A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias

André M. Machado; Mónica Felício; Elza Fonseca; Rute R. da Fonseca; L. Filipe C. Castro

doi:10.1016/j.dib.2018.03.013

A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias

André M. Machado, Mónica Felício, Elza Fonseca, Rute R. da Fonseca^*, L. Filipe C. Castro

^*Corresponding author for this work

Computational and RNA Biology

3 Citations (Scopus)

111 Downloads (Pure)

Abstract

Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae family are comparatively scarce. Here, we generated the first high-quality de novo assembly of the liver transcriptome of the Atlantic chub mackerel (Scomber colias). Through the use of RNA-Seq Illumina technology, 111,124,228 clean reads were obtained for the liver transcriptome. De novo assembly resulted in 93,731 transcripts with an N50 of 1462 bp. This dataset provides an important insight into the context of fisheries management.

Original language	English
Journal	Data in Brief
Volume	18
Pages (from-to)	276-284
Number of pages	9
ISSN	2352-3409
DOIs	https://doi.org/10.1016/j.dib.2018.03.013
Publication status	Published - 2018

Keywords

Atlantic chub mackerel
Liver
RNA-Seq
Scombridae
Stock management

Access to Document

10.1016/j.dib.2018.03.013Licence: CC BY

A resource for sustainable managementFinal published version, 506 KBLicence: CC BY

Cite this

@article{a6f4b354d81e4d28bacf99b75daa7c2b,

title = "A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias",

abstract = "Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae family are comparatively scarce. Here, we generated the first high-quality de novo assembly of the liver transcriptome of the Atlantic chub mackerel (Scomber colias). Through the use of RNA-Seq Illumina technology, 111,124,228 clean reads were obtained for the liver transcriptome. De novo assembly resulted in 93,731 transcripts with an N50 of 1462 bp. This dataset provides an important insight into the context of fisheries management.",

keywords = "Atlantic chub mackerel, Liver, RNA-Seq, Scombridae, Stock management",

author = "Machado, {Andr{\'e} M.} and M{\'o}nica Fel{\'i}cio and Elza Fonseca and {da Fonseca}, {Rute R.} and Castro, {L. Filipe C.}",

year = "2018",

doi = "10.1016/j.dib.2018.03.013",

language = "English",

volume = "18",

pages = "276--284",

journal = "Data in Brief",

issn = "2352-3409",

publisher = "Elsevier",

}

TY - JOUR

T1 - A resource for sustainable management

T2 - De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias

AU - Machado, André M.

AU - Felício, Mónica

AU - Fonseca, Elza

AU - da Fonseca, Rute R.

AU - Castro, L. Filipe C.

PY - 2018

Y1 - 2018

N2 - Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae family are comparatively scarce. Here, we generated the first high-quality de novo assembly of the liver transcriptome of the Atlantic chub mackerel (Scomber colias). Through the use of RNA-Seq Illumina technology, 111,124,228 clean reads were obtained for the liver transcriptome. De novo assembly resulted in 93,731 transcripts with an N50 of 1462 bp. This dataset provides an important insight into the context of fisheries management.

AB - Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae family are comparatively scarce. Here, we generated the first high-quality de novo assembly of the liver transcriptome of the Atlantic chub mackerel (Scomber colias). Through the use of RNA-Seq Illumina technology, 111,124,228 clean reads were obtained for the liver transcriptome. De novo assembly resulted in 93,731 transcripts with an N50 of 1462 bp. This dataset provides an important insight into the context of fisheries management.

KW - Atlantic chub mackerel

KW - Liver

KW - RNA-Seq

KW - Scombridae

KW - Stock management

U2 - 10.1016/j.dib.2018.03.013

DO - 10.1016/j.dib.2018.03.013

M3 - Journal article

C2 - 29896516

AN - SCOPUS:85044114889

SN - 2352-3409

VL - 18

SP - 276

EP - 284

JO - Data in Brief

JF - Data in Brief

ER -

A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias

Abstract

Keywords

Access to Document

Fingerprint

Cite this