Table 1.
Genome statistics of each of the hybrid-assembly T. endophyticum genomes.
Fig 1.
Distribution and total amount of DGC families per genome varies across isolates and Trichoderma clade.
The presence of different DGC families in a particular genome are indicated by a black cell, absence of a particular family is indicated by a white cell. DGC families are separated by cluster class. Trichoderma species lifestyle is indicated by presence/absence of color-coordinated cell, nutritional mode is indicated by either a circle (saprotroph) or a star (mycotroph). Trichoderma species lifestyle is indicated by the presence or absence of a color-coordinated cell, a potential endophyte lifestyle is indicated by a half-filled cell. Nutritional mode is indicated by either a circle (saprotroph) or a star (mycotroph). The total amount of DGC families identified in each genome is indicated by the red heatmap. Clade “Brevicompactum” is abbreviated as “Brevi”.
Fig 2.
Distribution and total amount of BGC families per genome varies across isolates and Trichoderma clade.
The presence of different BGC families are indicated by a black cell, BGC families are separated by class. The nutritional mode of each species is indicated by either a circle (saprotroph) or a star (mycotroph). BGC families present only in a single genome were removed for visualization purposes. Trichoderma species lifestyle is indicated by the presence or absence of a color-coordinated cell. Nutritional mode is indicated by either a circle (saprotroph) or a star (mycotroph). Endophyte cells half-filled indicated a potential endophytic lifestyle for that species. The total amount of DGC families identified in each genome are indicated by the red heatmap. Clade “Brevicompactum” is abbreviated as “Brevi”.
Fig 3.
Several mycoparasitism genes potentially related to the Trichoderma endophytic lifestyle were identified.
The phylogenetic and ecological (endophyte:non-endophyte ratio) signal of the distribution of the different mycoparasitism genes were determined by two methods. (A) Calculation of Blomberg’s K for each mycoparasitism gene distribution suggests that only two mycoparasitism genes are both overdispersed in the Trichoderma phylogeny (K < 0.8) and is not consistent with Brownian motion evolution (p > 0.05), while also being overrepresented in endophyte genomes (E:NE > 2). (B) Calculation of Pagel’s Lambda for each mycoparasitism gene distribution suggests that only a single mycoparasitism gene is both overdispersed in the Trichoderma phylogeny (Lambda < 0.8) and is not consistent with Brownian motion evolution (p > 0.05), while also being overrepresented in endophyte genomes (E:NE > 2).
Table 2.
Mycoparasitism gene orthogroups of interest that are found in greater numbers in endophytic Trichoderma genomes.
Fig 4.
Distribution and amount of chitinase gene classes per genome varies across isolates and Trichoderma clade.
Heatmap indicating the relative numbers of chitinase classes (green heatmaps) and chitinase domains (purple heatmaps) found in the genomes of 38 different Trichoderma isolates. Half-filled cells indicated a potential endophytic lifestyle for that species based on sequence identity and isolation in GenBank. Species lifestyle is indicated by color shading in cells, nutritional mode is indicated by either a circle (saprotroph) or a star (mycotroph). Clade “Brevicompactum” is abbreviated as “Brevi”.
Fig 5.
Horizontal transfer of ergot alkaloid BGCs from Xylariales to Brevicompactum and Eurotiales.
(A) IQ-TREE maximum likelihood gene phylogeny of easA with ultrafast bootstrap branch support. (B) Shared synteny and sequence similarity of ergot alkaloid BGCs. Gene-gene percent identity is highlighted in connecting shade. (C) Species phylogeny of genomes in easA gene phylogeny. Tip labels in (A) and (C) are colored by taxonomic order.