Identification of a Novel ß-Defensin Gene in Gilthead Seabream (Sparus aurata).

The excessive use of antibiotics in aquaculture favors the natural selection of multidrug-resistant bacteria, and antimicrobial peptides (AMPs) could be a promising alternative to this problem. The most studied AMPs in teleost fish are piscidins, hepcidins, and ß-defensins. In this work, we have found a new gene (defb2) encoding a type 2 ß-defensin in the genome of gilthead seabream, a species chosen for its economic interest in aquaculture. Its open reading frame (192 bp) encodes a protein (71 amino acids) that undergoes proteolytic cleavage to obtain the functional mature peptide (42 amino acids). The genetic structure in three exons and two introns and the six characteristic cysteines are conserved as the main signature of this protein family. In the evolutionary analysis, synteny shows a preservation of chromosomal localization and the phylogenetic tree constructed exposes the differences between both types of ß-defensin as well as the similarities between seabream and European seabass. In relation to its basal expression, ß-defensin 2 is mostly expressed in the intestine, thymus, skin, and gonads of the gilthead seabream (Sparus aurata). In head kidney leucoytes (HKLs), the expression was very low and did not change significantly when stimulated with various immunocompetent agents. However, the expression was significantly down-regulated in the liver, head-kidney, and blood 4 h post-injection with the fish pathogen Vibrio harveyi. When infected with nodavirus, the expression was downregulated in brain at 7 days post-infection. These results denote a possible complementarity between the expression patterns of ß-defensins and hepcidins. Further studies are needed to analyze gene duplications and expression patterns of ß-defensins and describe their mechanism of action in seabream and other teleost fish.

The telencephalon is a neuronal substrate for systemic inflammatory responses in teleosts via polyamine metabolism.

Systemic inflammation elicits sickness behaviors and fever by engaging a complex neuronal circuitry that begins in the preoptic area of the hypothalamus. Ectotherms such as teleost fish display sickness behaviors in response to infection or inflammation, seeking warmer temperatures to enhance survival via behavioral fever responses. To date, the hypothalamus is the only brain region implicated in sickness behaviors and behavioral fever in teleosts. Yet, the complexity of neurobehavioral manifestations underlying sickness responses in teleosts suggests engagement of higher processing areas of the brain. Using in vivo models of systemic inflammation in rainbow trout, we find canonical pyrogenic cytokine responses in the hypothalamus whereas in the telencephalon and the optic tectum il-1b and tnfa expression is decoupled from il-6 expression. Polyamine metabolism changes, characterized by accumulation of putrescine and decreases in spermine and spermidine, are recorded in the telencephalon but not hypothalamus upon systemic injection of bacteria. While systemic inflammation causes canonical behavioral fever in trout, blockade of bacterial polyamine metabolism prior to injection abrogates behavioral fever, polyamine responses, and telencephalic but not hypothalamic cytokine responses. Combined, our work identifies the telencephalon as a neuronal substrate for brain responses to systemic inflammation in teleosts and uncovers the role of polyamines as critical chemical mediators in sickness behaviors.

Fish microglia: Beyond the resident macrophages of the central nervous system - A review of their morphofunctional characteristics.

From classical to modern literature on microglia, the importance of the potential and variability of these immune cells in vertebrates has been pointed out. Recent aspects such as relationships and interactions between microglia and neurons in both normal and injured neural tissues, as well as their nexus with other organs and with the microbiota, or how these cells are modulated during development and adulthood are current topics of major interest. State-of-the-art research methodologies, including microscopy and potent in vivo imaging techniques, genomic and proteomic methods, current culture conditions together with the easy maintenance and manipulation of some fish embryos and adult specimens such as zebrafish (Danio rerio), have emerged and adapted to the phylogenetic position of some fish species. Furthermore, these advancements have facilitated the development of successful protocols aimed at addressing significant hypotheses and unresolved questions regarding vertebrate glia. The present review aims to analyse the available information on fish microglia, mainly the most recent one concerning teleosts, to establish an overview of their structural and immune functional features as a basis for their potentialities, heterogeneity, diversification, involvement, and relationships with neurons under normal and pathological conditions.

Barramundi (Lates calcarifer) rare coloration patterns: a multiomics approach to understand the "panda" phenotype.

The barramundi (Lates calcarifer), a significant aquaculture species, typically displays silver to bronze coloration. However, attention is now drawn to rare variants like the "panda" phenotype, characterized by blotch-like patterns of black (PB) and golden (PG) patches. This phenotype presents an opportunity to explore the molecular mechanisms underlying color variations in teleosts. Unlike stable color patterns in many fish, the "panda" variant demonstrates phenotypic plasticity, responding dynamically to unknown cues. We propose a complex interplay of genetic factors and epigenetic modifications, focusing on DNA methylation. Through a multiomics approach, we analyze transcriptomic and methylation patterns between PB and PG patches. Our study reveals differential gene expression related to melanosome trafficking and chromatophore differentiation. Although the specific gene responsible for the PB-PG difference remains elusive, candidate genes like asip1, asip2, mlph, and mreg have been identified. Methylation emerges as a potential contributor to the "panda" phenotype, with changes in gene promoters like hand2 and dynamin possibly influencing coloration. This research lays the groundwork for further exploration into rare barramundi color patterns, enhancing our understanding of color diversity in teleosts. Additionally, it underscores the "panda" phenotype's potential as a model for studying adult skin coloration.

High water temperature triggers early sexual maturation in the juvenile red spotted grouper Epinephelus akaara: Via regulation of reproduction-related hormones in the brain-pituitary-gonadal axis.

The red spotted grouper Epinephelus akaara is a marine species of economic importance and also at risk of extinction. This study investigated the effects of high water temperature on the growth and maturation of juvenile E. akaara females. From 160-420 days post-hatching (dph), the fish were maintained under natural water temperature (NT) and a constant high-water temperature (HT). From 240 dph, both the total length and body weight in the HT group were greater than in NT group. After 360 dph, the gonadosomatic index was also increased in the HT group compared to NT group. Mature oocytes were only observed in the HT group at 330, 360, and 390 dph. Both kiss1 and kiss2 levels increased at 240 and 270 dph in both groups; however, they were greater in the HT group at 240 dph. Similarly, gpr54 levels after 360 dph were greater in the HT group, suggesting that kisspeptin is related to maturation via its receptor gpr54. Levels of fshß and lhß were greater in the HT group after 360 dph. Estradiol-17ß (E2) levels after 160 dph (except 300 dph) were greater in the HT group than in the NT group, suggesting that the higher E2 levels trigger maturation, and is related to increased fshß and lhß. This study provides evidence that high water temperature is effective in accelerating growth and triggering early maturation of juvenile E. akaara, via regulating gpr54, fshß, lhß, and E2 levels.

Neuron mapping in the Molly fish optic tectum: An emphasis on the adult neurogenesis process.

Teleost fish exhibit the most pronounced and widespread adult neurogenesis. Recently, functional development and the fate of newborn neurons have been reported in the optic tectum (OT) of fish. To determine the role of neurogenesis in the OT, this study used histological, immunohistochemical, and electron microscopic investigations on 18 adult Molly fish specimens (Poecilia sphenops). The OT of the Molly fish was a bilateral lobed structure located in the dorsal part of the mesencephalon. It exhibited a laminated structure made up of alternating fiber and cellular layers, which were organized into six main layers. The stratum opticum (SO) was supplied by optic nerve fibers, in which the neuropil was the main component. Radial bipolar neurons that possessed bundles of microtubules were observed in the stratum fibrosum et griseum superficiale (SFGS). Furthermore, oligodendrocytes with their processes wrapped around the nerve fibers could be observed. The stratum album centrale (SAC) consisted mainly of the axons of the stratum griseum centrale (SGC) and the large tectal, pyriform, and horizontal neurons. The neuronal cells of the SO and large tectal cells of the SAC expressed autophagy-related protein-5 (APG5). Interleukin-1ß (IL-1ß) was expressed in both neurons and glia cells of SGC. Additionally, inducible nitric oxide synthase (iNOS) was expressed in the neuropil of the SAC synaptic layer and granule cells of the stratum periventriculare (SPV). Also, transforming growth factor beta (TGF-ß), SRY-box transcription factor 9 (SOX9), and myostatin were clearly expressed in the proliferative neurons. In all strata, S100 protein and Oligodendrocyte Lineage Transcription Factor 2 (Olig2) were expressed by microglia, oligodendrocytes, and astrocytes. In conclusion, it was possible to identify different varieties of neurons in the optic tectum, each with a distinct role. The existence of astrocytes, proliferative neurons, and stem cells highlights the regenerative capacity of OT. RESEARCH HIGHLIGHTS: The OT of the Molly fish exhibited a laminated structure made up of alternating fiber and cellular layers, which were organized into six main layers. Radial bipolar neurons that possessed bundles of microtubules were observed in the stratum fibrosum et griseum superficiale (SFGS). The stratum album central (SAC) consisted mainly of the axons of the stratum griseum centrale (SGC) and the large tectal, pyriform, and horizontal neurons. Inducible nitric oxide synthase (iNOS) was expressed in the neuropil of the SAC synaptic layer and granule cells of the stratum periventricular (SPV). Also, transforming growth factor beta (TGF-ß), SRY-box transcription factor 9 (SOX9), and myostatin were clearly expressed in the proliferative neurons. The existence of astrocytes, proliferative neurons, and stem cells highlights the regenerative capacity of OT.

DNA methylation reprogramming in teleosts.

Early embryonic development is crucially important but also remarkably diverse among animal taxa. Axis formation and cell lineage specification occur due to both spatial and temporal control of gene expression. This complex system involves various signaling pathways and developmental genes such as transcription factors as well as other molecular interactants that maintain cellular states, including several types of epigenetic marks. 5mC DNA methylation, the chemical modification of cytosines in eukaryotes, represents one such mark. By influencing the compaction of chromatin (a high-order DNA structure), DNA methylation can either repress or induce transcriptional activity. Mammals exhibit a reprogramming of DNA methylation from the parental genomes in the zygote following fertilization, and later in primordial germ cells (PGCs). Whether these periods of methylation reprogramming are evolutionarily conserved, or an innovation in mammals, is an emerging question. Looking into these processes in other vertebrate lineages is thus important, and teleost fish, with their extensive species richness, phenotypic diversity, and multiple rounds of whole genome duplication, provide the perfect research playground for answering such a question. This review aims to present a concise state of the art of DNA methylation reprogramming in early development in fish by summarizing findings from different research groups investigating methylation reprogramming patterns in teleosts, while keeping in mind the ramifications of the methodology used, then comparing those patterns to reprogramming patterns in mammals.

Metabolic Water As a Route for Water Acquisition in Vertebrates Inhabiting Dehydrating Environments.

Vertebrates have expanded their habitats during evolution, which accompanies diversified routes for water acquisition. Water is acquired by oral intake and subsequent absorption by the intestine in terrestrial and marine animals which are subjected to constant dehydration, whereas most water is gained osmotically across body surfaces in freshwater animals. In addition, a significant amount of water, called metabolic water, is produced within the body by the oxidation of hydrogen in organic substrates. The importance of metabolic water production as a strategy for water acquisition has been well documented in desert animals, but its role has attracted little attention in marine animals which also live in a dehydrating environment. In this article, the author has attempted to reevaluate the role of metabolic water production in body fluid regulation in animals inhabiting desiccating environments. Because of the exceptional ability of their kidney, marine mammals are thought to typically gain water by drinking environmental seawater and excreting excess NaCl in the urine. On the other hand, it is established that marine teleosts drink seawater to enable intestinal water and ion absorption, and the excess NaCl is excreted by branchial ionocytes. In addition to the oral route, we suggest through experiments using eels that water production by lipid metabolism is an additional route for water acquisition when they encounter seawater. It seems that metabolic water production contributes to counteract dehydration before mechanisms for water regulation are reversed from excretion in freshwater to acquisition in seawater.

Biology and functions of fish thrombocytes: A review.

This comprehensive review examines the role of fish thrombocytes, cells considered functionally analogous to platelets in terms of coagulation, but which differ in their origin and morphology. Despite the evolutionary distance between teleosts and mammals, genomic studies reveal conserved patterns in blood coagulation, although there are exceptions such as the absence of factors belonging to the contact system. Beyond coagulation, fish thrombocytes have important immunological functions. These cells express both proinflammatory genes and genes involved in antigen presentation, suggesting a role in both innate and adaptive immune responses. Moreover, having demonstrated their phagocytic abilities, crucial in the fight against pathogenic microorganisms, underscores their multifaceted involvement in immunity. Finally, the need for further research on the functions of these cells is highlighted, in order to better understand their involvement in maintaining the health of aquaculture fish. The use of standardized and automated methods for the analysis of these activities is advocated, emphaiszing their potential to facilitate the early detection of stress or infection, thus minimizing the economic losses that these adverse situations can generate in the field of aquaculture.

Immune aging in annual killifish.

Turquoise killifish (Nothobranchius furzeri) evolved a naturally short lifespan of about six months and exhibit aging hallmarks that affect multiple organs. These hallmarks include protein aggregation, telomere shortening, cellular senescence, and systemic inflammation. Turquoise killifish possess the full spectrum of vertebrate-specific innate and adaptive immune system. However, during their recent evolutionary history, they lost subsets of mucosal-specific antibody isoforms that are present in other teleosts. As they age, the immune system of turquoise killifish undergoes dramatic cellular and systemic changes. These changes involve increased inflammation, reduced antibody diversity, an increased prevalence of pathogenic microbes in the intestine, and extensive DNA damage in immune progenitor cell clusters. Collectively, the wide array of age-related changes occurring in turquoise killifish suggest that, despite an evolutionary separation spanning hundreds of millions of years, teleosts and mammals share common features of immune system aging. Hence, the spontaneous aging observed in the killifish immune system offers an excellent opportunity for discovering fundamental and conserved aspects associated with immune system aging across vertebrates. Additionally, the species' naturally short lifespan of only a few months, along with its experimental accessibility, offers a robust platform for testing interventions to improve age-related dysfunctions in the whole organism and potentially inform the development of immune-based therapies for human aging-related diseases.

Telencephalic eversion in embryos and early larvae of four teleost species.

The telencephalon of ray-finned fishes undergoes eversion, which is very different to the evagination that occurs in most other vertebrates. Ventricle morphogenesis is key to build an everted telencephalon. Thus, here we use the apical marker zona occludens 1 to understand ventricle morphology, extension of the tela choroidea and the eversion process during early telencephalon development of four teleost species: giant danio (Devario aequipinnatus), blind cavefish (Astyanax mexicanus), medaka (Oryzias latipes), and paradise fish (Macroposus opercularis). In addition, by using immunohistochemistry against tubulin and calcium-binding proteins, we analyze the general morphology of the telencephalon, showing changes in the location and extension of the olfactory bulb and other telencephalic regions from 2 to 5 days of development. We also analyze the impact of abnormal eye and telencephalon morphogenesis on eversion, showing that cyclops mutants do undergo eversion despite very dramatic abnormal eye morphology. We discuss how the formation of the telencephalic ventricle in teleost fish, with its characteristic shape, is a crucial event during eversion.

Effects of temperature acclimation on the upper thermal tolerance of two Arctic fishes.

The thermally dynamic nearshore Beaufort Sea, Alaska, is experiencing climate change-driven temperature increases. Measuring thermal tolerance of broad whitefish (Coregonus nasus) and saffron cod (Eleginus gracilis), both important species in the Arctic ecosystem, will enhance understanding of species-specific thermal tolerances. The objectives of this study were to determine the extent that acclimating broad whitefish and saffron cod to 5°C and 15°C changed their critical thermal maximum (CTmax) and HSP70 protein and mRNA expression in brain, muscle and liver tissues. After acclimation to 5°C and 15°C, the species were exposed to a thermal ramping rate of 3.4°C · h-1 before quantifying the CTmax and HSP70 protein and transcript concentrations. Broad whitefish and saffron cod acclimated to 15°C had a significantly higher mean CTmax (27.3°C and 25.9°C, respectively) than 5°C-acclimated fish (23.7°C and 23.2°C, respectively), which is consistent with trends in CTmax between higher and lower acclimation temperatures. There were species-specific differences in thermal tolerance with 15°C-acclimated broad whitefish having higher CTmax and HSP70 protein concentrations in liver and muscle tissues than saffron cod at both acclimation temperatures. Tissue-specific differences were quantified, with brain and muscle tissues having the highest and lowest HSP70 protein concentrations, respectively, for both species and acclimation temperatures. The differences in broad whitefish CTmax between the two acclimation temperatures could be explained with brain and liver tissues from 15°C acclimation having higher HSP70a-201 and HSP70b-201 transcript concentrations than control fish that remained in lab-acclimation conditions of 8°C. The shift in CTmax and HSP70 protein and paralogous transcripts demonstrate the physiological plasticity that both species possess in responding to two different acclimation temperatures. This response is imperative to understand as aquatic temperatures continue to elevate.

Manual for the study of tapeworms (Cestoda) parasitic in ray-finned fish, amphibians and reptiles.

Based on long-term and often frustrating experiences with the poor quality of tapeworms (Cestoda) collected throughout the world for taxonomic and phylogenetic studies, and considering the increasing obstacles to obtaining new material, a simple, easy-to-use and illustrated methodological guide (manual) is provided. It focusses mainly on key steps in examining hosts, collecting cestodes from poikilothermous vertebrates except elasmobranchs, i.e., from ray-finned fish (Actinopterygii), amphibians and 'reptiles' (a paraphyletic group comprising all sauropsids except birds), and fixing them for subsequent morphological and molecular study. It is proposed that the following methodological points should be followed: (i) ideally only freshly euthanised hosts (not previously frozen) should be used for parasitological examination; (ii) hosts examined should be documented by photographs; host tissue should also be preserved for future genotyping if necessary; (iii) tapeworms should be detached carefully to keep the scolex intact and properly cleaned before fixation; (iv) a small piece of cestode tissue should be always preserved in molecular grade ethanol for DNA sequencing; (v) tapeworms should be fixed as quickly as possible after collecting them and while they are still alive, always using hot (heated) fixatives; this prevents unnatural contraction or deformation and ensures uniform fixation; (vi) each sample (vial) should be properly labelled (a unique code should be given to every cestode sample); (vii) vouchers of sequenced specimens (hologenophores or paragenophores) should always be preserved for identification, and deposited in internationally recognised collections. It is hoped that this guide helps researchers and students to properly process valuable material of cestodes to make it suitable for reliable identification including genotyping and comparative anatomy, which is a prerequisite for any subsequent ecological, biogeographical, phylogenetic life cycle or molecular study.

In situ observation of a macrourid fish at 7259†m in the Japan Trench: swimbladder buoyancy at extreme depth.

A macrourid, Coryphaenoides yaquinae sp. inc., was observed to be attracted to bait and exhibiting normal foraging behaviour during a period of 80 min within view of a baited video camera on the sea floor at 7259 m - the deepest ever observation of a fish species with a swim bladder. The buoyancy provided by an oxygen-filled swim bladder at 74.4 MPa pressure was estimated to be 0.164 N, at a theoretical energy cost of 20 kJ, 200 times less than the cost of equivalent lipid buoyancy. During normal metabolism, 192 days would be required to fill the swimbladder. At these depths, oxygen is very incompressible, so changes in volume during ascent or descent are small. However, swimbladder function is crucially dependent on a very low rate of diffusion of oxygen across the swimbladder wall. The oxygen in the swimbladder could theoretically sustain aerobic metabolism for over 1 year but is unlikely to be used as a reserve.

The role of marine fish-produced carbonates in the oceanic carbon cycle is determined by size, specific gravity, and dissolution rate.

Rising CO2 emissions have heightened the necessity for increased understanding of Earth's carbon cycle to predict future climates. The involvement of marine planktonic species in the global carbon cycle has been extensively studied, but contributions by marine fish remain poorly characterized. Marine teleost fishes produce carbonate minerals ('ichthyocarbonates') within the lumen of their intestines which are excreted at significant rates on a global scale. However, we have limited understanding of the fate of excreted ichthyocarbonate. We analyzed ichthyocarbonate produced by three different marine teleosts for mol%MgCO3 content, size, specific gravity, and dissolution rate to gain a better understanding of ichthyocarbonate fate. Based on the species examined here, we report that 75 % of ichthyocarbonates are ≤0.91 mm in diameter. Analyses indicate high Mg2+ content across species (22.3 to 32.3 % mol%MgCO3), consistent with previous findings. Furthermore, ichthyocarbonate specific gravity ranged from 1.23 to 1.33 g/cm3, and ichthyocarbonate dissolution rates varied among species as a function of aragonite saturation state. Ichthyocarbonate sinking rates and dissolution depth were estimated for the Atlantic, Pacific, and Indian ocean basins for the three species examined. In the North Atlantic, for example, ~33 % of examined ichthyocarbonates are expected to reach depths exceeding 200 m prior to complete dissolution. The remaining ~66 % of ichthyocarbonate is estimated to dissolve and contribute to shallow water alkalinity budgets. Considering fish biomass and ichthyocarbonate production rates, our results support that marine fishes are critical to the global carbon cycle, contributing to oceanic alkalinity budgets and thereby influencing the ability of the oceans to neutralize atmospheric CO2.

A review of soluble factors and receptors involved in fish skin immunity: The tip of the iceberg.

The immune system of fish possesses soluble factors, receptors, pathways and cells very similar to those of the other vertebrates' immune system. Throughout evolutionary history, the exocrine secretions of organisms have accumulated a large reservoir of soluble factors that serve to protect organisms from microbial pathogens that could disrupt mucosal barrier homeostasis. In parallel, a diverse set of recognition molecules have been discovered that alert the organism to the presence of pathogens. The known functions of both the soluble factors and receptors mentioned above encompass critical aspects of host defense, such as pathogen binding and neutralization, opsonization, or modulation of inflammation if present. The molecules and receptors cooperate and are able to initiate the most appropriate immune response in an attempt to eliminate pathogens before host infection can begin. Furthermore, these recognition molecules, working in coordination with soluble defence factors, collaboratively erect a robust and perfectly coordinated defence system with complementary specificity, activity and tissue distribution. This intricate network constitutes an immensely effective defence mechanism for fish. In this context, the present review focuses on some of the main soluble factors and recognition molecules studied in the last decade in the skin mucosa of teleost fish. However, knowledge of these molecules is still very limited in all teleosts. Therefore, further studies are suggested throughout the review that would help to better understand the functions in which the proteins studied are involved.

Identification of maturation-inducing steroid in sturgeons via comprehensive analyses of steroids produced during oocyte maturation.

Although 17α, 20ß-dihydroxy-4-pregnen-3-one (DHP) and 17α, 20ß, 21-trihydroxy-4-pregnen-3-one (20ß-S) have been identified as maturation-inducing steroids (MIS) in several teleosts, to date, no MISs have been identified in sturgeons. As it remains possible that an unidentified steroid is an MIS in sturgeons, this study aimed to identify a sturgeon MIS via comprehensive analyses and maturation-inducing (MI) assay of C21 steroids. In vivo and in vitro comprehensive analyses of C21 steroids revealed that serum DHP concentrations were rapidly elevated in the oocyte maturation phase and the DHP production level was notably high among C21 steroids. MI assay indicated that the MI activity of DHP, 17α-hydroxyprogesterone (17OHP), a precursor of DHP, 17α, 20α-dihydroxy-4-pregnen-3-one (αDHP), and 20ß-S was high among C21 steroids, but the MI activity of these steroids were similar. In the C21 steroids produced in ovarian follicles during oocyte maturation, 17OHP, αDHP, and unidentified compounds had a low production level, and 20ß-S was suggested to be metabolized from DHP after oocyte maturation. Against this background, this study concluded that DHP is a steroid that possesses strong MI activity and is highly produced during oocyte maturation. Although this study could not identify an MIS in sturgeons by fractionation of plasma and subsequent bio assay, it was suggested that DHP is a major MIS in sturgeons.

Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei.

The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.

DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden.

Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes.