Filling Genomic Gaps in the Fungal Tree of Life

Abstract

Fungi are a massive and diverse group of organisms with the potential to produce many interesting and useful bioactive compounds and enzymes. Fungal genomes are used for the discovery of these compounds and enzymes, to research the evolutionary history of the fungal kingdom and biological processes. Less than one percent of all described fungal species have a reference genome available. Filling these gaps may result in the discovery of interesting novel pathways, enzymes and contribute to our understanding of fungal evolution. To fill these gaps, the genome assemblies of five selected type-strains from understudied families were subjected to comparative genomics analyses. First, the ArboPhyl phylogenomics workflow was created, using BUSCO-based phylogeny to accurately place the five species into the fungal tree of life. While the taxonomy of the five species was confirmed, one of them proved to be a new species which was named Thyridium absconditum, providing the Thyridiales order with a near chromosome level assembly of a type-strain. The tool TeloVision was developed to detect telomeres in the assemblies. TeloVision successfully detected a wide range of telomeric repeats (H. sapiens, A. thaliana, C. elegans, and various fungi) and has proven to be a useful tool for visualising genome assemblies. Finally, HighGene was developed to highlight gene content variation between related species. The principle relies on calculating a z-score to compare the abundance of functional classes between species and highlight outliers. Applied to KEGG, KOG, CAZymes, peptidases and transcription factor domains, a high number of plant biomass degradation related CAZymes were highlighted in multiple species. The developed tools can facilitate similar types of research in the future, and TeloVision might open avenues for telomeric research. The results of this work show that filling gaps in the fungal tree of life can lead to the discovery of new enzymes within families as well as providing support for the association between a species’ lifestyle and their genomic content.