Advances in genomics for flatfish aquaculture

Genes Nutr (2013) 8:5–17 DOI 10.1007/s12263-012-0312-8 REVIEW Advances in genomics for flatfish aquaculture Joan Cerdà • Manuel Manchado Received: 24 January 2012 / Accepted: 2 August 2012 / Published online: 19 August 2012 Ó Springer-Verlag 2012 Abstract Fish aquaculture is considered to be one of the most sustainable sources of protein for humans. Many different species are cultured worldwide, but among them, marine flatfishes comprise a group of teleosts of high commercial interest because of their highly prized white flesh. However, the aquaculture of these fishes is seriously hampered by the scarce knowledge on their biology. In recent years, various experimental ‘omics’ approaches have been applied to farmed flatfishes to increment the genomic resources available. These tools are beginning to identify genetic markers associated with traits of commercial interest, and to unravel the molecular basis of different physiological processes. This article summarizes recent advances in flatfish genomics research in Europe. We focus on the new generation sequencing technologies, which can produce a massive amount of DNA sequencing data, and discuss their potentials and applications for de novo genome sequencing and transcriptome analysis. The relevance of these methods in nutrigenomics and foodomics approaches for the production of healthy animals, as well as high quality and safety products for the consumer, is also briefly discussed. Special section: ‘‘Foodomics’’; Guest Editors Dr. A. Bordoni and F. Capozzi. J. Cerdà (&) Laboratory of Institut de Recerca i Tecnologia Agroalimentàries (IRTA)-Institut de Ciències del Mar, Consejo Superior de Investigaciones Cientı́ficas (CSIC), 08003 Barcelona, Spain e-mail: M. Manchado IFAPA Centro El Toruño, Junta de Andalucı́a, 11500 El Puerto de Santa Marı́a (Cádiz), Spain Keywords Genome sequencing
NGS technologies
Transcriptome
Microarray
Nutrigenomics Introduction Aquaculture is becoming an increasingly important source of fish protein available for human consumption. Fish meal is characterized by its high content in proteins and lipids (carbohydrates represent lower than 0.5 %) (Huss 1995). Although the chemical composition is highly dependent on the species, age, sex, environment, migratory behaviour or season, fish proteins represent a valuable source of essential amino acids including lysine, methionine and cysteine. By contrast, lipid content ranges between 0.3 and 45 % (w/w), but particularly in cold-water marine species of fish includes an important fraction (*40 %) of omega-3 polyunsaturated fatty acids (PUFAs) that have been associated with the prevention and treatment of cardiovascular disease, cancer and some other inflammatory disorders in humans (Hibbeln et al. 2006; Kolakowska et al. 2003). Moreover, fish meal carries other essential nutrients such as B vitamins as well as vitamin A and D in fatty fish, minerals (calcium and phosphorus) and some micronutrients essential for metabolism and endocrinological regulation such as iodine, fluorine and selenium. Different freshwater and marine fish species are being cultured worldwide, and among these, the flatfishes represent an important food resource. Flatfishes are considered as low-fat fish (2–4 % fat) with a firm, white, mild tasting flesh highly accepted by the consumers. As in other cold-water marine species of fish, they possess a high content of PUFAs such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids (71–93 mg EPA/100 g and 106–292 mg DHA/100 g) (Hibbeln et al. 2006). 123 6 Certain flatfishes, such as some flounders (Hippoglossoides dubius, H. pinetorum, Glyptocephalus stelleri) and plaice (Acanthopsetta nadeshnyi), have a high percentage of very long-chain 24:6(n-3) fatty acids (6–9 % of total fatty acids in the flesh) associated with their diet based on invertebrate such as polychaeta, crustaceans and molluscs (Ota et al. 1994). The possibility to transform them into fillets for multiple commercial preparations represents an added value that converts flatfish into a highly appreciated seafood product. Flatfishes comprise a relatively large group of fishes, mostly marine, which show unique developmental and reproductive processes. This includes a remarkable metamorphic alteration in bauplan during the larval to juvenile transition, and sophisticated courtship behaviours or unusual gametogenesis in the adults. However, the lack of basic knowledge of the control of these mechanisms hampers the farming of flatfishes and the establishment of a sustainable and profitable aquaculture industry. In recent years, different ‘omic’ technologies have been applied to flatfish research to enhance the knowledge of the biology of these species by unravelling the complex genetic control underlying different physiological processes. Although we are still some way from developing wide applications for flatfish aquaculture, it is expected that these ‘omics’ approaches will have a profound impact in the near future. In this short review, we summarize the advances in genomic research in flatfishes currently being cultured in Europe, and discuss the potentials and applications of new DNA sequencing technologies. The aquaculture of flatfish A total of 716 flatfish species belonging to 123 genera and about 11 families have been reported worldwide (reviewed by Munroe 2005). In the Northeast Atlantic area, there exist a total of 11 relevant species for fisheries belonging to the teleost order Pleuronectiformes. This includes Pleuronectidae, such as North Sea plaice (Pleuronectes platessa), Atlantic halibut (Hippoglossus hippoglossus) and winter flounder (Pseudopleuronectes americanus), Soleidae, such as the common sole (Solea solea) and Senegalese sole (S. senegalensis), and Bothidae, such as turbot (Scophthalmus maximus), brill (Scophthalmus rhombus) and megrim (Lepidorhombus whiffiagonis). In 1998, the number of flatfish landings in the Atlantic region reached 104,671 metric tons (MT) for plaice, 31,194 MT for common sole and 5,431 MT for turbot (Millner et al. 2005). However, due to their economic importance, increased fishing pressure has resulted in a drastic drop of flatfish landings with some difficulties to meet the current demands (ICES 2008). Also, overexploitation of wild stocks has 123 Genes Nutr (2013) 8:5–17 reduced genetic diversity in plaice (Hoarau et al. 2005), and is thought to underlie modified life-history traits with a shift towards earlier sexual maturation at smaller size in sole and plaice (Mollet et al. 2007; van Walraven et al. 2010). As a consequence, the development of aquaculture for some of these species has been proposed to supplement the demands for human consumption while reducing the pressure on natural populations. Currently, flatfish production is still much lower than that of salmonids or sea basses and sea breams. Within Europe, the main flatfishes being cultured are the turbot and Atlantic halibut, and a less (...truncated)