Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Abstract

Background: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.

Results: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.

Conclusions: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

Figure 1

Distribution of orthologues of T. atroviride, T. virens and T. reesei. The Venn diagram shows the distribution found for the three species of Trichoderma.

Figure 2

Mycoparasitism is an ancient life style of Trichoderma. (a) Position of Ta, Tv and Tr within the genus Hypocrea/Trichoderma. The positions of Tr, Tv and Ta are 4, 29 and 97, respectively - shown in bold), and a few hallmark species are given by their names. For the identities of the other species, see the gene accession numbers (Materials and methods). (b) Bayesian phylogram based on the analysis of amino acid sequences of 100 orthologous syntenic proteins (MCMC, 1 million generations, 10,449 characters) in Tr, Tv, Ta, Gibberella zeae and Chaetomium globosum. Circles above nodes indicate 100% posterior probabilities and significant bootstrap coefficients. The numbers in the boxes between (a) and (b) indicate the genome sizes and gene counts and percentage net gain regarding Ta. Photoplates show the mycoparasitic reaction after the contact between Trichoderma species and Rhizoctonia solani. Trichoderma species are always on the left side; dashed lines indicate the position of Trichoderma overgrowth of R. solani.