Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

André M. Machado
ORCID logo ,
Ole K. Tørresen
,
Naoki Kabeya
ORCID logo ,
Alvarina Couto
,
Bent Petersen
ORCID logo ,
Mónica Felício
,
Paula F. Campos
,
Elza Fonseca
,
Narcisa Bandarra
,
Mónica Lopes-Marques
,
Renato Ferraz
,
Raquel Ruivo
ORCID logo ,
Miguel M. Fonseca
,
Sissel Jentoft
* ORCID logo ,
Óscar Monroig
* ,
Rute Da Fonseca
* ,
L. Filipe C. Castro
*
Version 1 : Received: 10 September 2018 / Approved: 10 September 2018 / Online: 10 September 2018 (12:37:23 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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.

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 25579 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, an essential resource for their effective conservation, management and sustainable exploitation.

Keywords

European sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturated fatty acids

Subject

Biology and Life Sciences, Animal Science, Veterinary Science and Zoology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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