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A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina Pilchardus

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A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina Pilchardus G C A T T A C G G C A T genes Article “Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus André M. Machado 1,† , Ole K. Tørresen 2,† , Naoki Kabeya 3,† , Alvarina Couto 1,4, Bent Petersen 5,6 ,Mónica Felício 7, Paula F. Campos 1,4, Elza Fonseca 1,8, Narcisa Bandarra 7, Mónica Lopes-Marques 1, Renato Ferraz 1,9, Raquel Ruivo 1, Miguel M. Fonseca 1, Sissel Jentoft 2,10,* , Óscar Monroig 11,*, Rute R. da Fonseca 4,12,* and L. Filipe C. Castro 1,8,* 1 Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; [email protected] (A.M.M.); [email protected] (A.C.); [email protected] (P.F.C.); [email protected] (E.F.); [email protected] (M.L.-M.); [email protected] (R.F.); [email protected] (R.R.); [email protected] (M.M.F.) 2 Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway; [email protected] 3 Department of Aquatic Bioscience, The University of Tokyo, Tokyo 113-8654, Japan; [email protected] 4 The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark 5 Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark; [email protected] 6 Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah 08000, Malaysia 7 Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal; [email protected] (M.F.); [email protected] (N.B.) 8 Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal 9 Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4099-022 Porto, Portugal 10 Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630 Kristiansand, Norway 11 Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), 12595 Ribera de Cabanes, Spain 12 Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark * Correspondence: [email protected] (S.J.); [email protected] (Ó.M.); [email protected] (R.R.d.F.); fi[email protected] (L.F.C.C.) † These co-first authors contributed equally to this work. Received: 4 September 2018; Accepted: 2 October 2018; Published: 9 October 2018 Abstract: Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first Genes 2018, 9, 485; doi:10.3390/genes9100485 www.mdpi.com/journal/genes Genes 2018, 9, x FOR PEER REVIEW 2 of 13 Genes 2018, 9, 485 2 of 13 sardine, representing an essential resource for their effective conservation, management, and sustainableomics dataset exploitation. from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation. Keywords: European sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturatedKeywords: European fatty acids sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturated fatty acids 1. Introduction 1. Introduction Teleosts comprise the most species-rich group of vertebrates, with approximately 30,000 described speciesTeleosts [1]. During comprise the last the decades, most species-rich teleosts emerged group of as vertebrates, particularly with insightful approximately models 30,000for comparative described evolutionaryspecies [1]. During studies the [2]. last Moreover, decades, numerous teleosts emerged teleost fish as particularlyspecies are of insightful high commercial models for importance comparative for bothevolutionary fisheries studiesand aquaculture. [2]. Moreover, Fish numerousare not only teleost an important fish species source are ofof high protein commercial for human importance consumers, for butboth oily fisheries species and represent aquaculture. unique Fish sources are notof the only he analthy important omega-3 source long-chain of protein polyunsaturated for human consumers,fatty acids (LC-PUFAs),but oily species which represent have uniquebeen shown sources to of have the healthyessential omega-3 roles in long-chain cardiovascular polyunsaturated health and fattyneuronal acids development(LC-PUFAs), [3,4]. which Yet, have over-fishing been shown combined to have with essential global roleschanges in cardiovascularentail countless healththreats andto this neuronal taxon, makingdevelopment it an interesting [3,4]. Yet, target over-fishing for aquaculture combined which with already global provides changes approximately entail countless half threatsof the seafood to this consumedtaxon, making worldwide it an interesting [5]. The oily target fish forEuropean aquaculture sardine which (Sardina already pilchardus provides, Walbaum approximately 1792) (Figure half of 1) the is oneseafood of the consumed most commercially worldwide important [5]. The oilyspecies fish [6], European particularly sardine for the (Sardina canning pilchardus industry,, Walbaum and has 1792)high nutritional(Figure1) is value one ofprimarily the most linked commercially to its omega-3 important LC-PUFA species content. [ 6], particularly Interestingly, for the a steady canning and industry, sharp declineand has in high capture nutritional levels has value been primarily observed linked in the to last its omega-3decade, which LC-PUFA is currently content. dictating Interestingly, severe a cuts steady in fishingand sharp quotas decline within in capturethe European levels hasUnion been [7]. observed Recent inadvances the last decade,in captive which sardine is currently culture practices dictating representsevere cuts promising in fishing research quotas possibilities within the [8,9]; European however, Union the complete [7]. Recent absence advances of genomic in captive resources sardine from thisculture iconic practices species impose represents a severe promising bottleneck. research Genome possibilities data emer [8,ging9]; however, from high-thr the completeoughput sequencing absence of technologygenomic resources combined from with thismultiple iconic assembly species algorithms imposes a has severe represented bottleneck. a truly Genome transformative data emerging event in thefrom field high-throughput of comparative genomics sequencing [10]. technology Moreover, de combined novo assemblies with multiple based on assembly low coverage algorithms and short has readrepresented approaches a truly are transformativecost effective, and event provide in the valuable field of biological comparative information genomics [11–13] [10]. Moreover,. Here, we depresent novo theassemblies first draft based genome on low of the coverage European and sardine short read and approaches provide a relatively are cost effective, high-level and liver provide transcriptome valuable enablingbiological nutrigenomics information studies [11–13]. in Here, this iconic we present species. the The first genomic draft genome makeup ofof thethe EuropeanEuropean sardine was and furtherprovide compared a relatively to high-levelthat of other liver teleosts, transcriptome including enabling the closely nutrigenomics related clupeid, studies the Atlantic in this iconic herring species. [14]. AsThe a genomicproof of principle, makeup of we the selected European the sardineLC-PUFA was biosynthesis, further compared a metabolic to that pathway of other accounting teleosts, including for the productionthe closely relatedof omega-3 clupeid, fatty the acid Atlantic in fish herring[15], an [d14 characterized]. As a proof ofkey principle, genes with we selectedwell-established the LC-PUFA roles withinbiosynthesis, these pathways a metabolic [3,16]. pathway accounting for the production of omega-3 fatty acid in fish [15], and characterized key genes with well-established roles within these pathways [3,16]. Figure 1. Photograph of a specimen of European sardine, Sardina pilchardus (photograph credits to FigureMónica 1. Fel Photographício and Andr of aé M.specimen Machado). of European sardine, Sardina pilchardus (photograph credits to Mónica Felício and André M. Machado). 2. Methods, Results and Discussion 2. Methods, Results and Discussion 2.1. Sampling, DNA Extraction, Library Preparation
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