Table 2.
Genes/loci used in the phylogenetic analyses for members of the genus Nectria. Information on the primers, base pairs, PCR protocols, and models of nucleotide substitution are indicated.
| Locus | Primers used (reference) | PCR protocol: Annealing temp. & cycles | Nucleotide substitution models | Included sites (# of excluded sites) | Phylogenetically informative sites (%) | Uninformative polymorphic sites | Invariable sites |
|---|---|---|---|---|---|---|---|
| Act | Tact1, Tact2 (Samuels et al. 2006) | 65 °C, 30 s, 15′ | GTR+G | 613 (127) | 111 (18 %) | 43 | 459 |
| 48 °C, 30 s, 30′ | |||||||
| ITS | ITS5, ITS4 (White et al. 1990) | 53 °C, 1 min, 35′ | TIM3+I+G | 539 (279) | 62 (12 %) | 52 | 425 |
| LSU | LR5, LROR (Vilgalys n.d.) | 53 °C, 1 min, 35′ | TIM3+I+G | 807 (150) | 67 (8.3 %) | 39 | 701 |
| Rpb1 | crpb1a, rpb1c (Castlebury et al. 2004) | 50 °C, 2 min, 40′ | TIM2+I+G | 590 (540) | 233 (40 %) | 65 | 292 |
| Tef1 | tef1-728, tef1-1567 (Carbone & Kohn 1999, Rehner 2001) | 66 °C, 55 s, 9′ | GTR+I+G | 645 (261) | 142 (22 %) | 43 | 460 |
| 56 °C, 55 s, 35′ | |||||||
|
Tub |
βtub-T1, βtub-T2
(O'Donnell & Cigelnik
1997)
|
55 °C, 30 s, 35′
|
TPM3uf+I+G
|
479 (408)
|
192 (40 %)
|
32
|
255
|
| Total | 3673 | 807 (22 %) | 274 | 2592 |