Colletotrichum acutatum

Wang, Qiu-Tong, Liu, Xiao-Ting, Ma, Hai-Ying, Shen, Xiao-Ye & Hou, Cheng-Lin, 2019, Colletotrichum yulongense sp. nov. and C. rhombiforme isolated as endophytes from Vaccinium dunalianum var. urophyllum in China, Phytotaxa 394 (4), pp. 285-298 : 290

C. acutatum species complex

For the 6-locus (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) phylogenetic analysis of the C. acutatum species complex, 38 reference sequences were downloaded from GenBank ( Table 1) and one isolate obtained from V. dunalianum var. urophyllum in this study. The multi-gene dataset (gene boundaries of ITS: 1−558, GAPDH: 559−811, CHS- 1: 812−1084, HIS3: 1085−1471, ACT: 1472−1697, TUB2: 1698−2187) comprised 2187 characters including the alignment gaps, of which 250 were parsimony-informative, 271 parsimony-uninformative and 1666 constant. The MP analysis of sequences resulted in one most parsimonious tree ( Fig. 1 ) with a length (TL) of 886 steps, consistency index (CI) of 0.702, retention index (RI) of 0.844 and homoplasy index (HI) of 0.298. For the Bayesian analysis, MrModeltest 2.3 with the Akaike information criterion (AIC) was used to choose a substitution model for the two datasets. The model GRT+ I + G were chosen for the combined sequences. The analyses of the final MCMC chains were run from random trees for 1,000,000 generations and sampled every 100 generations. The tree generated from Bayesian analysis confirmed the tree topology obtained with parsimony. The phylogram constructed using combined dataset showed that V. dunalianum var. urophyllum isolate clustered into C. rhombiforme distinct clades with high bootstrap support (bootstrap support BS> 70 and Bayesian posterior probabilities PP> 0.95).

Figures

FIGURE 1. Phylogenetic tree derived from maximum parsimony analysis of the combined ITS, GAPDH, CHS-1, HIS3 ACT and TUB2 sequences of C. acutatum species complex, using C. orchidophilum CBS 632.80* as outgroup. Bootstrap values of more than 70 from 1000 replications are shown above the respective branches. Bayesian posterior probabilities (PP) were estimated and clades with PP> 0.95 are marked under the branches. The newly sequenced C. rhombiforme is in bold.