Diatom Genomics and Transcriptomics
Main Goals
- to describe the genetic potential of marine diatom species (Genomics)
- to systematically quantify genes expressed within a diatom cell under different environmental conditions (Transcriptomics)
The combination of genomics and transcriptomics allows us to identify genes involved in short-term response and long-term acclimation to changing environmental conditions and to evaluate the potential of these genes as indicators of physiological status. This work will improve our understanding of diatom evolution and physiology, and reveal insights into how different diatoms are adapted to different environmental niches in the marine system.
Specific topics of interest include:
- Whole genome sequences for diatom: Thalassiosira pseudonana (completed, led by E. Virginia Armbrust), Phaeodactylum tricornutum (completed, external collaboration with Dr. Chris Bowler), Pseudo-nitzschia multiseries (sequencing underway, led by Micaela S. Parker and E. Virginia Armbrust), Fragilariopsis cylindrus (external collaboration with Dr. Thomas Mock)
- Expressed sequence tag (EST) libraries for Pseudo-nitzschia australis (led by Micaela S. Parker) and Thalassiosira pseudonana (external collaboration with Dr. Thomas Mock)
- Tiling and gene-specific microarrays for Thalassiosira pseudonana (external collaboration with Dr. Thomas Mock)
- Single nucleotide polymorphisms in Thalassiosira pseudonana (led by Vaughn Iverson)
Additional people involved in these projects include Ellen Lin (molecular biology), Rhonda Marohl (molecular biology), Chris Berthiaume (bioinformatics), , and Tiffany Truong (undergraduate).