Dataset Information

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.

SUBMITTER: Machado AM

PROVIDER: S-EPMC5996228 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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

Machado André M AM Felício Mónica M Fonseca Elza E da Fonseca Rute R RR Castro L Filipe C LFC

Data in brief 20180313

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 mack ...[more]

PMID: 29896516

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Project description:Wild capture can be stressful for fish. Stress has the potential to induce mortality in released unwanted catches or negative flesh quality consequences in retained ones. Such effects compromise sustainable natural resource management and industry profitability. Mitigating stress during capture is therefore desirable. Biological indicators of stress can objectively inform fishers as to the functional welfare status of catches during fishing operations. If they are to be of practical use in mitigating stress during wild capture events, such indicators must be quantifiable, respond rapidly, reflect the level of induced stress and be easily observable. Atlantic mackerel (Scomber scombrus) are extensively targeted by purse seine fisheries in European waters but are particularly vulnerable to stress. Excessive crowding in the net is thought to be the principal stress mechanism. There is therefore a need to develop indicators of crowding stress for this species so that catch welfare can be improved. Here, we demonstrate that S. scombrus exhibit a skin colour change from predominately green to predominately blue when exposed to crowding stress. In sea cage trials, we induced various degrees of stress in groups of wild-caught S. scombrus by manipulating crowding density and its duration. Skin colour was quantified in air using digital photography. The colour change occurred rapidly (within the typical duration of crowding events in the fishery), and its magnitude was correlated to the severity and duration of crowding. Bluer fish were also associated with higher levels of plasma lactate. No appreciable colour change was observed in uncrowded (control) groups during the treatment period. Nonetheless, unstressed S. scombrus did turn blue <1 h after death. Together, these results indicate that skin colour change has the potential to be a useful real-time indicator of crowding stress for S. scombrus and could therefore be used to improve welfare during wild capture fishing.

Dataset Information

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

Publications

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

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