Liver transcriptome resources of four commercially exploited teleost species

Research output: Contribution to journalJournal articleResearchpeer-review

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Liver transcriptome resources of four commercially exploited teleost species. / Machado, André M.; Muñoz-Merida, Antonio; Fonseca, Elza; Veríssimo, Ana; Pinto, Rui; Felício, Mónica; da Fonseca, Rute R.; Froufe, Elsa; Castro, L. Filipe C.

In: Scientific Data, Vol. 7, 214, 2020.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Machado, AM, Muñoz-Merida, A, Fonseca, E, Veríssimo, A, Pinto, R, Felício, M, da Fonseca, RR, Froufe, E & Castro, LFC 2020, 'Liver transcriptome resources of four commercially exploited teleost species', Scientific Data, vol. 7, 214. https://doi.org/10.1038/s41597-020-0565-9

APA

Machado, A. M., Muñoz-Merida, A., Fonseca, E., Veríssimo, A., Pinto, R., Felício, M., ... Castro, L. F. C. (2020). Liver transcriptome resources of four commercially exploited teleost species. Scientific Data, 7, [214]. https://doi.org/10.1038/s41597-020-0565-9

Vancouver

Machado AM, Muñoz-Merida A, Fonseca E, Veríssimo A, Pinto R, Felício M et al. Liver transcriptome resources of four commercially exploited teleost species. Scientific Data. 2020;7. 214. https://doi.org/10.1038/s41597-020-0565-9

Author

Machado, André M. ; Muñoz-Merida, Antonio ; Fonseca, Elza ; Veríssimo, Ana ; Pinto, Rui ; Felício, Mónica ; da Fonseca, Rute R. ; Froufe, Elsa ; Castro, L. Filipe C. / Liver transcriptome resources of four commercially exploited teleost species. In: Scientific Data. 2020 ; Vol. 7.

Bibtex

@article{06ff43374f7543689a021f05488737a2,
title = "Liver transcriptome resources of four commercially exploited teleost species",
abstract = "The generation ofomicresources 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), andMicromesistius poutassou(MPO; blue whiting). A comprehensive assembly pipeline, usingde novosingle 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.",
keywords = "PROTEIN, GENERATION, FISH, GENE",
author = "Machado, {Andr{\'e} M.} and Antonio Mu{\~n}oz-Merida and Elza Fonseca and Ana Ver{\'i}ssimo and Rui Pinto and M{\'o}nica Fel{\'i}cio and {da Fonseca}, {Rute R.} and Elsa Froufe and Castro, {L. Filipe C.}",
year = "2020",
doi = "10.1038/s41597-020-0565-9",
language = "English",
volume = "7",
journal = "Scientific Data",
issn = "2052-4463",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Liver transcriptome resources of four commercially exploited teleost species

AU - Machado, André M.

AU - Muñoz-Merida, Antonio

AU - Fonseca, Elza

AU - Veríssimo, Ana

AU - Pinto, Rui

AU - Felício, Mónica

AU - da Fonseca, Rute R.

AU - Froufe, Elsa

AU - Castro, L. Filipe C.

PY - 2020

Y1 - 2020

N2 - The generation ofomicresources 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), andMicromesistius poutassou(MPO; blue whiting). A comprehensive assembly pipeline, usingde novosingle 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.

AB - The generation ofomicresources 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), andMicromesistius poutassou(MPO; blue whiting). A comprehensive assembly pipeline, usingde novosingle 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.

KW - PROTEIN

KW - GENERATION

KW - FISH

KW - GENE

U2 - 10.1038/s41597-020-0565-9

DO - 10.1038/s41597-020-0565-9

M3 - Journal article

C2 - 32636445

VL - 7

JO - Scientific Data

JF - Scientific Data

SN - 2052-4463

M1 - 214

ER -

ID: 246823680