Uncovering the Functional Genetics of Macroalgal Ulva Blooms using Transcriptome Analysis

Macroalgal Ulva is a bloom-forming genus of algae that has significantly impacted Narragansett Bay, Rhode Island. It has the capacity to accumulate large biomass during the summer months which negatively affects the environment and the economy of that region. U.compressa and U. rigida are the dominant species of Ulva impacting this area. Very little is known about the bloom dynamics due to the limited availability of genetic markers that can be used to identify the genetic make-up of individuals within the population. DNA obtained from U.rigida was sent to Washington State University to be sequenced on a PacBio third-generation sequencer. The data that we have received from this sequencing run is going to be used to create an initial genome assembly of that species. From there, the genome will be scanned to identify microsatellite regions that can be used to design primers which will help determine the genetic structure of the Ulva bloom. To identify the cause behind bloom-forming behavior, we are extracting RNA from both species and sequencing their transcriptome for gene expression analysis. Transcriptomes of three replicates from three different temperatures will be analyzed to identify a link between temperature and gene expression that influences bloom formation. Our goal is to use computational analysis to identify functional genes that show variation in sequences that may correlate to differences in temperature response. These functional genes will be validated by use of qRT-PCR.