Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds

Abstract

The extraordinary progress experienced by sequencing technologies and bioinformatics has made the development of omic studies virtually ubiquitous in all fields of life sciences nowadays. However, scientific attention has been quite unevenly distributed throughout the different branches of the tree of life, leaving molluscs, one of the most diverse animal groups, relatively unexplored and without representation within the narrow collection of well established model organisms. Within this Phylum, bivalve molluscs play a fundamental role in the functioning of the marine ecosystem, constitute very valuable commercial resources in aquaculture, and have been widely used as sentinel organisms in the biomonitoring of marine pollution. Yet, it has only been very recently that this complex group of organisms became a preferential subject for omic studies, posing new challenges for their integrative characterization. The present contribution aims to give a detailed insight into the state of the art of the omic studies and functional information analysis of bivalve molluscs, providing a timely perspective on the available data resources and on the current and prospective applications for the biomonitoring of harmful marine compounds.

Figure 1

Integrative omic studies constitute a powerful tool in addressing the links between environmental conditions, harmful effects and associated responses in marine bivalves. Environmental conditions affect different levels, starting from the genome and the state of the chromatin (epigenome). Changes on these levels influence gene expression and the pool of expressed mRNAs (transcriptome), which in turn has an obvious effect on protein synthesis (proteomics). The regulation of all these systems also produces modifications in the set of small metabolites produced by an organism (metabolome). Overall, the intricate interconnection among the different omes requires a holistic integrative approach in order to understand how organisms respond to changes in the surrounding environment.

Figure 2

Number of bioprojects registered at the NCBI database comparing traditional model organisms with two upcoming bivalve model organisms (the mussel M. galloprovincialis and the oyster C. gigas).

Figure 3

Process flow diagram of a NGS-based transcriptome analysis and potential applications for environmental biomonitoring. Specimens are subject to the desired experimental challenge and, upon collection, total RNA is extracted and sequenced using the technology of choice. Depending on the pre-existing genomic resources available for the organism of interest, sequencing reads are then mapped to an annotated reference genome or transcriptome to obtain read counts for each gene, and finally converted into digital gene expression data. The comparison of the gene expression profiles obtained from treated and control samples can lead to biological insights on the transcriptional response to the experimental stimulus, to the identification of potential gene expression biomarkers and also allows integrative analyses with other omic approaches (i.e., proteomics, metabolomics, etc.).