Research projects

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Core interests

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.

Research foci

Evolution of genome contents

Genome size variation in major plant taxonomic groups.
There are 2,500 fold differences in plant genome size, ranging from ~60 million bases in Genlisea margaretae, a carnivorous plant, to 150 billion bases in Paris japonica, the canopy plant. Unlike other eukaryotes, plants also tend to have younger new genes in gene families than other species. With the increasing ease in sequencing and assessing expression of the entire genome of any species, many parts of the genomes that are between known genes are now found to be expressed. In this area, our questions are:
  • 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?

For more information, check out our Plant Physiology paper comparing the evolutionary patterns of all gene families in four plant species and our Genome Research paper on novel protein coding genes.

Evolution of stress response

Gain and loss of stress responses among duplicate genes.
Under stressful environment, the expression of hundreds to thousands of genes changes at once. This response is essential for setting up proper physiological and developmental programs in plants so they can survive in adverse environment. Thus, proper response to stress is most likely under significant amount of selective pressure. In this area, we are interested in the following core questions:
  • 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.

Cis-regulatory logic

CRC v3.jpg
How is gene expression regulated under stress? Substantial knowledge has accumulated on how short DNA motifs, cis-regulatory elements, in the promoter regions are involved in controlling gene expression. We are interested in deciphering the cis-regulatory code, i.e., how cis-elements work in concert to specify gene expression in response to stress. The main questions in this area are:
  • 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

Four model species we study in the lab.
Our lab use multiple model systems to address questions in stress biology and genome evolution including the model plant A. thaliana, budding yeast, a green algae Chlamydomonas reinhardtii, and a marine algae Nannochloropsis oceanica. Aside from serving as good unicellular models for photosynthetic species, they are important for understanding how oil accumulates in these algae under nutrient limitation condition with implications in algal biofuel production. Our questions are:
  • 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.