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

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 sustainableomics datasetexploitation.from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.

Funding: We acknowledge the North Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) that supported this research through the Coral—Sustainable Ocean Exploitation (reference NORTE-01-0145-FEDER-000036). R.R.d.F. thanks the Danish National Research Foundation for its support of the Center for Macroecology, Evolution, and Climate (grant DNRF96). Acknowledgments: Some computational work was performed on the Abel Supercomputing Cluster (Norwegian metacenter for High Performance Computing (NOTUR) and the University of Oslo) operated by the Research Computing Services group at USIT, the University of Oslo IT-department (http://www.hpc.uio.no/). We would like to thank Jette Bornholdt, Amal Al-Chaer and George Pacheco for help with laboratory procedures, and the Bioinformatics Center of the University of Copenhagen for providing laboratory space. This work is part of the CIIMAR-lead initiative Portugal-Fishomics.