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Genes involved in gonadal sex differentiation have been traditionally thought to be fairly conserved across vertebrates, but this has been lately questioned. Here, we performed the first comparative analysis of gonadal transcriptomes across vertebrates, from fish to mammals. Our results unambiguously show an extraordinary overall variability in gene activation and repression programs without a phylogenetic pattern. During sex differentiation, genes such as dmrt1, sox9, amh, cyp19a and foxl2 were consistently either male- or female-enriched across species while many genes with the greatest expression change within each sex were not. We also found that downregulation in the opposite sex, which had only been quantified in the mouse model, was also prominent in the rest of vertebrates. Finally, we report 16 novel conserved markers (e.g., fshr and dazl) and 11 signaling pathways. We propose viewing vertebrate gonadal sex differentiation as a hierarchical network, with conserved hub genes such as sox9 and amh alongside less connected and less conserved nodes. This proposed framework implies that evolutionary pressures may impact genes based on their level of connectivity

Rearing density directly impacts fish welfare, which, in turn, affects productivity in aquaculture. Previous studies have indicated that high-density rearing during sexual development in fish can induce stress, resulting in a tendency towards male-biased sex ratios in the populations. In recent years, research has defined the relevance of the interactions between the environment and epigenetics playing a key role in the final phenotype. However, the underlying epigenetic mechanisms of individuals exposed to confinement remain elucidated. By using zebrafish (Danio rerio), the DNA methylation promotor region and the gene expression patterns of six genes, namely dnmt1, cyp19a1a, dmrt1, cyp11c1, hsd17b1, and hsd11b2, involved in the DNA maintenance methylation, reproduction, and stress were assessed. Zebrafish larvae were subjected to two high-density conditions (9 and 66 fish/L) during two periods of overlapping sex differentiation of this species (7 to 18 and 18 to 45 days post-fertilization, dpf). Results showed a significant masculinization in the populations of fish subjected to high densities from 18 to 45 dpf. In adulthood, the dnmt1 gene was differentially hypomethylated in ovaries and its expression was significantly downregulated in the testes of fish exposed to high-density. Further, the cyp19a1a gene showed downregulation of gene expression in the ovaries of fish subjected to elevated density, as previously observed in other studies. We proposed dnmt1 as a potential testicular epimarker and the expression of ovarian cyp19a1a as a potential biomarker for predicting stress originated from high densities during the early stages of development. These findings highlight the importance of rearing densities by long-lasting effects in adulthood conveying cautions for stocking protocols in fish hatcheries.

Rearing density directly impacts fish welfare, which, in turn, affects productivity in aquaculture. Previous studies have indicated that high-density rearing during sexual development in fish can induce stress, resulting in a tendency towards male-biased sex ratios in the populations. In recent years, research has defined the relevance of the interactions between the environment and epigenetics playing a key role in the final phenotype. However, the underlying epigenetic mechanisms of individuals exposed to confinement remain elucidated. By using zebrafish (Danio rerio), the DNA methylation promotor region and the gene expression patterns of six genes, namely dnmt1, cyp19a1a, dmrt1, cyp11c1, hsd17b1, and hsd11b2, involved in the DNA maintenance methylation, reproduction, and stress were assessed. Zebrafish larvae were subjected to two high-density conditions (9 and 66 fish/L) during two periods of overlapping sex differentiation of this species (7 to 18 and 18 to 45 days post-fertilization, dpf). Results showed a significant masculinization in the populations of fish subjected to high densities from 18 to 45 dpf. In adulthood, the dnmt1 gene was differentially hypomethylated in ovaries and its expression was significantly downregulated in the testes of fish exposed to high-density. Further, the cyp19a1a gene showed downregulation of gene expression in the ovaries of fish subjected to elevated density, as previously observed in other studies. We proposed dnmt1 as a potential testicular epimarker and the expression of ovarian cyp19a1a as a potential biomarker for predicting stress originated from high densities during the early stages of development. These findings highlight the importance of rearing densities by long-lasting effects in adulthood conveying cautions for stocking protocols in fish hatcheries.

High-throughput DNA sequencing technologies have revolutionized the field of microbial and fish genomics, providing unprecedented insights into marine organisms’ genetic and functional diversity. These technologies allow for the comprehensive profiling of microbial communities, revealing the identities and functions of microbes within ocean ecosystems. This enables us to understand the intricate relationships between microbial species, their metabolic pathways, and their responses to environmental changes. For fish genomics, high-throughput sequencing has enabled whole genome sequencing, transcriptomics, and epigenomic studies at an unimaginable resolution and scale. Epigenetics studies heritable changes in gene expression not caused by alterations in DNA sequence but mediated through mechanisms like DNA methylation, histone modifications, and non-coding RNAs. This process introduces additional complexity to our understanding of marine life. The wealth of DNA and RNA data has shed light on fish evolutionary biology, physiology, and responses to environmental stressors, including climate change and anthropogenic activities. As our understanding of the ocean microbiome and fish genomics expands, we are confronted with unprecedented data complexity and volume. This necessitates a collaborative effort across disciplines, notably integrating mathematical tools and principles to analyze and interpret vast and diverse omics data from the ocean. Mathematical tools contribute significantly to our understanding of marine microbial interaction networks by capturing their inherent complexities and dynamics. These networks, which depict ecological interactions such as mutualism or parasitism, can help predict the response of marine ecosystems to environmental fluctuations, thereby serving as tools for ecosystem conservation and management. Yet, mathematical approaches for building microbial networks are far from perfect, with few methods addressing causality, network stability

The Institut de Ciències del Mar (ICM) is the largest marine research centre of the Spanish Research Council (CSIC) • Most multidisciplinary marine science hub in Spain • 2022 - 314 staff (179 women, 135 men) • 2022 - Budget 19.7 million euro (57% soft funding) • 2022 - >300 scientific papers, 94% in OA, 87% Q1 • Leading role in Southern Europe and the Mediterranean • First and only marine science research center to achieve the ‘Severo Ochoa Centre of Excellence’ accreditation

[EN] Epigenetic mechanisms play a vital role in gene expression regulation and phenotype determination. This thesis aimed to comprehensively investigate the transcriptome, the methylome and the influence of intrinsic (such as sex) and environmental factors (such as temperature) on the European sea bass (Dicentrarchus labrax). First, we focused on understanding the genetic expression of the gonads during early sex differentiation. By doing so, we proposed a novel approach combining weighted gene coexpression network analysis (WGCNA) with differential gene expression analysis (DEGs) for improved transcriptomic analysis. Further, we also explored gonadal sex differentiation across different vertebrate species, identifying key genes and potential novel markers. Then, we focused on the development of epigenetic biomarkers. As a result, DNA methylation marks were identified as indicators of the thermal environment experienced during early development. Additionally, a cost-effective method for epigenetic biomarker development and its integration with genetic selection in aquaculture was developed. Lastly, the impact of sex and temperature on the methylome was explored, revealing multigenerational effects and markers for genetic resistant females to temperature-induced masculinization. These findings have implications for aquaculture and contribute to our understanding of adaptive mechanisms and epigenetic inheritance, [CAT] Els mecanismes epigenètics juguen un paper vital en la regulació de l'expressió gènica i en la determinació del fenotip. Aquesta tesi tenia com a objectiu investigar el transcriptoma, el metiloma i la influència de factors intrínsecs (com el sexe) i factors ambientals (com la temperatura) en el llobarro (Dicentrarchus labrax). En primer lloc, ens vam centrar en comprendre l'expressió gènica de les gònades durant els primers estadis de la diferenciació sexual. Mitjançant això, proposem una nova aproximació metodològica que combina l'anàlisi de xarxes de co-expressió gènica ponderada (WGCNA) amb l'anàlisi de l'expressió gènica diferencial (DEGs) per a una millor anàlisi transcriptòmica. A més, vam explorar la diferenciació sexual gonadal en diferents espècies de vertebrats, identificant gens clau i possibles marcadors nous. A continuació, ens vam centrar en el desenvolupament de biomarcadors epigenètics. Com a resultat, es van identificar marques de metilació del DNA com a indicadors de l'entorn tèrmic experimentat durant el desenvolupament primerenc. A més, es va desenvolupar un mètode amb baix cost i alta efectivitat per al desenvolupament de biomarcadors epigenètics i la seva integració amb la selecció genètica en l'aqüicultura. Finalment, vam explorar l'impacte del sexe i la temperatura en el metiloma, revelant efectes multigeneracionals i marcadors per a femelles genèticament resistents a la masculinització induïda per la temperatura. Aquests resultats tenen implicacions per a l'aqüicultura i contribueixen a la nostra comprensió dels mecanismes adaptatius i de la herència epigenètica

Female-to-male sex reversals (pseudomales) are common in lower vertebrates and have been found in natural populations, which is a concern under rapid changes in environmental conditions. Pseudomales can exhibit altered spermatogenesis. However, the regulatory mechanisms underlying pseudomale spermatogenesis remain unclear. Here, we characterized spermatogenesis in Chinese tongue sole (Cynoglossus semilaevis), a species with genetic and environmental sex determination, based on a high-resolution single-cell RNA-seq atlas of cells derived from the testes of genotypic males and pseudomales. We identified five germ cell types and six somatic cell types and obtained a single-cell atlas of dynamic changes in gene expression during spermatogenesis in Chinese tongue sole, including alterations in pseudomales. We detected decreased levels of Ca2+ signaling pathway-related genes in spermatogonia, insufficient meiotic initiation in spermatocytes, and a malfunction of somatic niche cells in pseudomales. However, a cluster of CaSR genes and MAPK signaling factors were upregulated in undifferentiated spermatogonia of pseudomales. Additionally, we revealed that Z chromosome-specific genes, such as piwil2, dhx37, and ehmt1, were important for spermatogenesis. These results improve our understanding of reproduction after female-to-male sex-reversal and provide new insights into the adaptability of reproductive strategies in lower vertebrates

This essential guide will allow you to understand how new developments in our knowledge of epigenetic mechanisms and epigenetic inheritance can be applied to improve aquaculture production and aquatic resource management and conservation. Epigenetics is the study of heritable changes in gene expression that are independent of alterations in the nucleotide sequence. It integrates genomic and environmental influences to shape the phenotype. Epigenetics is a field with particular relevance to aquaculture and aquatic organisms, since it underpins acclimatory responses to diverse and changing environments and inheritance of desired phenotypes. Epigenetics in Aquaculture provides a comprehensive introduction to epigenetics, epigenetic mechanisms, epigenetic inheritance, and research methods. It also provides the current state of the art on research and development on epigenetics in the major functions of aquatic organisms in the framework of aquaculture production. The fact that aquaculture is the fastest-growing sector of food production makes the book especially timely. Readers will also find: * Detailed treatment of subjects including aquatic faunal reproduction, sex determination, growth regulation, nutritional programming, disease resistance, stress response and much more * Survey of current research lacunae and the projected future of the discipline * An authorial team of internationally renowned experts Epigenetics in Aquaculture is a valuable reference for researchers, biologists and advanced students in any area of marine science, oceanography, aquaculture, environmental science, and food production

Aquaculture is the fastest food production sector in the world and prospects are that this position will be maintained for years come. [...]

The field of epigenetics in aquaculture is very young, but promising. [...]

The sex ratio is a key ecological demographic parameter crucial for population viability. However, the epigenetic mechanisms operating during gonadal development regulating gene expression and the sex ratio remain poorly understood. Moreover, there is interest in the development of epigenetic markers associated with a particular phenotype or as sentinels of environmental effects. Here, we profiled DNA methylation and gene expression of 10 key genes related to sex development and stress, including steroidogenic enzymes, and growth and transcription factors. We provide novel information on the sex-related differences and on the influence of elevated temperature on these genes in zebrafish, a species with mixed genetic and environmental influences on sex ratios. We identified both positive (e.g., amh, cyp11c and hsd11b2) and negative (e.g., cyp11a1 and dmrt1) correlations in unexposed males, and negative correlation (amh) in exposed females between DNA methylation and gene expression levels. Further, we combined DNA methylation analysis with machine learning procedures and found a series of informative CpGs capable not only of correctly identifying sex (based on cyp19a1a DNA methylation levels) but also of identifying whether males and females had been exposed to abnormally elevated temperature when young (based on amh and foxl2a DNA methylation levels, respectively). This was achieved in the absence of conspicuous morphological alterations of the gonads. These DNA methylation-based epigenetic biomarkers represent molecular resources that can correctly recapitulate past thermal history and pave the way for similar findings in other species to assess potential ecological effects of environmental disturbances in the context of climate change

Epigenetic changes such as DNA methylation modifications at specific loci in the genome in response to environmental cues can appear long before the appearance of transcriptomic or other phenotypic changes with potential consequences for performance. Thus, epigenetic DNA methylation-based biomarkers hold great promise in aquaculture and conservation biology because they can have prognostic value. However, to the best of our knowledge, a clear demonstration of such biomarkers has not been provided yet. Temperature during early stages of development is the main abiotic factor determining larval quality, with effects potentially persisting until adulthood and influencing performance. The objective of this study was to test whether epigenetic biomarkers could be developed as reliable indicators of the quality of the thermal environment during European sea bass (Dicentrarchus labrax) early development and their relation to long-lasting phenotypic consequences. We exposed European sea bass embryos and newly hatched larvae to different temperature regimes and sampled fish thereafter at three time points: at larval, juvenile and adult stages. Here, we provide an analytical strategy combining Reduced Representation Bisulfite sequencing (RRBS) and RNA-sequencing (RNA-seq) to develop epigenetic and transcriptomic biomarkers with both prognostic and diagnostic value. Specifically, we report a series of DNA-methylation biomarkers linked to short-term, mid-term, long-term, and very-long term effects of temperature in both somatic and reproductive tissues. Among the different biomarkers identified, one promising example is the methylation status of keratin-associated protein 10–4 (krtap10–4), which fulfills the criteria of an epigenetic biomarker with both prognostic and diagnostic value. This study constitutes a first step toward providing the European sea bass farming sector with a set of epigenetic biomarkers that can be used to screen batches of larvae to determine the quality

Epigenetic clocks are accurate tools for age prediction and are of great interest for fisheries management and conservation biology. Here, we review the necessary computational steps and tools in order to build an epigenetic clock in any species focusing on fish. Currently, a bisulfite conversion method which allows the distinction of methylated and unmethylated cytosines is the recommended method to be performed at single nucleotide resolution. Typically, reduced representation bisulfite sequencing methods provide enough coverage of CpGs to select from for age prediction while the exact implemented method depends on the specific objectives and cost of the study. Sequenced reads are controlled for their quality, aligned to either a reference or a deduced genome and methylation levels of CpGs are extracted. Methylation values are obtained in biological samples of fish that cover the widest age range possible. Using these datasets, machine learning statistical procedures and, in particular, penalized regressions, are applied in order to identify a set of CpGs the methylation of which in combination is enough to accurately predict age. Training and test datasets are used to build the optimal model or “epigenetic clock”, which can then be used to predict age in independent samples. Once a set of CpGs is robustly identified to predict age in a given species, DNA methylation in only a small number of CpGs is necessary, thus, sequencing efforts including data and money resources can be adjusted to interrogate a small number of CpGs in a high number of samples. Implementation of this molecular resource in routine evaluations of fish population structure is expected to increase in the years to come due to high accuracy, robustness and decreasing costs of sequencing. In the context of overexploited fish stocks, as well as endangered fish species, accurate age prediction with easy-to-use tools is much needed for improved fish populations management and conservation

The distribution of age classes is a key demographic parameter of populations and thus proper age estimation is crucial for fisheries management and for conservation biology. Age estimation in fishes has traditionally relied on the analysis of growth marks in hard structures such as otoliths. However, besides being lethal this method is time-consuming, can have low accuracy in some species and cannot be applied in others. Thus, there is a need for the development of new methods. DNA methylation is an epigenetic modification consisting in the addition of a methyl group in cytosine-guanine loci. Aging is associated with changes in DNA methylation. Among a background of global and weak genome hypomethylation, there are some loci in which age-associated DNA methylation changes are of a “clock-like” nature and thus predictable. Chronological age estimators built from DNA methylation are termed ‘epigenetic clocks’. Epigenetic clocks have been developed in the last ten years for many species, notably vertebrates, including already several fish species. Here, we review the piscine epigenetic clocks built so far and outline the major considerations to be taken into account for the development of new epigenetic clocks for additional species, which include the number of samples to be collected and tissues to be targeted. The steps on how to develop such a clock and the techniques available to do so are also discussed. Next, we focus on the features of epigenetic clocks as measuring devices, considering aspects such as accuracy, precision and reproducibility. Finally, we discuss the possibility of developing a multi-species piscine epigenetic clock and how processing automation can greatly reduce the cost per sample. One important knowledge gap is to determine how environmental changes, especially temperature and food availability, may affect the tick rate of piscine epigenetic clocks. Improved age prediction through the use of piscine epigenetic clocks can contribute to better

La producció mundial de l’aqüicultura l’any 2018 fou de 114,5 milions de tones (Mt), enfront dels 96,4 Mt de la pesca, segons les darreres dades de la FAO. Per tant, actualment l’aqüicultura ja representa més del 50 % del total de biomassa d’origen aquàtic destinada al consum humà, una xifra que no ha deixat de créixer des de la seva industrialització en les darreres quatre dècades. Tot i així, hi ha una part de l’aqüicultura que depèn de la producció d’oli i farina de peix i, per tant, en darrer terme de la pesca. A més, l’expansió de l’aqüicultura s’enfronta a reptes derivats del consum d’aigua dolça en l’aqüicultura continental, l’ocupació de les zones costaneres en l’aqüicultura marina, la lluita contra patògens degut a la seva intensificació, i el fet que cada cop els pinsos utilitzats són més d’origen vegetal, en el que podem anomenar la creixent interdependència dels sectors terra i mar. El que ja és innegable, però, és que l’aqüicultura forma part del sistema alimentari mundial i, per tant, la seva contribució ja no té marxa enrere. Una activitat sostenible vol dir que persisteix en el temps i que, a més, està feta de forma que l’impacte ambiental sigui el menor possible o, idealment, nul. Determinar el grau de sostenibilitat de l’aqüicultura no és gens fàcil perquè és tan elevat el volum de dades que s’han de tenir en compte i creuar que la tasca escapa a l’objectiu d’aquest escrit. Si que és adient, però, fer algunes consideracions al respecte tenint en compte la disponibilitat tant d’informes periòdics de la FAO, de la Comissió Europea i d’altres ens supranacionals, així com d’articles originals i revisions sobre el tema publicats a les revistes científiques, i això és el que es pretén aquí

El Consejo Superior de Investigaciones Científicas (CSIC) es el mayor organismo público de investigación en España y el tercero en Europa. Tiene como misión el fomento, la coordinación, el desarrollo y la difusión de la investigación científica y tecnológica de carácter multidisciplinar. Su fin último es contribuir al avance del conocimiento y al desarrollo económico, social y cultural, así como a la formación de personal y al asesoramiento de entidades públicas y privadas en estas materias. Dentro de un marco de ciencia de excelencia con compromiso social, emergen acciones de transferencia del conocimiento como esta. Así, gracias a la ayuda del CSIC y del programa INTERCOONECTA de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID), dependiente del Ministerio de Asuntos Exteriores, Unión Europea y Cooperación, se ha hecho posible esta programación titulada: Mejora de la productividad y la gestión acuícola mediante el empleo de herramientas de diagnóstico y gestión, y mediante programas de selección en especies nativas de Latinoamérica y el Caribe, salvajes o cultivadas, de importancia ecológica y comercial. [...]

Contar con más proteína animal de origen acuícola en la dieta de los seres humanos es imprescindible si se considera una población mundial cuyo aumento se estima en alrededor de un 50% en 2050, lo cual conlleva a una necesidad de incrementar hasta en un 70% la producción de alimento. En la actualidad se pueden producir especies acuáticas aplicando tecnologías disponibles que permiten mitigar el dolor potencial en peces, cefalópodos y crustáceos. [...]

[EN] The program, funded by the AECID and the CSIC, involved 86 teachers and more than 150 students from 18 Latin American and Caribbean countries, [ES] En total, han participado en el programa, financiado por la AECID y el CSIC, 86 profesores y más de 150 alumnos de 18 países de Latinoamérica y el Caribe, [CAT] En total, han participat en el programa, finançat per l'AECID i el CSIC, 86 professors i més de 150 alumnes de 18 països de Llatinoamèrica i el Carib

[EN] The book, the first one on the subject, deciphers the importance of epigenetics in the environmental adaptation and culture of algae, mollusks, crustaceans, and fish, [ES] La obra, pionera en el tema, ahonda en la importancia de la epigenética en las adaptaciones ambientales y el cultivo de algas, moluscos, crustáceos y peces, [CAT] L’obra, pionera en el tema, aprofundeix en la importància de l'epigenètica en les adaptacions ambientals i el cultiu d'algues, mol·luscs, crustacis i peixos