Phylogenomics and systematics studies in Ustilaginomycotina
Ustilaginomycotina contains a diverse group of basidiomycetous fungi that are primarily comprised of biotrophic pathogens, the so-called “smut fungi”. The smut fungi are one of the most important groups of phytopathogens infecting several economic crops such as corn, wheat and sugarcane. In addition to smut fungi, recent phylogenetic studies have shown that Ustilaginomycotina also contains allied taxa such as non-smut phytopathogens, animal pathogens and yeast species for which a pathogenic stage is not known. Currently, the subphylum comprises ca. 1700 species belonging to 12 orders and four classes. However, ordinal-level relationships for this group are unresolved, which creates an obstacle for exploring their Biology in broader contexts such as evolutionary histories of pathogenicity, host specificity and fungal dimorphism. An additional obstacle is the lack of reference genomic data for fungal species in Ustilaginomycotina. Thus, for this project, whole genome sequences for eight Ustilaginomycotina species, representing various trophic strategies across six orders, were generated through the 1000 Fungal Genome Project. Because three of the selected taxa were new to science, three new species and one new genus are also described based on molecular, morphological, cytological and physiological data. all available genomic data from public databases and newly generated genomes were utilized for phylogenomic reconstruction. Total number of 19 species, 14 from Ustilaginomycotina, three from Agaricomycotina and two from Pucciniomycotina, were included in the final analyses. A bioinformatics pipeline was designed for single-copy orthology screening, sequence alignment and phylogenetic tree reconstruction. Starting from a subset of 246 orthologs from the Fungal Phylogenomic Database (FunyBASE), the final 93 protein models were selected for species tree reconstruction using three different strategies: concatenation and maximum-likelihood; concatenation and parsimony; and species tree estimation from gene trees. The constructed phylogenomic tree was then used for expanded supertree analyses in order to place other taxa within Ustilaginomycotina that were without representative genomes. After resolving the ordinal-level relationships, the tree was used to test hypotheses regarding the origin and evolution of certain traits within Ustilaginomycotina. For instance, these data suggest that teliospore formation and smut-like morphology are likely to be synapomorphic characters in Ustilaginomycotina, and there are subsequent derivations to two specific developmental types, the Ustilago type in Ustilaginales and the Tilletia type in Tilletiales, Doassansiales and Entylomatales. Genome compaction is a striking feature of the sampled Ustilaginomycotina, compared to genomes from other basidiomycetous subphyla (Pucciniomycotina and Agaricomycotina). Genes related to pathogenicity and tumoriogenesis studied in U. maydis appear to be found only within Ustilaginaceae, suggesting these may have been arisen during specialization to grass species. In terms of reproductive biology, two mating-type loci are present in all studied taxa, but they are varied in several aspects such as placement in the genome, a copy number of mating genes in each locus, synteny conservation and encoded protein sequences.
Aime, Purdue University.
Off-Campus Purdue Users:
To access this dissertation, please log in to our