Table 5.
β -giardin (bg) multiple alignment sequence isolates in this study with reference sequences retrieved from GenBank, representing position of intra-genotypic substitutions in sub-assemblages of assemblages A and B.
| Isolates/GenBank accession no. | Nucleotide position from the start of the gene | |||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Assemblage A | 177 | 204 | 216 | 273 | 285 | 303 | 333 | 357 | 393 | 417 | 432 | 435 | 460 | 468 | 498 | 516 | 534 | 541 | 564 | 567 | 606 | 624 | ||||
| AII-A2 | AY072723 | C | A | G | G | C | A | T | G | T | T | G | T | C | T | A | C | G | G | C | G | T | G | |||
| AI-A1 | X85958 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | C | . | |||
| AII-A3 | AY072724 | . | . | . | . | . | . | . | . | . | . | . | . | T | C | . | . | . | . | . | . | . | . | |||
| AII-A4 | AY545642 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | A | . | . | C | . | |||
| AII-A3 | IGT2,11-14, 20-22, 25-26, 30, 37, 39-40, 117, 143; IGR81,287 | . | . | . | . | . | . | . | . | . | . | . | . | T | C | . | . | . | . | . | . | . | . | |||
| AII-A2 | IGT8, 19, 29, 31, 41 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | |||
| AII-A3 | IGT9; IGA340 | . | . | . | . | . | . | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . | |||
| AII-A3 | IGT213 | . | . | . | . | . | G | . | . | . | . | . | . | . | C | . | . | . | . | . | . | . | . | |||
| A | IGT93 | T | . | R | . | . | . | Y | . | . | Y | A | C | . | Y | . | . | R | . | . | S | . | S | |||
| A | IGT7H | . | R | . | R | Y | R | . | Y | Y | Y | A | . | T | C | M | Y | R | . | T | S | . | . | |||
| Assemblage B | 210 | 228 | 273 | 303 | 327 | 354 | 357 | 384 | 393 | 432 | 435 | 438 | 450 | 471 | 538 | 541 | 550 | 564 | 594 | 609 | 610 | 636 | 639 | 645 | 648 | |
| BIII-B2 | AY072726 | C | A | G | G | C | C | C | C | C | A | C | C | C | C | G | G | G | T | G | C | G | G | G | C | G |
| BIV-B3 | AY072727 | . | . | A | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV-B1 | AY072725 | T | . | A | . | T | T | T | . | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | A |
| BIV-B4 | AY072728 | . | G | A | . | . | T | T | . | . | . | . | . | . | . | . | . | . | C | . | T | . | . | . | T | . |
| BIV-B5 | AY647265 | . | . | A | . | . | T | T | . | . | . | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . |
| BIV-B6 | AY647266 | T | . | A | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV-B3 | IGT1,3,6,10,17,23,24,27,28,35,164; IGR12 | . | . | A | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV-B6 | IGT4 | T | . | A | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGT5 | T | . | A | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | A | . | . | . | . |
| BIV | IGT7,15,16,34 | . | . | A | . | . | T | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGT18; IGR197 | . | . | R | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGT32 | . | . | A | . | . | . | T | . | . | . | . | . | . | . | . | . | . | R | . | . | . | . | . | . | . |
| BIV | IGT33 | . | . | A | . | . | . | T | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGT36, 38; IGR101,386 | T | . | A | . | . | T | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGT52 | . | G | A | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGT110; IGA305 | T | . | A | . | . | T | T | . | . | . | . | . | . | . | . | . | . | . | A | . | . | . | . | . | . |
| BIV | IGT152 | . | . | R | . | . | . | T | . | . | . | . | . | . | . | T | C | C | . | . | . | . | . | . | . | . |
| BIV | IGT165 | Y | . | R | R | . | T | K | T | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGT182 | . | . | A | . | . | T | T | T | T | G | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGA458 | . | . | A | . | . | . | T | . | . | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . |
| BIV | IGR519 | . | . | R | . | . | . | T | . | . | . | . | . | . | . | . | . | . | . | . | . | . | A | T | . | . |
Accession numbers of the isolates used as sub-assemblage reference isolates are included in bold. Numbers in bold represent nucleotide substitutions from the start of the gene, which differentiate between sub-assemblages introduced by Weilinga and Thompson and Cacciò et al. (15, 17) position and breakdown of intra-genotypic substitutions. Heterogeneous positions are indicated by standard IUPAC codes in bold. Dots indicate nucleotide identity to the AII (AY072723) or BIII (AY072726) reference sequences.