Evolutionary Genomics of Nematode-Trapping Fungi

University dissertation from Lund University, Dept. of Biology

Abstract: Nematode-trapping fungi are ubiquitous, soil-living organisms with the ability to infect and kill nematodes. These fungi have developed specialized infection structures for the capture of nematodes. Many nematode species are parasites on plants and animals, which have resulted in an interest to use nematode-trapping fungi as biological control agents. Through bioinformatics approaches, I have used comparative genomics and transcriptomics (RNASeq) to gain insights into the evolution of parasitism in the nematode-trapping fungus, Monacrosporium haptotylum (Ascomycetes; Orbiliales). M. haptotylum is the second nematode-trapping fungus to have its genome sequenced. The genome assembly contains 40.4 million base pairs with 28x coverage and 10,959 predicted protein-encoding genes. Here, I report analyses of the knob forming species M. haptotylum genome in comparison with the net-forming species Arthrobotrys oligospora. The analysis showed that two genomic mechanisms are likely to be involved in the evolution of parasitism in nematode-trapping fungi. First, gene duplications leading to the expansion of gene families resulting in a large number of species-specific genes. Many of these genes were highly expressed and upregulated during infection. Second, the differential gene expression of orthologs between the two fungi during early stages of infection, suggest that differential gene expression has been an important mechanism for the evolution of parasitism in nematode-trapping fungi. Comparative studies of the genomes of the two nematode-trapping fungi with 14 other sequenced fungal genomes show that the lineages of M. haptotylum and A. oligospora diverged about 14-18 million years ago. A total of 7,455 proteins from M. haptotylum were clustered into 3,124 protein domain families and 7,555 proteins from A. oligospora into 3,782 protein domain families. Analysis of the M. haptotylum genome with other ascomycetes genomes revealed a large number of expanded protein families. The expanded gene families contained several peptidases, cell wall degrading enzymes, tyrosinases, and extracellular proteins with WSC and mucin domains. Many of these genes were highly upregulated and highly expressed during infection. In addition the transcripts encoding small-secreted proteins (SSPs) were also highly expressed during infection. In the second part of my thesis, the patterns and mechanisms for expansion and functional divergence of subtilisin-like serine proteases in nematode-trapping fungi were analyzed in more detail. Phylogenetic analyses showed that the genome of M. haptotylum contains many paralogs of these proteases that have arisen through gene duplication. Many of the serine proteases were highly expressed and regulated during infection. The genomic sequence of M. haptotylum and its comparison with A. oligospora has provided a first glimpse into the genomic basis of the evolution of parasitism in nematode-trapping fungi.