A haplotype-resolved draft genome of the European sardine ( Sardina pilchardus )
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (GigaScience)
Abstract
Background
The European sardine ( Sardina pilchardus Walbaum, 1792) has a high cultural and economic importance 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. Consequently, there is an urgent need to better understand the causal factors of this continuing decrease in the sardine stock. Important biological and ecological features such as levels of population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.
Findings
The sardine genome of a single female individual was sequenced using Illumina HiSeq X Ten 10X Genomics linked-reads generating 113.8 Gb of data. Three draft genomes were assembled: two haploid genomes with a total size of 935 Mbp (N50 103Kb) each, and a consensus genome with a total size of 950 Mbp (N50 97Kb). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of eleven tissues were sequenced and used 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 more than 2.3 million phased SNPs with heterozygous loci.
Conclusions
A draft genome was obtained with the 10X Genomics linked-reads technology, despite a high level of sequence repeats and heterozygosity that are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data are a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.
Article activity feed
-
Now published in GigaScience doi: 10.1093/gigascience/giz059
Bruno Louro 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGianluca De Moro 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarlos Garcia 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCymon J. Cox 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this …
Now published in GigaScience doi: 10.1093/gigascience/giz059
Bruno Louro 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGianluca De Moro 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarlos Garcia 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCymon J. Cox 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAna Veríssimo 2CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephen J. Sabatino 2CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAntónio M. Santos 2CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdelino V. M. Canário 1CCMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, PortugalFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Adelino V. M. CanárioFor correspondence: acanario@ualg.pt
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz059 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101710 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101711
-
-
-