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

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.

Functional characterization of fatty acyl desaturase Fads2 and Elovl5 elongase in the Boddart’s goggle-eyed goby,Boleophthalmus boddarti(Gobiidae) suggest an incapacity for long-chain polyunsaturated fatty acid biosynthesis

“…In most teleost, the Elovl5 elongates C18 and C20 PUFA at much higher rate than C22 PUFA, with the latter often at conversion rate of below 5%. While the capacity to elongate C22 PUFA seemed exclusive to Elovl2 rather than Elovl5, this paralog has only been isolated and characterised from salmonids and several clupeocephalan species (Agaba et al, 2004, Morais et al, 2009, Oboh et al, 2016, Machado et al, 2018, Ferraz et al, 2019). To date, elov5 from two euryhaline herbivorous species, spotted scat ( Scatophagus argus ) and rabbitfish ( Siganus canaliculatus ) have been reported to have moderate but measurable elongation capacity of C22 substrates (Monroig et al, 2012, Xie et al, 2016).…”

“…As for elongases, elovl5 is the principal ortholog isolated from various teleost species and is primarily responsible for the elongation of C18 and C20 PUFA substrates. Another ortholog, the elovl2 elongase participates in the Sprecher pathway and is limited to small number of species (Morais et al, 2009, Monroig et al, 2009, Oboh et al, 2016, Machado et al, 2018). The diversification of teleost Fads and Elovl is postulated to be the outcome of species adaptation towards the availability of LC-PUFA in their respective natural diet (Morais et al, 2012).…”

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

“…By closing several gaps within scaffolds and merging other scaffolds into longer and fewer scaffolds (117 259), this procedure resulted into a slightly longer genome size of 949.62 Mb, which slightly deflated the scaffold N50 length to 96.6 Kb (Table 2). The assembly metrics of the three assemblies are described in Table 2 together with a recently published Illumina paired-end assembled sardine genome (UP_Spi) [20]. The total assembly size of our genome (SP_G) is 950 Mb and the UP_Spi is 641 Mb (Table 2).…”

“…For the fourth iteration, GeneMark-ES v4.32 (GeneMark, RRID:SCR_011930) [33], a self-training gene prediction software, was executed and the resulting HMM file was integrated into the Maker pipeline. As further evidence for the annotation, in the last run of Maker, the genome was queried using blastx v2.7.1 (BLASTX, RRID:SCR_001653) (protein2genome parameter in Maker), against the deduced proteomes of herring (GCF_000966335.1), ( Clupea harengus , NCBI:txid7950, Fishbase ID:24) zebrafish ( Danio rerio , NCBI:txid7955, Fishbase ID:4653) (GCF_000002035.6), blind cave fish ( Astyanax mexicanus , NCBI:txid7994, Fishbase ID:2740) (GCF_000372685.2), European sardine [20] and all proteins from teleost fishes in the UniProtKB/Swiss-Prot database (UniProtKB, RRID:SCR_004426) [34]. After the five Maker runs the selected 40 777 genes models are the ab initio predictions supported by the transcriptome and proteome evidence.…”

“…We conducted a phylogenetic analysis of ray-finned fish (Actinopterygii) taxa based on 17 fish species. The sardine protein data set used in the phylogenetic analysis was obtained by querying the deduced proteins from our sardine genome against the one-to-one orthologous cluster dataset (106 proteins from 17 species) obtained from [20].…”