column) with respect to the 35-nucleotide C. albicans sequence was calculated. Conserved nucleotides are depicted in uppercase bold letters, and variable positions are depicted in lowercase letters. Hyphens have been introduced to improve alignments. Asterisks denote those organisms for which the pyrosequencing profile was not unique to the species in question, as judged by BLAST searches performed against the public synchronized DNA databases (see text and Table 3).