From Shiu Lab
We are interested in answering how genomic changes contribute to physiological diversity and adaptation using photosynthetic organisms and yeast as model systems. Particularly, our focus is on the influence of environmental perturbations, such as changes in the abiotic or biotic conditions or nutrient availability in shaping genomes.
Evolution of genome contents
- What is evolutionary pressure that shapes the differences we see between genomes?
- How frequently can new genes be generated? What are the mechanisms? Are these new genes evolutionarily transient or important in survival of the species?
- What is the significance of expression in regions between known genes?
Evolution of stress response
- How did stress response evolve over time, particular among genes that got duplicated?
- What is the molecular basis for stress response evolution? What is the influence of changes in cis-element, transcription factors, and epigenetic regulation?
- How frequent may novel responses arise? What is the mechanism? How do such novel responses affect survival?
For more information on our research in this area, please take a look at our Plant Physiology paper on the relationships between stress response and gene family evolution and our PLoS Genetics paper on how stress responses have evolved in the model plant, Arabidopsis thaliana.
- How can we predict stress responsive gene expression based on DNA sequence, in a condition, time, as well as cell-type specific manner?
- What is the influence of cis-elements location, copy number, and combinatorial relation on gene expression?
- What is the role of epigenetic modifications in the cis-regulatory code?
For more information on our research in this area, check out our PNAS paper analyzing stress expression data from Arabidopsis thaliana with systems biology approaches in the first comprehensive analysis of plant cis-regulatory code.
Algae as a model system to study stress biology and evolution
- How did algal gene content evolve as revealed through comparative studies of multiple genomes?
- What is the cis-regulatory code of algal gene expression under nutirent limitation?
- How did algal stress response and its regulatory mechanism evolve?
For more information about our research in this area, check out our Plant Physiology paper discussing how nitrogen deprivation affect gene expression in C. reinhardtii. Also, check out our collaborative project website on the Biological Foundation of Algal Biofuels.