Liver transcriptome resources of four commercially exploited teleost species
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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 journal › Journal article › Research › peer-review
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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