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Pleuronectiformes) to Boost Aquaculture Production Edinburgh Research Explorer Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production Citation for published version: Robledo Sanchez, D, Hermida, M, Rubiolo, JA, Fernández, C, Blanco, A, Bouza, C & Martínez, P 2016, 'Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production', Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. https://doi.org/10.1016/j.cbd.2016.12.001 Digital Object Identifier (DOI): 10.1016/j.cbd.2016.12.001 Link: Link to publication record in Edinburgh Research Explorer Document Version: Peer reviewed version Published In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 01. Oct. 2021 ÔØ ÅÒÙ×Ö ÔØ Integrating genomic resources of flatfish (Pleuronectiformes) to boost aqua- culture production Diego Robledo, Miguel Hermida, Juan A. Rubiolo, Carlos Fern´andez, Andr´es Blanco, Carmen Bouza, Paulino Mart´ınez PII: S1744-117X(16)30091-0 DOI: doi:10.1016/j.cbd.2016.12.001 Reference: CBD 435 To appear in: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics Received date: 28 September 2016 Revised date: 9 December 2016 Accepted date: 13 December 2016 Please cite this article as: Robledo, Diego, Hermida, Miguel, Rubiolo, Juan A., Fern´andez, Carlos, Blanco, Andr´es, Bouza, Carmen, Mart´ınez, Paulino, Integrat- ing genomic resources of flatfish (Pleuronectiformes) to boost aquaculture produc- tion, Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics (2016), doi:10.1016/j.cbd.2016.12.001 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production Diego Robledoa, Miguel Hermidab, Juan A. Rubiolob, Carlos Fernándezb, Andrés Blancob, Carmen Bouzab, Paulino Martínezb* aDepartment of Zoology, Genetics and Physical Anthropology, Faculty of Biology (CIBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain bDepartment of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain Running title: Flatfish integrative genomics in aquaculture * Corresponding author Dr. Paulino Martínez Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade deACCEPTED Santiago de Compostela, MANUSCRIPT 27002 Lugo, Spain Tel/Fax: + 34 982822428 E-mail: [email protected] ACCEPTED MANUSCRIPT Abstract Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (> 210x coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2,500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification. ACCEPTED MANUSCRIPT Key words: Pleuronectiformes, aquaculture, genetic map, transcriptome, genome, comparative mapping, evolution ACCEPTED MANUSCRIPT Introduction Pleuronectiformes is an order of fish with special adaptations to demersal life. Their origin has been the focus of a long controversy since Darwin's time. Flatfish suffer a drastic metamorphosis from the bilateral symmetry of pelagic larvae to the flat morphology typical of the group, which represents its most oustanding adaptation to demersal life. Additionally, the sea bottom poses new environmental challenges as compared to pelagic life such as low light conditions, skin damage risk, and low temperature and oxygen concentration (Figueras et al., 2016). All available data suggest a quick adaptive radiation of this group ~40 MYA (Friedman, 2008), reflected by a high molecular evolutionary rate (Vernau et al., 1994; Castro et al., 2006) and major genomic reorganizations (Figueras et al., 2016). This probably explains the low inter- family/suborder statistical support reported in phylogenetic studies (Pardo et al., 2005; Azevedo et al., 2008), especially between the two suborders of the group, Psettoidei and Pleuronectoidei (Campbell et al., 2014). This low phylogenetic support has led some authors to not discard a polyphyletic origin of the group (Campbell et al., 2014). Genetic evidences on the diversification of flatfish adaptation to sea bottom have been reported from the whole genome sequencing projects of the tongue sole (Cynoglossus semilaevis; Chen et al., 2014) and the turbot (Scophthalmus maximus; Figueras et al., 2016), suggesting that different strategies may have been involved in the adaptation to a demersal lifestyle. Flatfish are a group of great commercial value. Fisheries of several flatfish species are exploited all overACCEPTED the world reaching a total MANUSCRIPT production of ~150,000 tonnes (Gibson et al., 2014). Reduction of captures as a consequence of fisheries exhaustion has , promoted flatfish aquaculture mainly in Europe and Asia (Cerdá and Manchado, 2013). Although the usual inland production of flatfish increases production costs, the high appreciation by consumers allows higher market prices, making it profitable. Flatfish aquaculture production increased from 52,005 tonnes in 2003 to 131,254 tonnes in 2014, with PR China and Spain as the leading countries (FAO, 2014). Production records of the main six farmed species indicate that turbot has the largest production (77,000 tonnes; (https://aquatrace.eu/leaflets/turbot), followed by Japanese flounder (Paralichthys olivaceus; 44,733 tonnes), and tongue sole (7,120 tonnes) (FAO, 2014). Other farmed species with high potential are Atlantic halibut (Hippoglossus ACCEPTED MANUSCRIPT hippoglossus; 1,327 tonnes), Senegalese sole (Solea senegalensis; 1,066 tonnes) and common sole (S. solea; 88 tonnes). Improving nutrition and growth, controlling reproduction and sex ratio, and obtaining disease resistant broodstock are transversal issues to improve flatfish production (Cerdá and Manchado, 2013). Specifically, larval viability is a major concern in Atlantic halibut (Shields et al., 1999); reproduction represents the main bottleneck for Senegalese and common soles (Imsland et al., 2003; Oliveira et al., 2011); obtaining more resistant or tolerant broodstock to some diseases is the main challenge for turbot (enteromyxosis and scuticociliatosis; Rodríguez-Ramilo et al., 2013; Robledo et al., 2014) and Japanese flounder (scuticociliatosis and lymphocystosis; Fuji et al., 2007; Kang and Kim, 2015); and sex control in turbot and tongue sole is highly relevant because of their size dimorphism in favour of females (Liao et al., 2014; Taboada et al., 2014a). An important but uneven effort has been done to understand the physiological, molecular and genetic basis of these traits in the different flatfish with the goal of improving production. Further, heritabilities have been estimated for growth-related traits to predict their response to selection in turbot (Gjerde et al., 1997; Guan et al., 2016), Japanese flounder (Liu et al., 2014), tongue sole (Liu et al., 2016) and common sole (Blonk et al., 2010), and genotype x environment interactions have been evaluated in turbot (Guan et al., 2016) and common sole (Mas-Muñoz et al., 2013). These and other
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