{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T04:26:46Z","timestamp":1772252806696,"version":"3.50.1"},"reference-count":63,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T00:00:00Z","timestamp":1539043200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NORTE2020","award":["NORTE-01-0145-FEDER-000031"],"award-info":[{"award-number":["NORTE-01-0145-FEDER-000031"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/genes9100485","type":"journal-article","created":{"date-parts":[[2018,10,9]],"date-time":"2018-10-09T11:10:44Z","timestamp":1539083444000},"page":"485","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["\u201cOut of the Can\u201d: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6857-7581","authenticated-orcid":false,"given":"Andr\u00e9 M.","family":"Machado","sequence":"first","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1932-8212","authenticated-orcid":false,"given":"Ole K.","family":"T\u00f8rresen","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2055-6554","authenticated-orcid":false,"given":"Naoki","family":"Kabeya","sequence":"additional","affiliation":[{"name":"Department of Aquatic Bioscience, The University of Tokyo, Tokyo 113-8654, Japan"}]},{"given":"Alvarina","family":"Couto","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"},{"name":"The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2472-8317","authenticated-orcid":false,"given":"Bent","family":"Petersen","sequence":"additional","affiliation":[{"name":"Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark"},{"name":"Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah 08000, Malaysia"}]},{"given":"M\u00f3nica","family":"Fel\u00edcio","sequence":"additional","affiliation":[{"name":"Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal"}]},{"given":"Paula F.","family":"Campos","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"},{"name":"The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark"}]},{"given":"Elza","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal"}]},{"given":"Narcisa","family":"Bandarra","sequence":"additional","affiliation":[{"name":"Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal"}]},{"given":"M\u00f3nica","family":"Lopes-Marques","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"}]},{"given":"Renato","family":"Ferraz","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"},{"name":"Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4099-022 Porto, Portugal"}]},{"given":"Raquel","family":"Ruivo","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"}]},{"given":"Miguel M.","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8707-531X","authenticated-orcid":false,"given":"Sissel","family":"Jentoft","sequence":"additional","affiliation":[{"name":"Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway"},{"name":"Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630 Kristiansand, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8712-0440","authenticated-orcid":false,"given":"\u00d3scar","family":"Monroig","sequence":"additional","affiliation":[{"name":"Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Cient\u00edficas (IATS-CSIC), 12595 Ribera de Cabanes, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2805-4698","authenticated-orcid":false,"given":"Rute R.","family":"Da Fonseca","sequence":"additional","affiliation":[{"name":"The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark"},{"name":"Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark"}]},{"given":"L. Filipe","family":"C. Castro","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2018,10,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1146\/annurev-animal-030117-014821","article-title":"The divergent genomes of teleosts","volume":"6","author":"Ravi","year":"2018","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"6249","DOI":"10.1073\/pnas.1719358115","article-title":"Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data","volume":"115","author":"Hughes","year":"2018","journal-title":"Proc. Natl. Acad. Sci. 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