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RESEARCH PRODUCT

An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming

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Abstract Recent advancements within state-of-the-art genomic tools and the generation of the first version of the Atlantic cod genome (Star et al., 2011) have proven to be valuable resources, improving our understanding of this species’ biology. In this chapter we describe some aspects and implications of using these resources to identify genes and molecular pathways involved in Atlantic cod growth and development, as well as responses to nutritional changes, pathogens and other immune stimuli, and environmental stressors (e.g., temperature, stress, or pollutants). Additionally, we highlight the immunological puzzle of the Atlantic cod that lacks components of the adaptive immune system previously thought to be an essential feature of all jawed vertebrates. Furthermore, we present a new and substantially improved version of the Atlantic cod genome by combining recent developments within bioinformatics tools and the inclusion of data from both short as well as long read sequencing technologies. The new version of the Atlantic cod genome will be of high impact; facilitating applied functional genomics research to improve our understanding of gene function and variants affecting important phenotypic traits such as growth, sexual maturation, and disease resistance. Moreover, large-scale resequencing efforts of selected specimens would further aid in deducing genomic effects of natural selection, identifying specific changes involved in local adaptation in the wild as well as in artificial selection related to breeding programs. This will allow for a systems biology approach where effects of a large number of gene variants (and regulatory pathways) can be causally related to phenotypic variation, for example, knowledge that will be crucial in selecting family material for the emerging cod aquaculture.