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.

Generally detected genes in comparative transcriptomics in bivalves: Toward the identification of molecular markers of cellular stress response

“…decrease in lysosomal membrane stability, indicators of oxidative stress (lipid peroxidation and antioxidant enzyme activities) and genotoxicity (DNA integrity) (Moore et al, 2004). These biological effects are non-specific in regard to different groups of contaminants and highly sensitive to chemical stressors (Lehtonen and Schiedek, 2006;van der Oost et al, 2003). With corresponding to the general biological effects, responses to stress stimuli are supported by a more or less important reprogram of the gene expression, where a specific gene can be alternatively induced or suppressed depending on its physiological role, as demonstrated for yeast cells challenged with a set of stress agents (Gasch et al, 2000).…”

“…The last 10 years have seen the introduction and wide spread adoption of transcriptomic techniques used in comparative mRNA profiling studies for the identification of biomarkers for specific conditions of bivalves or components of biological processes and pathways (Li et al, 2013;Suárez-Ulloa et al, 2013). On the basis of these transcriptomic studies, we performed a meta-analysis with current comparative transcriptional data of bivalves, in order to explore the generally detected protein-coding genes and discuss the association of the genes with CRS in bivalves.…”

The genome of the Pacific oyster Crassostrea gigas brings new insights on the massive expansion of the C1q gene family in Bivalvia

“…Based on a comparative transcriptomics analysis, we have hypothesized that a massive expansion event occurred in the class Bivalvia independently from the establishment of a large complement of C1qDC genes in the Chordates lineage (Gerdol et al, 2011). The increasing accessibility of RNA-seq datasets from non-model organisms and the recent release of the Crassostrea gigas, Pinctada fucata and M. galloprovincialis draft genomes (Nguyen et al, 2014;Takeuchi et al, 2012;Zhang et al, 2012) are leading to the explosion of bivalve-omics, making deeper investigations finally possible (Suárez-Ulloa et al, 2013). Taking advantage of the valuable oyster genome data, we have investigated the expansion of the C1qDC gene family in bivalves, their functional and structural diversification and their expression levels during development and in adult tissues.…”

Toxicological effects of benzo(a)pyrene, DDT and their mixture on the green mussel Perna viridis revealed by proteomic and metabolomic approaches

“…"Omics" approaches (Su arez- Ulloa et al, 2013) can help reveal the toxicological mechanism of pollutants and identify the broader ranges of biomarkers at molecular levels (Ji et al, 2013c;Li et al, 2006;Wu et al, 2005;Wu and Wang, 2011;Zhang et al, 2011aZhang et al, , 2006. In the proteomic approach, two-dimensional electrophoresis (2-DE)-based proteomics remains widely applied to display complex functional protein networks because of its high resolution and low expense Wei et al, 2015).…”