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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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>The 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 &amp;gt;2.3 million phased single-nucleotide polymorphisms with heterozygous loci.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>A 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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/gigascience\/giz059","type":"journal-article","created":{"date-parts":[[2019,5,21]],"date-time":"2019-05-21T23:56:35Z","timestamp":1558482995000},"source":"Crossref","is-referenced-by-count":16,"title":["A haplotype-resolved draft genome of the European sardine (\n                    <i>Sardina pilchardus<\/i>\n                    )"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8164-581X","authenticated-orcid":false,"given":"Bruno","family":"Louro","sequence":"first","affiliation":[{"name":"CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005\u2013139 Faro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5542-0278","authenticated-orcid":false,"given":"Gianluca","family":"De Moro","sequence":"additional","affiliation":[{"name":"CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005\u2013139 Faro, Portugal"}]},{"given":"Carlos","family":"Garcia","sequence":"additional","affiliation":[{"name":"CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005\u2013139 Faro, Portugal"}]},{"given":"Cymon J","family":"Cox","sequence":"additional","affiliation":[{"name":"CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005\u2013139 Faro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3396-9822","authenticated-orcid":false,"given":"Ana","family":"Ver\u00edssimo","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO, Laborat\u00f3rio Associado, Universidade do Porto, Vair\u00e3o, Portugal"}]},{"given":"Stephen J","family":"Sabatino","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO, Laborat\u00f3rio Associado, Universidade do Porto, Vair\u00e3o, Portugal"}]},{"given":"Ant\u00f3nio M","family":"Santos","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO, Laborat\u00f3rio Associado, Universidade do Porto, Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6244-6468","authenticated-orcid":false,"given":"Adelino V M","family":"Can\u00e1rio","sequence":"additional","affiliation":[{"name":"CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005\u2013139 Faro, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2019,5,21]]},"reference":[{"issue":"11","key":"2024111714570671300_bib1","doi-asserted-by":"crossref","first-page":"2019","DOI":"10.1139\/f89-251","article-title":"The monotypic sardines, Sardina and Sardinops - Their taxonomy, distribution, stock structure, and zoogeography","volume":"46","author":"Parrish","year":"1989","journal-title":"Can J Fish Aquat Sci"},{"issue":"6","key":"2024111714570671300_bib2","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1016\/S1054-3139(03)00141-3","article-title":"Morphometric variation among sardine (Sardina pilchardus) populations from the northeastern Atlantic and the western Mediterranean","volume":"60","author":"Silva","year":"2003","journal-title":"ICES J Mar Sci"},{"issue":"3","key":"2024111714570671300_bib3","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1016\/j.ympev.2006.09.018","article-title":"Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences","volume":"43","author":"Lavoue","year":"2007","journal-title":"Mol Phylogenet Evol"},{"issue":"3","key":"2024111714570671300_bib4","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1006\/jmsc.2001.1060","article-title":"Sardine and horse mackerel recruitment and upwelling off Portugal","volume":"58","author":"Santos","year":"2001","journal-title":"ICES J Mar Sci"},{"issue":"1","key":"2024111714570671300_bib5","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1146\/annurev-marine-122414-033819","article-title":"Climate, anchovy, and sardine","volume":"9","author":"Checkley","year":"2017","journal-title":"Annu Rev Mar Sci"},{"key":"2024111714570671300_bib6","author":"ICES","year":"2017","journal-title":"Report of the Working Group on Southern Horse Mackerel, Anchovy and Sardine (WGHANSA), 24\u201329 June 2017, Bilbao, Spain. 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