Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data

Abstract

Ribosomal DNA sequences were assessed for their usefulness in distinguishing among Trichoderma isolates and for their robustness in resolving their phylogenetic relationships. DNA sequences from the D2 region of the 28S rRNA gene were determined for 50 Trichoderma isolates representing seven species. Eight distinct sequence types existed, and were mostly consistent with groupings based on morphology. Sequence variability within the D2 region alone was not sufficient to provide a reliable phylogeny. Sequences from the ITS1, 5.8S and ITS2 regions were subsequently determined for 18 of the isolates. Eight distinct ITS sequence types were detected among these 18 isolates. The ITS sequence types were generally consistent with morphology, ITS1 sequence data supported the identification of the Th3 T. harzianum group of Muthumeenakshi et al. (1994) as T. atroviride. The data also confirmed that the biocontrol strains of this study were different from those causing disease problems in the mushroom industry in Europe and North America. Results from the phylogenetic analysis stress the importance of testing the robustness of data used to predict phylogenies. Two ITS sequence data sets for the same group of isolates produced significantly different phylogenies. Congruence analysis detected that T. inhamatum (GJS90-90) was corrupting tree topologies and ' first order pruning ' was performed by removing its sequence from the two ITS data sets. Subsequent differences in the topologies of pruned ITS1 and ITS2 trees were attributed to a lack of phylogenetic information in the ITS2 sequence region. Although ITS sequences successfully differentiated among morphologically distinct isolates within Trichoderma, it did not provide a sufficient phylogenetic signal to resolve all of their relationships.

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea

“…Despite the suggestion by other authors (Chaverri et al, 2003b;Dodd et al, 2000;Lieckfeldt and Seifert, 2000) of occurrence of paralogous ITS1 or 2 copies, we have so far not seen any in an analysis of over 1000 Trichoderma and Hypocrea isolates. While several species showed two or more haplotypes of ITS1 and 2, these diVered in most cases only in 1-3 nucleotides, and clustered together in phylogenetic analyses.…”

Trichodermaspecies onAgaricus bisporusfarms in Serbia and their biocontrol

“…The study classified T. virens in a separate clade, which was in accordance with a study by Dodd et al . (). However, by analysing ITS sequences and the D2 region of 28S rRNA of numerous Trichoderma isolates, these authors resolved the clade as consisting of only T. harzianum , while T. atroviride and T. koningii formed another clade.…”

Taxonomy and phylogenetic relationships of two species of Hypocrea with Trichoderma anamorphs

“…1) or by PCR amplification of genomic DNA using the primers ITS4 and ITS5 (WHITE et al 1990 a 50 µL reaction volume using a 55 ºC annealing temperature. The amplification was performed as described elsewhere (DODD et al 2000). Similarly, a section of the translation-elongation factor gene was amplified using primers EF1-728F (CARBONE & KOHN 1999) and EF-2 (O'DONNELL, CIGELNIK & NIRENBERG 1998).…”