Ontogeny of bivalve immunity: assessing the potential of next‐generation sequencing techniques

Abstract

Living organisms are constantly evolving to secure their survival via adaptations at the molecular and cellular level. Most marine bivalves have microscopic planktonic larval stages until settlement to the benthic environment. These pelagic stages are generally more sensitive than their adult counterparts to environmental and pathogen threats. Adaptive capacities could improve survival of these early stages. Recent advancements in data mining and pipeline analysis should shed light on the currently unknown processes that occur during these first stages. Existing data on early stages are fragmented compared with the abundance of information available for adult. Exploring diversity through aquaculture and lessening the impact of common issues, for example, massive mortalities of larvae, especially within the current conditions of a changing climate, ultimately rests on our knowledge of the molecular processes responsible for phenotypic plasticity. Although it is somewhat difficult to assess immune mechanisms by tracking circulating immunocytes in larvae, studies on the development of immune processes are now feasible at the transcript level. Next-generation techniques offer outstanding solutions for wide-range transcriptome analysis. We present a short review of the early ontogeny of the immune system in marine bivalves, with particular focus on next-generation sequencing applications. Like all reviews of this nature, there is a trade-off between the depth of the coverage and the number of subjects discussed. We will thus restrict the scope to bivalve immunity and focus on the central concepts across a wide range of topics, that is, the ontogeny of immunity and advancements in molecular studies.

An updated molecular basis for mussel immunity

“…For these reasons, we have undertaken a revision of sequence and literature data to update our knowledge on the gene-encoded molecules shaping the strength and peculiarities of the innate responses of mussels in the context of their fluctuating holobiome. Starting from the first "immunome" description [20] and expanding the analysis to NGS datasets related to the blue mussel [13,21] and other bivalve species [22e24] we propose a step forward in the understanding of pathogen recognition and clearance in M. galloprovincialis. Since the de novo assembly of RNA-seq data can provide only a partial view of the genes involved in mussel immune responses, we have often used the Pacific oyster C. gigas genome for comparison.…”

Characterization of the <i>TRAF3IP1</i> gene in Yesso scallop (<i>Patinopecten yessoensis</i>) and its expression in response to bacterial challenge

“…The innate immune system is especially important to the survival of these organisms because they lack adaptive immunity (Bassim et al, 2015). With innate immunity, they have evolved elaborate mechanisms to protect themselves against pathogenic invasion.…”

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

“…Experiments were conducted on hatchery-reared animals and the task was to induce mortality through deficiency in ArA and EPA. Although studies to date have shown a direct nutritional effect on larvae and juvenile development (Thompson et al, 1993;Sánchez-Lazo and Martínez-Pita, 2014), it remains unclear which genes have a critical impact on growth and survival or which pathways are particularly implicated in vulnerability or resistance during early development (Bassim et al, 2014a). For this reason, we explored the association of the developmental changes of early larvae and the dynamic interactions of differentially expressed transcripts that may influence growth and mortality mechanisms.…”