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“Out of the can”: a draft genome assembly, liver transcriptome, and nutrigenomics of the european sardine, sardina pilchardus

AuthorsMachado, André M.; Tørresen, Ole K.; Kabeya, Naoki; Couto, Alvarina; Petersen, Bent; Felício, Mónica; Campos, Paula F.; Fonseca, Elza; Bandarra, Narcisa; Lopes-Marques, Mónica; Ferraz, Renato; Ruivo, Raquel; Fonseca, Miguel M.; Jentoft, Sissel; Monroig, Óscar ; da Fonseca, Rute R.; Castro, L. Filipe C.
KeywordsEuropean sardine
Draft genome
Comparative genomics
Long chain polyunsaturated fatty acids
Issue Date9-Oct-2018
PublisherMultidisciplinary Digital Publishing Institute
CitationGenes 9(10): 485 (2018)
AbstractClupeiformes, 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.
Publisher version (URL)https://doi.org/10.3390/genes9100485
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