Comparison of the genomes of two mycoparasitic and one saprotrophic Trichoderma species revealed remarkable differences: in contrast to the genomes of other multicellular ascomycetes, such as aspergilli [15, 17], those of Trichoderma appear to be have the highest level of synteny of all genomes investigated (96% for Tr and still 78/79% for Tv and Ta, respectively, versus 68 to 75% in aspergilli), and most of the differences between Ta and Tv versus Tr or other ascomycetes occur in the non-syntenic areas. Nevertheless, at a molecular level the three species are as distant from each other as apes from Pices (fishes) or Aves (birds) , suggesting a mechanism maintaining this high genomic synteny. Espagne et al.  proposed that a discrepancy of genome evolution between P. anserina, N. crassa and the aspergilli and saccharomycotina yeasts is based on the difference between heterothallic and homothallic fungi: in heterothallics the presence of interchromosomal translocation could result in chromosome breakage during meiosis and reduced fertility, whereas homothallism allows translocations to be present in both partners and thus have fewer consequences on fertility. Since Trichoderma is heterothallic , this explanation is also applicable to it. However, another mechanism, meiotic silencing of unpaired DNA  - which has also been proposed for P. anserina , and which eliminates progeny in crosses involving rearranged chromosomes in one of the partners - may not function in Trichoderma because one of the essential genes (SAD2 ) is missing.
Our data also suggest that the ancestral state of Hypocrea/Trichoderma was mycoparasitic. This supports an earlier speculation  that the ancestors of Trichoderma were mycoparasites on wood-degrading basidiomycetes and acquired saprotrophic characteristics to follow their prey into their substrate. Indirect evidence for this habitat shift in Tr was also presented by Slot and Hibbett , who demonstrated that Tr - after switching to a specialization on a nitrogen-poor habitat (decaying wood) - has acquired a nitrate reductase gene (which was apparently lost earlier somewhere in the Sordariomycetes lineage) by horizontal gene transfer from basidiomycetes.
Furthermore, the three Trichoderma species have the lowest number of transposons reported so far. This is unusual for filamentous fungi, as most species contain approximately 10 to 15% repetitive DNA, primarily composed of TEs. A notable exception is Fusarium graminearum , which, like the Trichoderma species, contains less than 1% repetitive DNA . The paucity of repetitive DNA may be attributed to RIP, which has been suggested to occur in Tr  and for which we have here provided evidence that it also occurs in Ta and Tv. It is likely that this process also contributes to prevent the accumulation of repetitive elements.
The gene inventory detected in the three Trichoderma species reveals new insights into the physiology of this fungal genus: the strong expansion of genes for solute transport, oxidoreduction, and ankyrins (a family of adaptor proteins that mediate the anchoring of ion channels or transporters in the plasma membrane ) could render Trichoderma more compatible in its habitat (for example, to successfully compete with the other saprotrophs for limiting substrates). In addition, the expansion of WD40 domains acting as hubs in cellular networks  could aid in more versatile metabolism or response to stimuli. These features correlate well with a saprotrophic lifestyle that makes use of plant biomass that has been pre-degraded by earlier colonizers. The expansion of HET proteins (proteins involved in vegetative incompatibility specificity) on the other hand suggests that Trichoderma species may frequently encounter related yet genetically distinct individuals. In fact, the presence of several different Trichoderma species can be detected in a single soil sample . Unfortunately, vegetative incompatibility has not yet been investigated in any Trichoderma species, and based on the current data, should be a topic of future research.
Finally, the abundance of SSCPs in Trichoderma may be involved in rhizosphere competence: the genome of the ectomycorrhizal basidiomycete Laccaria bicolor also encodes a large set of SSCPs, which accumulate in the hyphae that colonize the host root .
Gene expansions in Tv and Ta that do not occur in Tr may comprise genes specific for mycoparasitism. As a prominent example, proteases have expanded in Ta and Tv, supporting the hypothesis that the degradation of proteins is a major trait of mycoparasites . Likewise, the increase in chitinolytic enzymes and some ß-glucanase-containing GH families is remarkable and illustrates the importance of destruction of the prey's cell wall in this process. With respect to the chitinases, the expansion of those bearing CBM50 modules was particularly remarkable: proteins containing these modules were recently classified into several different groups by de Jonge and Thomma . Proteins that consist solely of CBM50 modules are type-A LysM proteins, and there is evidence for the role of these as virulence factors in plant pathogenic fungi. The high numbers of LysM proteins that are found in Trichoderma, however, indicate other/additional roles for these proteins in fungal biology that are not understood yet. Also, the expansion of the GH75 chitosanases was intriguing: chitosan is a partially deacetylated derivative of chitin and, depending on the fungal species and the growth conditions, in mature fungal cell walls chitin is partially deacetylated. It has also been reported that fungi deacetylate chitin as a defense mechanism [45, 46]. Chitosan degradation may therefore be a relevant aspect of mycoparasitism and fungal cell wall degradation that has also not been regarded yet. Overall, the carbohydrate-active enzyme machinery present in Trichoderma is compatible with saprophytic behavior but, interestingly, the set of enzymes involved in the degradation of 'softer' plant cell wall components, such as pectin, is reduced. A possible plant symbiotic relationship  might rely on a mycoparasitic capacity along with a reduced specificity for pectin, minimizing the plant defense reaction.
Although the genes encoding proteins for the synthesis of typical fungal secondary metabolites (PKS, NRPS, PKS-NRPS) are also abundant, they are not significantly more expanded than in some other fungi. An exception is Tv and its 28 NRPS genes. However, our genome analysis revealed also a high number of oxidoreductases, cytochrome P450 oxidases, and other enzymes that could be part of as yet unknown pathways for the synthesis of further secondary metabolites. In support of this, several of these genes were found to be clustered in the genome (data not shown), and were more abundant in the two mycoparasitic species Ta and Tv. Together with the expanded set of oxidoreductases, monooxygenases, and enzymes for AMP activation of acids, phosphopathetheine attachment, and synthesis of isoquinoline alkaloids in Ta and Tv, these genes may define new secondary metabolite biosynthetic routes.