The use of -omic tools in the study of disease processes in marine bivalve mollusks
Graphical abstract
Introduction
The -omic-based disciplines focus on the analysis of structure and function of the genetic material (genomics and epigenomics), expressed genes (transcriptomics), proteins (proteomics), and low molecular weight metabolites (metabolomics) in an organism using an array of recently developed analytical high-throughput technologies. Additionally, these techniques allow for the study of species composition or expressed gene pathways in a complex mix of microorganisms (metagenomics/metatranscriptomics). These technologies have allowed researchers to better determine the complex relationships between genotypes, phenotypes, and the environment by simultaneously analyzing large numbers of individuals, genes, proteins, or metabolites in samples directly collected from the environment (reviewed in Carvalho and Creer, 2010). Therefore, these tools are particularly suited to study the complex interactions between hosts, pathogens, and the environment that lead to disease outbreaks (Fig. 1). In recent decades, there has been an explosion of the application of -omic technologies to address fundamental and applied research questions in human and veterinary medicine, from elucidation of novel mechanisms of immunity in model and non-model host species (Dheilly et al., 2014) to applications of whole-genome sequencing of pathogens to the development of diagnostic, prevention, and treatment tools (Firth and Lipkin, 2013). This explosion has been facilitated by the development of tools for the analysis of genomes of non-model species, as well as the decrease in the cost of high-throughput analysis technologies.
The field of aquatic pathology has benefited from these major investments in studying the genomes, transcriptomes, and, to a lesser extent, the proteomes, metabolomes, and epigenomes of species of commercial and ecological interest. These tools have been also applied to the study of key pathogens causing major mortalities in these species. This review builds upon and expands several excellent reviews on the -omics of bivalve species (Cancela et al., 2010, Gestal et al., 2008, Guo et al., 2008, Peng, 2013, Rodrigues et al., 2012, Romero et al., 2012, Saavedra and Bachère, 2006, Schmitt et al., 2012, Suárez-Ulloa et al., 2013, Wang et al., 2013, Yue, 2014) to provide some examples on how -omic tools have been used in the study of immunity and host–pathogen interactions in molluscan bivalves, and how this knowledge has been applied to two key areas in the management of the impact of infectious diseases on wild and cultured populations of these species: (a) the development of disease resistant strains (Section 5); and (b) the development of diagnostic tools (Section 8).
Section snippets
Genetic and genomic resources available for disease research and management in bivalve species
Most of the health management issues affecting marine bivalve molluscs can be addressed through improved knowledge of (1) the genetic mechanisms underlying relevant traits such as fast growth (which reduces risks to some disease-related losses by decreasing harvest time) and resistance/tolerance to diseases, (2) existing environmental stressors and anticipated stressors resulting from environmental change, and (3) the ability of bivalves to limit the uptake and accumulation of human pathogens
The application of -omic tools to the study of bivalve immunity
Studies on the patterns of gene expression in bivalves in response to disease challenge have used medium-throughput approaches to sequencing and analysis of gene expression including EST analysis, suppression subtractive hybridization, microarrays and, more recently, high-throughput RNAseq (Table 1). This recent burst in bivalve transcriptome studies focused on responses to pathogens have led to the extensive characterization of immune-related genes in several bivalve species (Fig. 2),
The application of -omic tools to the study of host–pathogen interactions in bivalves
Transcriptomic and proteomic studies have also significantly increased our understanding of host–pathogen interactions in marine bivalves. In this section, we provide some examples on how these technologies have been applied to the study of bivalve responses to viral, bacterial, and parasitic challenge and attempt to summarize the most general findings from these studies.
Application of -omic tools to the study of mechanisms of disease resistance in bivalves
Functional genomics and proteomics methods can take advantage of the availability of disease-resistant families or lines to evaluate potential genes and processes involved in disease resistance. For example, candidate genes potentially associated with disease resistance to OsHV-1 identified through these studies include a superoxide dismutase [Cu–Zn] and inhibitor of NF-kappaB 2 (Green and Montagnani, 2013, Normand et al., 2014, Sauvage et al., 2010, Segarra et al., 2014c). Two studies, one
Functional genomics and proteomics of bivalve pathogens: mechanisms of immune avoidance
As expected, pathogens have co-evolved mechanisms to avoid and exploit immune defenses in bivalves (see for example review by Schmitt et al., 2012), and -omic tools can help provide insights into some of these mechanisms. The availability of cultures for bivalve pathogens allows for the study of in vitro responses of the pathogens to environmental stress or host extracts. Characterization of ESTs in P. marinus (Joseph et al., 2010) identified many genes potentially involved in the uptake,
Epigenomics, immunity, and disease processes in bivalves
Not all the heritable variation present in natural populations can be detected by differences in DNA sequences. Epigenetics is the science that studies those DNA sequence (genome)-independent changes that can result in phenotypic changes. Examples of epigenetic mechanisms include DNA methylation, non-coding RNAs, histone modifications and chromatin remodeling. These mechanisms alter gene expression without changing the underlying DNA sequence (Bogdanović, 2014, Cao, 2014).
Eukaryotic DNA
The use of -omic tools in pathogen identification and disease diagnosis
Another important area in bivalve health management potentially benefiting from -omic technologies is the area of diagnosis. Accurate and rapid diagnosis of pathogens is critical in the management of diseases and in studying infections and immune responses in host organisms. Diagnosis of diseases has been greatly improved by the development of molecular or genetic diagnostic tools. Robust end-point and quantitative PCR-based diagnostic protocols have been developed for all major bivalve
Metagenomics and population genomics
High-throughput sequencing technologies provide the ability to fully characterize the diversity of complex microbial populations in marine environments (the microbiomes), both at the taxonomic (e.g. DNA barcoding, sequencing of 16S or 18S rDNA libraries) and functional (e.g. metagenomics, metatranscriptomics, metabolite production, gene pathway analysis) levels without relying on culture techniques (Kuczynski et al., 2012, Sharpton, 2014). These powerful methods require relatively small amounts
Conclusions and future perspectives
Although the -omic resources available for marine bivalve molluscs pale in comparison to those for many model and commercially important vertebrate species, the rate at which new, low-cost, high-throughput genomic technologies are being developed has led to an expansion in the number of studies aimed at gaining a better understanding of disease processes in bivalves. The analysis of genomes and transcriptomes has revealed that many immune-related gene families are expanded in most bivalve taxa
Conflict of interest
The authors wish to disclose that there are no known conflicts of interest associated with this publication and there has been no significant financial support for this work that could have influenced its outcome.
Acknowledgements
The authors thank 2 anonymous reviewers for very useful editorial suggestions and the editors of this special issue for their invitation to write this review. We thank Springer Science and Business Media for their kind permission to reprint Fig. 2, published originally in Zhang et al. (2014a).
References (235)
- et al.
Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to brown ring disease
Fish Shellfish Immunol.
(2014) - et al.
Dinoflagellate phylogeny revisited: using ribosomal proteins to resolve deep branching dinoflagellate clades
Mol. Phylogenet. Evol.
(2014) - et al.
Identification of Mytilus edulis genetic regulators during early development
Gene
(2014) - et al.
New tools for the study and direct surveillance of viral pathogens in water
Curr. Opin. Biotechnol., Energy Biotechnol./Environ. Biotechnol.
(2008) - et al.
Transcriptomic analysis of Ruditapes philippinarum hemocytes reveals cytoskeleton disruption after in vitro Vibrio tapetis challenge
Dev. Comp. Immunol.
(2012) - et al.
Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in Rhizaria
Curr. Biol.
(2013) - et al.
An analysis of dinoflagellate metabolism using EST data
Protist
(2013) - et al.
Deep sequencing-based transcriptome profiling analysis of Chlamys farreri exposed to benzo[a]pyrene
Gene
(2014) - et al.
A preliminary study of differentially expressed genes of the scallop Chlamys farreri against acute viral necrobiotic virus (AVNV)
Fish Shellfish Immunol.
(2013) - et al.
Bioinformatics analysis of hemocyte miRNAs of scallop Chlamys farreri against acute viral necrobiotic virus (AVNV)
Fish Shellfish Immunol.
(2014)
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454
BMC Genomics
Proteomic signatures of the oyster metabolic response to herpesvirus OsHV-1 μVar infection
J. Proteomics
No more non-model species: the promise of next generation sequencing for comparative immunology
Dev. Comp. Immunol.
Proteomic analysis of eggs from Mytilus edulis females differing in mitochondrial DNA transmission mode
Mol. Cell. Proteomics
The galectin CvGal1 from the eastern oyster (Crassostrea virginica) binds to blood group A oligosaccharides on the hemocyte surface
J. Biol. Chem.
Comparison of protein expression profiles between three Perkinsus spp., protozoan parasites of molluscs, through 2D electrophoresis and mass spectrometry
J. Invertebr. Pathol.
The effect of thermal stress on protein composition in dogwhelks (Nucella lapillus) under normoxic and hyperoxic conditions
Comp. Biochem. Physiol. A
Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates
Curr. Biol.
Poly I: C induces a protective antiviral immune response in the Pacific oyster (Crassostrea gigas) against subsequent challenge with Ostreid herpesvirus (OsHV-1 μvar)
Fish Shellfish Immunol.
Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas
Gene
Chapter nine – preparation and metatranscriptomic analyses of host-microbe systems
Mutation in promoter region of a serine protease inhibitor confers Perkinsus marinus resistance in the eastern oyster (Crassostrea virginica)
Fish Shellfish Immunol.
Comparative proteomic analysis of challenged zhikong scallop (Chlamys farreri): a new insight into the anti-Vibrio immune response of marine bivalves
Fish Shellfish Immunol.
Identification of differentially expressed proteins involved in the early larval development of the Pacific oyster Crassostrea gigas
J. Proteomics
Age-dependent expression of stress and antimicrobial genes in the hemocytes and siphon tissue of the Antarctic bivalve, Laternula elliptica, exposed to injury and starvation
Cell Stress Chaperones
Differential expression of genes involved in immunity and biomineralization during brown ring disease development and shell repair in the Manila clam, Ruditapes philippinarum
J. Invertebr. Pathol.
Responses of Mytilus galloprovincialis to bacterial challenges by metabolomics and proteomics
Fish Shellfish Immunol.
In silico whole genome EST analysis reveals 2322 novel microsatellites for the silver-lipped pearl oyster, Pinctada maxima
Mar. Genomics
Analysis of EST and lectin expressions in hemocytes of Manila clams (Ruditapes philippinarum) (Bivalvia: Mollusca) infected with Perkinsus olseni
Dev. Comp. Immunol.
Yields of cultured Pacific oysters Crassostrea gigas Thunberg improved after one generation of selection
Aquaculture
Serine protease inhibitor cvSI-1 potential role in the eastern oyster host defense against the protozoan parasite Perkinsus marinus
Developmental Comparative Immunol.
Oysters as hot spots for mimivirus isolation
Arch. Virol.
Evidence for interspecies transmission of oyster herpesvirus in marine bivalves
J. Gen. Virol.
Molecular cloning and copy number variation of a ferritin subunit (Fth1) and its association with growth in freshwater pearl mussel Hyriopsis cumingii
PLoS One
High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus
BMC Genomics
Invertebrate epigenomics: the brave new world of the spineless
Briefings Funct. Genomics
Genetic variability and selective breeding for traits of aquacultural interest in the Pacific oyster (Crassostrea gigas)
Bull. Aquaculture Assoc. Canada
Tailored microarray platform for the detection of marine toxins
Environ. Sci. Technol.
Diversity of animal immune receptors and the origins of recognition complexity in the deuterostomes
Dev. Comp. Immunol.
Can selective breeding reduce the heavy metal content of Pacific oysters (Crassostrea gigas) and are trade-offs with growth or survival?
J. Shellfish Res.
Genomic approaches in aquaculture and fisheries
The functional role of long non-coding RNAs and epigenetics
Biol. Proc. Online
Eight PCR primers to amplify EST-linked microsatellites in the Eastern oyster, Crassostrea virginica genome
Mol. Ecol. Notes
Mass mortality in Pacific oysters is associated with a specific gene expression signature
Mol. Ecol.
The transcriptomic responses of the eastern oyster, Crassostrea virginica, to environmental conditions
Mol. Ecol.
Metagenomic assessment of the eastern oyster-associated microbiota
Genome Announc.
Eukaryotic DNA methylation as an evolutionary device
BioEssays
A view on the role of epigenetics in the biology of malaria parasites
PLoS Pathog.
New resources for marine genomics: bacterial artificial chromosome libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas)
Mar. Biotechnol.
Cited by (45)
Search for new biomarkers of tolerance to Perkinsus olseni parasite infection in Ruditapes decussatus clams
2023, Fish and Shellfish ImmunologyWithering syndrome induced gene expression changes and a de-novo transcriptome for the Pinto abalone, Haliotis kamtschatkana
2022, Comparative Biochemistry and Physiology - Part D: Genomics and ProteomicsCitation Excerpt :This combined approach can be especially useful when attempting to understand the complex interactions between host, pathogen, and environment (Gomez-Chiarri et al., 2015). For example, transcriptomic tools have been used to identify immune-related changes and function in response to pathogen challenges in bivalves, as well as the interaction of environmental impacts on disease resistance pathways (Gomez-Chiarri et al., 2015). Transcriptome analysis during infection can also highlight organ-specific changes caused by disease.
Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production
2019, Comparative Biochemistry and Physiology - Part D: Genomics and ProteomicsFrom the raw bar to the bench: Bivalves as models for human health
2019, Developmental and Comparative ImmunologyCitation Excerpt :Microbial dysbiosis in the marine environment and aquaculture is strongly associated with mortality events and disease (Egan and Gardiner, 2016). In response, high-throughput sequencing of microbiomes has been used as a tool for disease management of bivalve species of aquaculture interest (Bentzon-Tilia et al., 2016; Gómez-Chiarri et al., 2015a). Additional research is needed to decipher this crosstalk between the bivalve host's immune receptors and the microbiome.