Table 3.
Genes/loci used in the phylogenetic analyses for members of Nectria cinnabarina species complex (NCSC). 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′ | TrN+G | 649 (91) | 47 (7 %) | 40 | 562 |
| 48 °C, 30 s, 30′ | |||||||
| ITS | ITS5, ITS4 (White et al. 1990) | 53 °C, 1 min, 35′ | TrNef+G | 475 (592) | 38 (8 %) | 19 | 418 |
| LSU | LR5, LROR (Vilgalys n.d.) | 53 °C, 1 min, 35′ | TIM1+I+G | 814 (260) | 18 (2 %) | 14 | 782 |
| Rpb1 | crpb1a, rpb1c (Castlebury et al. 2004) | 50 °C, 2 min, 40′ | TrN+G | 621 (123) | 111 (18 %) | 120 | 390 |
| Tef1 | tef1-728, tef1-1567 (Carbone & Kohn 1999, Rehner 2001) | 66 °C, 55 s, 9′ | TrN+G | 828 (186) | 158 (19 %) | 36 | 634 |
| 56 °C, 55 s, 35′ | |||||||
|
Tub |
βtub-T1, βtub-T2
(O'Donnell & Cigelnik
1997)
|
55 °C, 30 s, 35′
|
TPM3uf+G
|
527 (135)
|
88 (17 %)
|
138
|
301
|
| Total | 3914 | 460 (12 %) | 367 | 3087 |