Evolution in Tremellomycetes

The Tremellales (Agaricomycotina, Basidiomycota, Fungi) are a very ecologically diverse group including human pathogens and a better knowledge of its ecology and evolutionary complexity will be of broad scientific interest. There are important aspects requiring study in the group: 1) they have a uniquely diverse range of nutritional habits, but little is still known on the evolution of them; 2) their biodiversity and speciation modes are still far from known, and need investigation, especially as fungal-inhabiting species represent a source of chemical compounds of therapeutic interest 3) most symbionts and parasitic species are host-specific, and there are interesting coevolutionary patterns to be clarified, and 4) hardly anything is known on the factors influencing specificity. These questions, require sound phylogenetic hypothesis both at deep and shallow levels. We will use target enrichment sequencing to generate a much-needed comprehensive phylogenetic hypothesis of the Tremellales as a whole, and in teo species complexes. Our aim is producing a bait design that can be used to construct phylogenetic hypotheses both at deep and shallow timescales in the Tremellales. Using our phylogenies, we will test the following hypotheses: 1: There are evolutionary connections between the nutritional habit, the mating system, the taxon-specific CAZYmes and proteolytic enzymes, and the genes involved in regulating the transitions between yeast and filamentous forms. 2: Animal parasitism, including human parasitism, appeared secondarily in the evolutionary story of the Tremellales. 3: Yeast growth is a derived stage along the Tremellales and yeast groups appeared secondarily because of a loss of the ability to form hyphae 4: Lichenicolous species in the Tremellaes are distributed in independent lineages, each of them deserving the description of a new genus. 5: Speciation of lichenicolus species of the Tremellales is driven by adaptations to their hosts. 6: Cell wall carbohydrates are related to host adaptation in the Tremellales and varies between the yeast and filamentous phases in two lichenicolous tremellalean species. This is the first time that a large phylogenomic study of the Tremellales is undertaken, including a good and balanced representation of all nutritional habits in the group. It is timely to do this because: 1) during the past years, lab and phylogenomic analyses methods have developed enormously allowing to work with genomic data from herbarium specimens and to avoid dependency on cultures or fresh material; 2) the knowledge of Tremellales diversity has dramatically improved in the past 10 years, resulting in a much more representative taxon sampling, 3) the number of sequenced and well-annotated genomes of tremellalean fungi has also remarkably increased representing almost all tremellalean families, and where thousands of orthologous relevant genes have already been identified in the genomes, which is a great advance regarding successful probe-design for target-capture.