Abstract
BackgroundThe European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.FindingsThe genome of a single female individual was sequenced using Illumina HiSeq X Ten 10x Genomics linked reads, generating 113.8 gigabase pairs of data. Three draft genomes were assembled: 2 haploid genomes with a total size of 935 megabase pairs (N50 103 kilobase pairs) each, and a consensus genome of total size 950 megabase pairs (N50 97 kilobase pairs). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of 11 tissues were sequenced to aid the functional annotation of the genome, resulting in 40,777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of >2.3 million phased single-nucleotide polymorphisms with heterozygous loci.ConclusionsA draft genome was obtained, despite a high level of sequence repeats and heterozygosity, which are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data will be a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.
Highlights
The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution
We provide a European sardine draft genome, an essential tool to assess the genetic structure of the sardine population(s) and for genetic studies of the life history and ecological traits of this small pelagic fish, which will be instrumental for conservation and fisheries management
Because the size of our genome (SP G) and UP Spi assembly sizes are of different orders of magnitude, in addition to N50 we present NG50 values [21] for an estimated genome size of 950 megabase pairs (Mb) (Table 2)
Summary
The European sardine (Sardina pilchardus Walbaum, 1792) (National Center for Biotechnology Information [NCBI]: txid27697, Fishbase ID:1350) (Fig. 1) is a small pelagic fish occurring in temperate boundary currents of the Northeast Atlantic down to Cape Verde off the west coast of Africa, and throughout the Mediterranean to the Black Sea [1]. Two subspecies are generally recognized: Sardina pilchardus pilchardus occupies the northeastern Atlantic and the North Sea whereas S. pilchardus sardina occupies the Mediterranean and Black seas, and the North African coasts south to Cape Verde, with a contact zone near the Strait of Gibraltar [1, 2].
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