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Genes 2018, 9(10), 485; https://doi.org/10.3390/genes9100485

Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

1
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal
2
Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
3
Department of Aquatic Bioscience, The University of Tokyo, Tokyo 113-8654, Japan
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
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
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
These co-first authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 4 September 2018 / Revised: 1 October 2018 / Accepted: 2 October 2018 / Published: 9 October 2018
(This article belongs to the Section Animal Genetics and Genomics)
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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 omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation. View Full-Text
Keywords: European sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturated fatty acids European sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturated fatty acids
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Machado, A.M.; Tørresen, O.K.; Kabeya, N.; Couto, A.; Petersen, B.; Felício, M.; Campos, P.F.; Fonseca, E.; Bandarra, N.; Lopes-Marques, M.; Ferraz, R.; Ruivo, R.; Fonseca, M.M.; Jentoft, S.; Monroig, Ó.; da Fonseca, R.R.; C. Castro, L.F. “Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes 2018, 9, 485.

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