TABLE 1.
Oligonucleotide primers designed in this study
| Primer | Target |
Sequence (5′→3′) | Amplicon size (bp)b | |
|---|---|---|---|---|
| Gene | Accession no. (position)a | |||
| alp2/3-D | alp2/alp3 | AF208158 (1070)/AF245663 (1311) | CATTAACCGTCACTCCAGAGCAAC | |
| alp2-R | alp2 | AF208158 (1582) | CTTCATCTGTTGACTTATCTGGATAG | 513* |
| alp3-R | alp3 | AF245663 (1637) | CTTTTGGTTCGTTGCTATCCTTAAG | 327* |
| PI1-UP | gbs80 | AE009948 (632375) | GGTCGTCGATGCTCTGGATTC | 881 |
| PI1-DN | gbs80 | AE009948 (633255) | GTTGCCCAGTAACAGCTTCTCC | 881 |
| PI2a-UP | gbs67 | AE009948 (1417645) | CTATGACACTAATGGTAGAAC | 575 |
| PI2a-DN | gbs67 | AE009948 (1417071) | CACCTGCAATAGACATCATAG | 575 |
| PI2b-UP | san_1519 | AAJR01000022 (10160) | ACACGACTATGCCTCCTCATG | 721 |
| PI2b-DN | san_1519 | AAJR01000022 (10880) | TCTCCTACTGGAATAATGACAG | 721 |
| PI1_all-UP | sal_0710 | NZ_AAJP01000027 (23718) | ACCTATGTTGCTGATTCGGCTGAAAATG | 684† |
| PI1_all-DN | sal_0709 | NZ_AAJP01000027 (23035) | TACGGACACTTTCTAGTGCCTTTGGATC | 684† |
| neuB1-UP | neuB | EF990364 (10162) | CAAGCGGTGAATATTTTACG | 2,797 |
| neuA-DN | neuA | EF990364 (12958) | CATTGCTTCCTTTATATGCCATG | |
| neuB2-UP | neuB | EF990364 (10653) | CTTGGGACAAGAAGCGCAAG | |
| neuC1-UP | neuC | EF990364 (11153) | GCGTTGATTTATAATGTCCCAG | |
| neuC2-UP | neuC | EF990364 (11672) | CTGATTGGTAATTCGTCTTCTGG | |
| neuD-UP | neuD | EF990364 (12133) | GAAGATGGCTCAATAGATGCAG | |
a
That is, the position of primer from the 5′ end.
b
*, together with the primer alp2/3-D; †, size if the isolate lacks the PI-1 islet (if this locus is present, a 16.7-kb fragment would be expected).