Dietary carbohydrate in land-locked salmon

A common-garden experiment was carried out to compare two genetically distinct strains of Atlantic salmon (Salmo salar) fed diets with either high (CHO) or low (NoCHO) digestible carbohydrate (starch). Twenty salmon from either a commercial farmed strain (F) or a land-locked population (G) were placed in two tanks (10 fish of each population in each tank) and fed either CHO or NoCHO feeds. At the end of the experiment fish were fasted for 8 h, euthanized and blood and liver collected. Both diet and population had an effect on circulating glucose levels with G showing hypoglycaemia and dietary starch increasing this parameter. In contrast, G showed increased plasma triacylglycerol levels regardless of dietary treatment suggesting faster conversion of glucose to triacylglycerol. This different ability to metabolise dietary starch among strains was also reflected at a molecular (gene) level as most of the metabolic pathways evaluated were mainly affected by the factor population rather than by diet. The data are promising and suggest different regulatory capacities towards starch utilization between land-locked salmon and the farmed stock. Further analyses are necessary in order to fully characterise the capacity of land-locked salmon to utilise dietary carbohydrate

Epigenetics in teleost fish: from molecular mechanisms to physiological phenotypes

The final publication is available at Elsevier via https://doi.org/10.1016/j.cbpb.2018.01.006. © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease

Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications

DNA methylation is an important epigenetic mechanism involved in many biological processes, i.e. gametogenesis and embryonic development. However, increased copy numbers of DNA methylation related genes (dnmt, tet and tdg) have been found during chordate evolution due to successive whole genome duplication (WGD) events. Their evolutionary history and phylogenetic relationships remain unclear. The present study is the first to clarify the evolutionary history of DNA methylation genes in chordates. In particular, our results highlight the fixation of several dnmt3-related genes following successive WGD throughout evolution. The rainbow trout genome offered a unique opportunity to study the early evolutionary fates of duplicated genes due to a recent round of WGD at the radiation of salmonids. Differences highlighted in transcriptional patterns of these genes during gametogenesis and ontogenesis in trout indicated that they might be subjected to sub- or neo-functionalisation after WDG. The fixation of multiple dnmt3 genes in genomes after WGD could contribute to the diversification and plastic adaptation of the teleost

Caractérisation des gènes nanog, c-myc, pou2 et sox2 au cours du développement précoce chez le poisson rouge (carassius auratus)

Le poisson rouge est une espèce utilisée régulièrement dans le cadre du transfert nucléaire somatique. Cependant, peu de données moléculaires concernant entre autre des gènes impliqués dans le développement précoce sont disponibles dans cette espèce dont le génome n est pas séquencé. L objectif du travail était donc de séquencer et de caractériser au cours du développement embryonnaire et dans la nageoire de poisson rouge les orthologues des gènes Pou5f1 (pou2 chez les téléostéens), Sox2, c-Myc et Nanog connus chez les mammifères pour leur implication et leur importance dans le développement des mammifères. Par la mise en place d analyses in silico, notre travail a permis de préciser l identité des gènes séquencés chez le poisson rouge et leur histoire phylogénétique. Notre étude montre notamment que c-myc a subi deux duplications au sein des téléostéens, dont une spécifique aux cyprininae, sous-famille à laquelle appartient le poisson rouge. L étude détaillée du profil d expression et de méthylation de l ADN des gènes au cours du développement embryonnaire et dans les cellules de nageoire a révélé des différences avec les données existantes dans la littérature relatives aux autres téléostéens modèles tels que le poisson-zèbre ou le médaka mais aussi avec les mammifères. Outre l intérêt de ces travaux pour l étude et la compréhension de l implication de pou2, nanog, c-myc et sox2 au cours du développement précoce des embryons de téléostéens, les caractéristiques moléculaires des gènes mises en évidence dans cette étude pourront être utilisés comme témoin de la reprogrammation du génome de la cellule de nageoire après transfert nucléaire somatique.The goldfish is a species widely considered when studying somatic nuclear transfer biotechnology. However, few molecular data notably related to early developmental genes are available in this species whose genome is not sequenced. Thus this work aimed at sequencing and characterizing during early goldfish development and in fin tissue orthologous genes of mammalian Pou5f1 (pou2 chez les téléostéens), Sox2, c-Myc and Nanog known to be involved and important during development in mammals. Using in silico analyses, we were able to confirm the identity of sequenced genes in goldfish and to clarify their phylogenetic history among teleosts. Our results especially show that two gene duplications occured at the c-myc locus in teleosts, one of them specifically in cyprininae sub-family which goldfish belongs to. The throughout study of both expression and DNA methylation patterns during embryonic development and in fin tissue highlighted differences between data previously published in zebrafish or medaka as well as in mammals. Our work provides new insight into important developmental genes identities, expression and DNA methylation in teleosts and paves the way for further functional analysis. Finally, molecular characteristics of the genes described in this study can be used as markers to monitor the reprogrammation of fin cell genome after somatic nuclear transfer.RENNES1-BU Sciences Philo (352382102) / SudocSudocFranceF

Expression patterns of DNA methyltransferase genes during gametogenesis and early development in rainbow trout Oncorhynchus mykiss

RésuméRésuméDNA methylation is one of the most extensively studied epigenetic mechanisms that modulate gene expression and cellular differentiation. It plays critical roles during gametogenesis and early development of vertebrates. Previous studies in mammals demonstrated that DNA methylation is accomplished through the activities of DNA methyltransferases (Dnmts). Dnmt1 is associated with the maintenance of methylation status, whereas Dnmt3a and Dnmt3b are essential for de novo methylation. The present study aimed at investigating the dynamic transcription pattern of dnmt genes during gametogenesis and early development for the first time in rainbow trout (Oncorhynchus mykiss), an economically important fish speciesDue to the fact that the teleost experienced a third round of whole genome duplication (WGD) apart from the two round of WGD that occurred at the root of the vertebrate lineage, the evolutionary of dnmt genes remains unclear. Indeed, there are three common fates for the duplicated genes after WGD: loss one of the duplicate gene, sub- or neo-functionalisation. In the present study, two ohnologs of dnmt1 (dnmt1a and dnmt1b) and eight paralogs of dnmt3 (including 3 paralogs of dnmt3a: dnmt3aa, dnmt3ab1, dnmt3ab2, and 5 paralogs of dnmt3b: dnmt3ba1, dnmt3ba2, dnmt3bba1, dnmt3bba2 and dnmt3bbb) were identified in rainbow trout. Spatial expression patterns of dnmt genes were analysed using the PhyloFish database to identify the main expression territories of these genes. Results showed that, both dnmt1 ohnologs were preferentially expressed in unfertilised eggs. dnmt3a paralogs were highly expressed in brain, whereas dnmt3ba1, dnmt3ba2, dnmt3bbb were predominantly expressed in skin, head kidney and ovary, respectively, which could be possibly linked to a sub- or neo-functionalisation after WDG.The dynamic expression patterns of dnmt genes were analysed in trout gonads during gametogenesis (between two spawn). Our results showed that there was a remarkable increase in the mRNA levels of dnmt1a and three of the five dnmt3b paralogs in oocytes compared with ovaries in females. In males, we observed the highest mRNA level of dnmt1a together with the lowest mRNA levels of dnmt3ab1 and dnmt3bba1 at the late-spermatogenesis stage. Besides, mRNA levels of dnmt genes were also analysed during early development of trout from stage 0 (oocyte) to stage 36 (alevin). All dnmt genes displayed a similar expression pattern, with no or low mRNA levels from stage 0 up to 15, followed by a sharp increase at the setting up of the most of the vital organs (stage 22/23) and then decreased after hatching. By contrast, there was relatively high transcript abundance of dnmt3bbb from the beginning of embryogenesis, suggesting its functionally importance during early development.In conclusion, the dynamic expression patterns of dnmt genes during gametogenesis and early development suggested that epigenetic mechanisms actively participated in these physiological processes in trout. The distinct transcription patterns of dnmt3b paralogs indicated that they may subject to sub- or neo-functionalisation after WDG

New insights on intermediary metabolism for a better understanding of nutrition in teleosts

International audienceThe rapid development of aquaculture production throughout the world over the past few decades has led to the emergence of new scientific chal lenges to improve fish nutrition. The diet formulations used for farmed fish have been largely modified in the past few years. However, bottlenecks still exist in being able to suppress totally marine resources (fish meal and fish oil) in diets without negatively affecting growth performance and flesh quality. A better understanding of fish metabolism and its regulation by nutrients is thus mandatory. In this review, we discuss four fields of research that are highly important for improving fish nutrition in the future: ( a ) fish genome complexity and subsequent consequences for metabolism, ( b )) microRNAs (miRNAs) as new actors in regulation of fish metabolism, ( c ) the role of autophagy in regulation of fish metabolism, and ( d ) the nutritional programming of metabolism linked to the early life of fish

Parental high carbohydrates/low protein diets in rainbow trout modulate DNA-methylation landscape in their progeny

International audienceFor aquaculture sustainability, broodstock diet for carnivorous species will rapidly evolve toward a decrease of the protein-to-carbohydrate ratio, with the substitution of the protein-rich fishmeal by plant-derived carbohydrates (Callet et al., 2020). Numerous studies have reported that parental high carbohydrate (HC)/ low protein (LP) nutrition could affect their progeny epigenetic landscape and subsequently their metabolism in various species (Gao et al., 2020). In carnivorous fish species, even though the effects of parental nutrition have already been demonstrated (Hou et al., 2020), the consequences of parental HC/LP have never been explored until now. To investigate this question, two-year old male and female trout were fed either a control diet (0% carbohydrate and 63.89% protein) or a diet containing a high proportion of carbohydrates (35% carbohydrate and 42,96% protein) for an entire reproductive cycle for females (10 months) and 5 months for males. Crossed-fertilizations were carried out in order to obtain four groups of fish. Samplings and DNA extractions were performed at different life stages in order to quantify the proportions of the four forms of methylatedmethyl- cytosine (5-mC) derivatives (5-mC, 5-hmC, 5-fC, and 5-caC and 5-C), by HPLC-UV analysis. Before the first feeding, the maternal HC-LP nutrition induced at the same time a decrease of 5-mC proportion decrease and an increase of 5-caC proportion increase in their progeny (whole fry). These effects were enhanced by the paternal nutrition (Callet et al. 2021). The underlying mechanisms probably include the modulation of the expression of the genes coding for the enzymes responsible for the de novo methylation, as transcriptomic analyses revealed that dnmt3bbb relative expression was significantly reduced by the parental nutrition. Such outcome is maintained over time and regardless of the diet given, as the maternal HC-LP nutrition also triggered a decrease of both 5-mC and 5-hmC proportions in the liver, after a 9-month feeding trial.Interestingly, a previous study has also reported a global DNA-hypomethylation in juvenile trout which were directly fed with a high carbohydrate diet (Marandel et al., 2016). Overall, the data accumulation suggests that HC-LP nutrition, whether directly or indirectly via parental nutrition, highly modulates the DNA-methylation landscape in trout

A reassessment of the carnivorous status of salmonids: hepatic glucokinaseis expressed in wild fish in Kerguelen islands

RésuméRésuméInternational audienc