The use of –omic tools in the study of disease processes in marine bivalves

Authors: GOMEZ CHIARRI, MARTA - University Of Rhode Island; GUO, XIMING - Rutgers University; TANGUY, ARNAUD - National Council For Scientific Research-Cnrs; HE, YAN - Ocean University Of China; Proestou, Dina

Submitted to: Journal of Invertebrate Pathology
Publication Type: Review Article
Publication Acceptance Date: 5/5/2015
Publication Date: 5/25/2015
Citation: Gomez Chiarri, M., Guo, X., Tanguy, A., He, Y., Proestou, D.A. 2015. The use of –omic tools in the study of disease processes in marine bivalves. Journal of Invertebrate Pathology. 131, pp. 137-154.

Interpretive Summary: Several diseases hinder the productivity and profitability of the shellfish aquaculture industry, but how shellfish hosts and their respective pathogens interact is often poorly understood. A better knowledge of bivalve host-pathogen interactions is needed to inform and develop new approaches for disease management and increased productivity. Studies aimed at gaining a better understanding of disease processes in commercially important bivalves have increased exponentially due to the emergence and application of high-throughput genomic technologies. This review article provides a catalogue of the genetic and -omic tools available for bivalve species. Examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis.

Technical Abstract: Our understanding of disease processes and host-pathogen interactions in model species has benefited greatly from the application of medium and high-throughput genomic, metagenomic, epigenomic, transcriptomic, and proteomic analyses. The rate at which new, low-cost, high-throughput -omic technologies are being developed has also led to an exponential increase in the number of studies aimed at gaining a better understanding of disease processes in bivalves. This review provides a catalogue of the genetic and -omic tools available for bivalve species and examples of how -omics has contributed to the advancement of marine bivalve disease research, with a special focus in the areas of immunity, bivalve-pathogen interactions, mechanisms of disease resistance and pathogen virulence, and disease diagnosis. The analysis of bivalve genomes and transcriptomes has revealed that many immune and stress-related gene families are expanded in bivalve taxa examined thus far. In addition, the analysis of proteomes confirms that responses to infection are influenced by epigenetic, post-transcriptional, and post-translational modifications. The few studies performed in bivalves show epigenetic modifications are non-random, suggesting a role for epigenetics in regulating the interactions between bivalves and their environments. Despite the progress –omic tools have enabled in the field of marine bivalve disease processes, there is much more work to be done. To date, only three bivalve genomes have been sequenced completely, with assembly status at different levels of completion. Transcriptome datasets are relatively easy and inexpensive to generate, but their interpretation will benefit greatly from high quality genome assemblies and improved data analysis pipelines. Finally, metagenomic, epigenomic, proteomic, and metabolomic studies focused on bivalve disease processes are currently limited but their expansion should be facilitated as more transcriptome datasets and complete genome sequences become available for marine bivalve species.