Molecular physiology of copepods - from biomarkers to transcriptomes and back again

Planktonic copepods are a diverse and abundant group of small (~mm sized) aquatic animals that play a critical role in linking the base of the food chain with higher trophic levels. These invertebrates are a primary food source for marine fish larvae. Their ubiquitous presence is thus of vital importance for recruitment of fish stocks and also as promising live feed for finfish production in aquaculture. This paper reviews the application of molecular approaches to understanding copepod physiology, particularly in non-parasitic species. The review includes both targeted gene approaches and untargeted transcriptomic approaches, with suggestions for best practices in each case. Issues particularly relevant to studies of copepods include heterogeneity within species, morphologically cryptic species, experimental artifacts associated with sample handling, and limited annotation of copepod genes and transcripts. The emergence of high-throughput sequencing and associated increased availability of genomic and transcriptomic databases have presented a huge opportunity to advance knowledge of copepod physiology. The research community can leverage this opportunity through efforts to maintain or improve data accessibility, database annotation, and documentation of analytical pipelines.