Reasearch
＜Course Outline＞
１）Developing a New Taxonomic Approach by Integrating Cutting-Edge Genomic Information Techniques with Classical Identification Approaches:
▶︎Unraveling by Genome: Yeasts are microorganisms that play essential roles in our lives through fermented products such as bread and alcohol, and as model organisms they are also a valuable research resource in fundamental biology. In addition, many diverse yeast species inhabit the natural environment. This project aims to link genomic information with phenotypic data to elucidate the relations between diverse yeast traits and their phylogeny.
▶Bundling by Genome: Despite being fungi, yeasts lack distinctive morphological features, so characterization of species and genera has relied mainly on physiological and biochemical characteristics. However, classification of filamentous fungi and mushrooms has been based mainly on morphological diversity. To construct a yeast taxonomic system that is consistent with the overall fungal taxonomy, we will use genomic information to unify the data of these different fields.
２）Continuously Updating and Verifying the Taxonomic System using the Developed Method:
▶Exploration with a Broad Perspective: Yeasts are taxonomically diverse fungi and include Ascomycota and Basidiomycota. By exploring the similarities and differences between yeasts and other fungi, and characterizing yeasts within the taxonomic system, we will approach the question of what type of fungi are yeasts.
▶ Investigating with a Sensitive Perspective: Even within the same yeast species, the characteristics of each strain vary. By clarifying these differences and identifying common characteristics, we aim to establish indicators of genetic proximity among strains and discover new functions in yeast strains that are essential for fermentation.
Research Theme 1: Developing a Yeast Taxonomic System Based on Genomic Information
▶Genomic information has become increasingly important in the taxonomy of bacteria and archaea. It allows the construction of robust phylogenetic trees and investigation of genetic distance by in-silico hybridization with closely related species when describing new species. This trend is now extending to fungi, including yeasts. This research will incorporate genomic information into yeast taxonomy to harmonize it with traditional data—such as physiological, biochemical, and morphological characteristics—and DNA-DNA hybridization experiments, for comprehensive classification.
Clarification of phylogenetic relationships is essential for building a taxonomic system. Traditionally, fungal phylogenetic trees have been constructed by examining the sequence divergence of single or multiple genes, such as the D1/D2 and ITS regions of ribosomal RNA genes, as well as RPB2. However, it has become clear that some fungal groups include problems, such as polyphyletic genera are dispersed across multiple phylogenetic groups. Our research aims to establish a robust backbone tree based on genomic information that provides a foundation for a taxonomic system encompassing yeasts and other fungi.
Based on genomic information from numerous species of ascomycetous and basidiomycetous yeasts, we will examine differences between the target group and other fungal groups from a new perspective, developing and validating markers for their identification and for characterizing yeasts. We will also explore new indicators of genetic proximity to represent species and to classify varieties, if needed, for further subdivision within species.
Research Theme 2: Development and Validation of a New Yeast Classification Method
▶Although yeasts and filamentous fungi (molds) are both fungi, different criteria have traditionally been used to identify their species and genera: filamentous fungi are classified primarily based on detailed morphological observations, whereas yeasts are classified based on physiological, biochemical, and chemotaxonomic characteristics. Recent studies on model organisms such as Saccharomyces cerevisiae and Aspergillus nidulans have begun to reveal connections between these phenotypic traits and genes. However, many phenotypic traits have not yet been evaluated as taxonomic criteria. By analyzing these traits across a broad range of yeast species, this project aims to develop a classification method applicable to both filamentous fungi and yeasts.
Some basidiomycetous yeasts have been reported to exhibit unique nuclear behavior: the nucleus migrates into the budding daughter cell before dividing. Therefore, the nuclear division patterns of basidiomycetous yeasts are thought to differ from those of ascomycetous yeasts such as S. cerevisiae. This study will investigate whether this nuclear behavior is common across all basidiomycetous yeasts, and whether any show nuclear division within the mother cell, similar to S. cerevisiae.
Filamentous fungi and mushrooms, which form mycelia, produce a variety of secondary metabolites and are closely linked to human life. Although yeasts are generally unicellular throughout most of their life cycle, some species form mycelia. We culture yeasts under various conditions to explore the diversity of mechanisms of mycelium formation, and investigate factors such as the culture environment and growth factors needed for mycelium formation in yeasts.