Fig 1.
Phylogeny of Hypocreales and the composition of their pcwdCAZomes.
A. Bayesian phylogram obtained based on the curated concatenated alignments of 100 orthologous neutrally evolving proteins of Hypocreales and two other Sordariomycetes. Black dots above nodes indicate posterior probability support > 0.95. The colors of the branches indicate the major nutritional strategy in the group (see insert) as described in Supporting Information S1 Text. B. The size of each pcwdCAZome per species is shown as a circle; n.a. means not available. The heat map shows the gene number for each GH family in the Hypocreales fungi examined; cluster analysis was performed with Euclidian distance and complete linkage for rows. The corresponding data matrix is presented in Supporting Information S3 Table. GH indicates glycosyl hydrolase family.
Fig 2.
Principal component analysis based on the diversity of Hypocreales genes in GH families involved in plant cell wall degradation.
Size of the dot corresponds to the total size of pcwdCAZome as shown in Fig 1B. Brown, blue, and green colors indicate parasitism on insects, fungi, and plants, respectively. Saprotrophic fungi are shown in grey.
Fig 3.
Evolution by vertical gene transfer of GH36 α-1,4-galactosidase Clade B (reference sequence Trire2:124016 of T. reesei QM 6a) in Trichoderma.
Results for all pcwdCAZymes in Trichoderma are presented in Supporting Information S2 Fig.
Fig 4.
Evolution of selected pcwdCAZymes by putative lateral gene transfer.
A. Evolution of GH6 cellobiohydrolase CEL6 (Trire2:72567) obtained by LGT from Pestalotiopsis fici. B. The GH11 endo-ß-1,4-xylanase gene (Trire2:74223) and its duplicated copies, which have incongruent tree topologies compared to the phylogenomic tree (see Fig 1A). Talaromyces stipitatus (Eurotiales) was confirmed to be an LGT donor for the clade containing Trire2:123818. The phylogenetic position of the GH11 clade including T. atroviride Triat2:90109 is unresolved (Supporting Information S2 Fig, S4 Table).
Fig 5.
Evolution of swollenin in Trichoderma.
The reference sequence Trire2:123992 of T. reesei QM 6a. Green plants have been identified as putative donors for LGT of this gene.
Fig 6.
Evolutionary origin of Trichoderma pcwdCAZome obtained via putative LGT from Pezizomycotina donors mapped on Bayesian multilocus phylogram.
A. The multilocus Bayesian phylogram of Ascomycota. B. The magnified Hypocreales clade from the phylogram on A. A &B: Black dots above nodes indicate posterior probability > 0.99. Individual lines correspond to LGT events, and the thickness of lines is proportional to the number of genes obtained from this donor. Statistically confirmed donor fungi are shown in bold. Colors correspond to the major groups of proteins composing the pcwdCAZome of Trichoderma (pie chart on C).
Fig 7.
Composition and origin of the pcwdCAZome of Trichoderma based upon nine genomes.
A. Summary of the evolutionary analysis and tests for LGT of individual proteins in Trichoderma pcwdCAZomes (N = 122) presented in Supporting Information S3 Table–S4 Table, S2 Fig. B. Schematic drawing of the primary plant cell wall. Cellulose, hemicellulose, and pectin are colored brown, green, and orange, respectively. C: The diversity and evolution of individual groups of Trichoderma pcwdCAZome. Brown, green, and orange rectangles correspond to enzymes involved in the degradation of cellulose, hemicellulose, and pectin, respectively. See B for the legend. Auxiliary proteins are shown in blue. Dark-shaded lines correspond to genes obtained through putative LGT, while light-shaded lines indicate additional cases of incongruent phylogeny and/or insufficient data. Numbers on white, black, or grey backgrounds correspond to the maximum total numbers of genes in each family that evolved through LGT, vertical evolution, or unknown mechanisms, respectively.
Fig 8.
Mycoparasitism of Trichoderma on Basidiomycota (A) and Ascomycota (B). Macrophotography for A shows T. simmonsi TUCIM 6527 on Stereum sp. Bar indicates 1 cm. SEM images show hyphae of T. guizhouense NJAU 4742 on three hosts.
Fig 9.
Mycoparasitism of GFP-labeled T. reesei TUCIM 4817 on Pestalotiopsis fici TUCIM 5788.
A. Dual confrontation assay after 10 days of incubation at 28°C in darkness. B. Hyphal interactions observed using light microscopy (400x magnification). C. Confocal image showing endoparasitism of T. reesei on hyphae of P. fici on a glass slide prepared as shown in S3 Fig. D. Hyphae of P. fici TUCIM 5788 and a fluorescent chlamydospore of T. reesei. E. T. reesei TUCIM 4817 mycelium. Scale bar on C–E—40 μm.
Fig 10.
Adelphoparasitism of Trichoderma on members of the same genus (A), same family (B), and same order (C, D). Parasites were inoculated on the right side of each plate, and hosts are on the left side. Images were taken after 10 days of incubation at 28°C in the dark. Parasitism is assigned as a function of active overgrowth of the opponent colony. NCBI accession numbers for the DNA barcodes for fungi are given in Supporting Information S6 Table. Note to A: In this experiment, the host fungus T. guizhouense NJAU 4742 did not produce conidia (see other images in Supporting Information S3 Fig).