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07 07, 2020;7 (1): 214.

Liver transcriptome resources of four commercially exploited teleost species.

Andr�� M Machado, Antonio Mu��oz-Merida, Elza Fonseca, Ana Ver��ssimo, Rui Pinto, M��nica Fel��cio, Rute R da Fonseca, Elsa Froufe, L Filipe C Castro
Author Information
  1. Andr�� M Machado: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal. andre.machado@ciimar.up.pt. ORCID
  2. Antonio Mu��oz-Merida: CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agr��rio de Vair��o, 4485-661, Vair��o, Portugal. ORCID
  3. Elza Fonseca: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal.
  4. Ana Ver��ssimo: CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agr��rio de Vair��o, 4485-661, Vair��o, Portugal.
  5. Rui Pinto: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal.
  6. M��nica Fel��cio: Portuguese Institute for the Sea and Atmosphere, I.P. (IPMA), Lisbon, Portugal.
  7. Rute R da Fonseca: Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. ORCID
  8. Elsa Froufe: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal. ORCID
  9. L Filipe C Castro: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal. filipe.castro@ciimar.up.pt.
PMID: 32636445 DOI: 10.1038/s41597-020-0565-9

Abstract

The generation of omic resources is central to develop adequate management strategies for species with economic value. Here, we provide high-coverage RNA-seq datasets of liver tissue (containing between 80,2 and 88,4 million of paired-end reads) from four wildtype teleost species with high commercial value: Trachurus trachurus (TTR; Atlantic horse mackerel), Scomber scombrus (SSC; Atlantic mackerel), Trisopterus luscus (TLU; pout), and Micromesistius poutassou (MPO; blue whiting). A comprehensive assembly pipeline, using de novo single and multi-kmer assembly approaches, produced 64 single high-quality liver transcriptomes - 16 per species. The final assemblies, with N50 values ranging from 2,543-3,700���bp and BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness values between 81.8-86.5% of the Actinopterygii gene set, were subjected to open reading frame (ORF) prediction and functional annotation. Our study provides the first transcriptomic resources for these species and offers valuable tools to evaluate both neutral and selected genetic variation among populations, and to identify candidate genes for environmental adaptation assisting in the investigation of the effects of global changes in fisheries.

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MeSH Term

Animals
Fisheries
Fishes
Genetic Variation
Genetics, Population
Liver
Open Reading Frames
Transcriptome
Dataset Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 1

Word Cloud

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