Digital Genome

 
 

 

Revolutionary progress in understanding plant biology is being driven through advances in DNA sequencing technology. The department has played a key role in the sequencing and genome annotation efforts of the model plant Arabidopsis thaliana and the soil alga Chlamydomonas reinhardtii. Now that many genomes from algae to mosses to trees are publicly available, this information can be mined using bioinformatics to build models. These models can be tested, ultimately with the goal of rational design of plants for a wide spectrum of applications.
 
Sue Rhee’s lab has pioneered a genome-wide gene association network Aranet that can assign functions to genes for which no function had previously been assigned (to date about 50% of the plant genome) by their associations with genes of known function. They are also building protein interaction and metabolic pathway networks in plants to systematically identify signaling and metabolic pathways and relationships among these pathways.
 
Eva Huala’s lab develops and applies ontologies and text mining methods to capture biological knowledge about the function of plant genes. The Huala lab also maintains and improves the Arabidopsis genome annotation and provides online bioinformatics tools allowing plant biologists worldwide to mine the rich Arabidopsis datasets.
 
Arthur Grossman’s lab uses the algal genomes to identify genes that are specific to the green lineage, the so-called Greencut, to uncover the yet unknown regulatory systems critical for photosynthetic function. The whole department has developed an interest in this approach as a tool to understand the evolution of multicellularity and sexual reproduction in the plant lineage, and the evolution of plant specific characters such as plasmodesmata and the interactions between plants and other organisms.