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>

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: RNA-Seq, Scombridae, Stock management, Atlantic chub mackerel, Live

Report of the 4th Workshop on Age Reading of horse mackerel, Mediterranean horse mackerel and blue jack mackerel (Trachurus trachurus, T. mediterraneus and T. picturatus) (WKARHOM)

Based on the previous work from WKARHOM3 (ICES, 2018), the Working Group on Biological Parameters (ICES, 2020) identified the need for a new otolith exchange followed by an age read-ing Workshop. The Workshop on Age reading of Horse Mackerel, Mediterranean Horse Macke-rel and Blue Jack Mackerel (Trachurus trachurus, T. mediterraneus and T. picturatus) (WKAR-HOM4) had several main objectives; to review the current protocols of ageing Trachurus species, to update the advances in the validation of the ageing criteria (i.e. the annual deposition of one annulus, coherency of the interpretation), to evaluate the new precision of ageing data of Tra-churus species and to update guidelines, common ageing criteria and reference collections of otoliths. An online otolith exchange was performed using SmartDots during 2021 and 2022, and results including the three Trachurus species were published in advance of the meeting, showing a low Percentage of Agreement (PA) both when considering all the readers (44-55%) and the advanced readers only (52-54%) (Massaro and Jurado-Ruzafa, 2022). For T. trachurus the Coef-ficient of Variation (CV) was lower for the sliced samples (22-18%) than for whole otoliths sam-ples (44-38%). Readers participating in the exchange, following discussion during the WKAR-HOM4 meeting, agreed that the main cause of age determination error for T. trachurus was due to the different otolith preparation techniques (whole/sliced). These differences reflect the stunted growth and compactness of the annuli in older specimens (from the 4th-5th annuli on-wards). Anyway, for the three Trachurus species, there are several difficulties in age determina-tion: identification of the first growth annulus, presence of many false rings (mainly in the first and second annuli) and the interpretation and identification of the edge characteristics (opaque/translucent). The second reading exercise was performed during the workshop orga-nized in four different events (i.e. Trachurus trachurus whole otoliths -135 images-, T. trachurus sliced otoliths -95 images- T. mediterraneus whole otoliths -150 images- and T. picturatus whole otoliths –121 images). For T. trachurus no enhancement among readers’ precision was observed in all cases, in terms of PA and CV. Conversely, for T. mediterraneus and T. picturatus a notice-able improvement in terms of PA and decrease of CV occurred compared to the pre-workshop exchange. Finally, this group updated the ageing guidelines and a reference collection of images for all the species, with the aim to employ these tools for all laboratories.ICESN

Pequena pesca na costa continental portuguesa : caracterização socioeconómica, descrição da atividade e identificação de problemas

No âmbito do projeto PRESPO “Desenvolvimento Sustentável da Pesca Artesanal no Espaço Atlântico” (Programa INTERREG IIIB, Espaço Atlântico, União Europeia, Fundos FEDER) foi realizado um inquérito ao longo de toda a costa continental portuguesa que cobriu grande parte dos portos de pesca atualmente ativos, o que permitiu conhecer, de forma detalhada, a atividade de pesca associada à frota da pequena pesca.Num contexto nacional, a pequena pesca assume crescente importância em virtude da sua forte implantação ao longo de toda a costa portuguesa, da grande diversidade de artes de pesca e espécies capturadas, do elevado valor comercial dos produtos desta actividade, do grande número de pescadores e outros agentes envolvidos, da importância ambiental, sócio‐económica e cultural a nível local, regional e/ou nacional e da diminuição da importância dos pesqueiros tradicionais explorados pela frota longínqua. Acresce o facto de nalgumas regiões a pequena pesca constituir, no conjunto das estruturas produtivas, uma das componentes com maior relevância. O segmento de frota associado à pequena pesca é caracterizado por embarcações com reduzida autonomia de operação e comprimento de fora‐a‐fora inferior a 9 metros. Esta frota, que corresponde a cerca de 80% da frota portuguesa, opera, de uma maneira geral, dentro das 3 milhas tanto ao longo do litoral oceânico, como em sistemas lagunares costeiros e sistemas estuarinos. As áreas de actuação da frota associada à pequena pesca fazem com que esta actividade esteja fortemente vinculada a pequenas comunidades piscatórias que se distribuem ao longo de toda a costa portuguesa. Não é, por isso, de estranhar que os problemas associados a esta importante actividade sejam frequentemente locais,cuja resolução exige abordagens que deverão ter em conta os habitats sobre os quais a pesca se exerce, o tipo de artes de pesca utilizadas, as espécies‐alvo e acessórias, o esforço de pesca, bem como o contexto sócio‐económico da região. Apesar da importância da pequena pesca, esta actividade tem merecido reduzida atenção a nível nacional, assim como ao nível da União Europeia, já que grande parte dos estudos desenvolvidos pela comunidade científica são sobretudo dirigidos para as frotas industriais ou semi‐industriais que exploram os grandes recursos. Esta situação deriva, por um lado, do facto da pequena pesca ter um peso directo muito pequeno no PIB dos diferentes países comunitários e, por outro lado, pelas dificuldades em seguir esta actividade. Importa, contudo, sublinhar que se directamente acontribuição da pequena pesca para o PIB é baixa, indirectamente é bastante alta pois tem repercussões positivas em outras actividades económicas como seja a restauração e o turismo.União Europeiainfo:eu-repo/semantics/publishedVersio

“Out of the can”: a draft genome assembly, liver transcriptome, and nutrigenomics of the european sardine, sardina pilchardus

Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.We acknowledge the North Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) that supported this research through the Coral—Sustainable Ocean Exploitation (reference NORTE-01-0145-FEDER-000036). R.R.d.F. thanks the Danish National Research Foundation for its support of the Center for Macroecology, Evolution, and Climate (grant DNRF96).Peer reviewe