Using evolutionary gene networks to investigate genomic modifications in response to a parasitic lifestyle


Thursday, May 12, 2011
Redfield Auditorium - 12:00 Noon
Dr. Chris Lane
Assistant Professor Department of Biological Sciences
University of Rhode Island

Over the last 5 years, the cost of sequencing DNA has plummeted while the output of a new wave of "next generation" sequencers has increased on a nearly logarithmic scale. The confluence of these factors has made large-scale sequencing projects, including metagenomics and full eukaryotic genome sequencing, available to individual labs on reasonable budget. As a result, there has been an explosion of sequence data in public databases and comparative genomic studies are being enabled beyond "model" organisms. With the infusion of data, however, it is critical to devise strategies to effectively utilize the large number of sequences. Evolutionary Gene Networks (EGNs) are a fast and efficient tool for the comparative analysis of genomic data that enable the user to visualize data on a broad scale. These networks can be employed at the sequence assembly stage to verify quality, or serve to compare genes and gene families across a wide range of taxa. We have used EGNs to assemble and analyze the genome of the facultative pathogenic oomycete Achlya hypogyna and the proteome of the free-living oomycete Thraustotheca clavata. In comparison with several obligate oomycete pathogens, our data indicate that gene family evolution is highly correlated with life style.