ECSRI Projects:

Shellfish RI 2009: High throughput genomics approach for immune-related marker identification in the Eastern oyster

Research conducted at University of Rhode Island, Kingston, RI
Principal Investigators: Marta Gómez-Chiarri, Dina Proestou, Chris Lane

The goal of this research is to improve our understanding of immunity and mechanisms of disease resistance in the Eastern oyster, Crassostrea virginica. Cultured oysters in the Northeast US are severely impacted by bacterial and parasitic pathogens, including the causative agents of juvenile oyster disease, dermo disease, and MSX disease.

Due to great diversity among and within groups of pathogens infecting oysters, key features of a successful immune response include high levels of diversity in the molecules capable of recognizing and responding to infectious bacteria and parasites. We will take advantage of advances in high-throughput sequencing technology and basic characteristics of the immune response to identify novel molecules involved in oyster immune defenses.

Previous sequencing-based approaches have been limited by the cost of sequencing. Furthermore, these previous efforts have used a limited number of tissues and/or organisms and, in general, have only been able to identify genes involved in immunity based on sequence identity to immune-related genes in other organisms.

However, many of the genes produced in oysters in response to infection are probably unknown or show low levels of identity to genes in other organisms. Our approach exploits several basic characteristics of an ideal immune system to identify novel genes involved in the immune response of oysters. These basic characteristics of immunity include:
a) rapid upregulation in response to immune challenge;
b) great diversity; and
c) flexibility (ability to respond to different pathogens in different environments).

We will construct and sequence libraries of genes produced in response to infection with two pathogens of oysters: a bacterial pathogen that causes juvenile oyster disease and the parasitic pathogen that causes dermo disease. We will sequence those libraries, and identify the genes common and unique to the response to the infection.

By sequencing and comparing the genes expressed in response to two different groups of oysters with the genes produced in non-infected oysters, we expect to collect a tremendous amount of data from a non-model organism at a relatively low cost in a short period of time. This information will substantially enhance our understanding of the molecular response to bacterial and parasitic infections in oysters.

The genomic resources for oysters have substantially expanded in the last five years and these data will provide another enormous advancement in the techniques that can be applied to this mainstay of oyster aquaculture in the US. The identification and annotation of genes involved in the general response of oysters to infection will be an important step in breeding a more resistant oyster strain that will increase the yield of farmers, while reducing the time to market.