Diversity of eukaryotics is far greater than most people realize. In the Yuanning-Li lab, we are trying to use DNA records to study patterns and process of eukaryotic evolution on different time scales and with different types of genomic information. Combining a molecular systematic and/or genomic approach with information from organismal evolution has proved a powerful approach to study everything from the origin of major eukaryotic lineages (especially for marine invertebrates and fungi) to the recent adaptation to deep-sea chemosynthetic environments. Research in the lab focuses on utilizing computational approaches and genome-scale data to gain insight into molecular phylogenetics, evolutionary biology, comparative genomics, and bioinformatics.
We analyzed 120 budding yeast genomes to examine evolution of genome organization.
Budding yeasts exhibit lower macrosynteny than animals and filamentous fungi.
Budding yeasts exhibit high levels of microsynteny conservation on par with mammals.
Genes in metabolic clusters are deeply conserved across the subphylum.
Genome-scale phylogeny of the fungal kingdom based on 290 genes and 1,644 species
85% of inferred phylogenetic relationships among fungi are robustly supported
Certain unresolved relationships may be due to ancient diversification events
Fungal higher rank taxonomy broadly reflects organisms' genome sequence divergence