title: The use of -omic tools in the study of disease processes in marine bivalve mollusks.
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 expansion 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 the 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 that 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.
authors.affiliation: Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, 169 CBLS, Kingston, RI 02881, USA. Electronic address: gomezchi@uri.edu.
authors.forename: Marta
authors.initials: M
authors.lastname: Gómez-Chiarri
authors.affiliation: Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA.
authors.forename: Ximing
authors.initials: X
authors.lastname: Guo
authors.affiliation: CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, 29680 Roscoff, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Tanguy
authors.affiliation: Key laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: He
authors.affiliation: USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, 469 CBLS, Kingston, RI 02881, USA.
authors.forename: Dina
authors.initials: D
authors.lastname: Proestou
mesh_terms: D000818:Animals; D049872:Bivalvia / Q000235:genetics*; D023281:Genomics; D054884:Host-Pathogen Interactions / Q000502:physiology*; D040901:Proteomics
keywords: Bivalve mollusk; Epigenomics; Genomics; Host–pathogen; Metagenomics; Proteomics