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The evolution of sex determination (SD) mechanisms in teleost fishes is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified, even sometimes among closely related species. Pangasiids are a group of economically important catfishes in many South-Asian countries, but little is known about their sex determination system. Here, we generated novel genomic resources for 12 Pangasiid species and provided a first characterization of their SD system. Based on an Oxford Nanopore long-read chromosome-scale high quality genome assembly of the striped catfish Pangasianodon hypophthalmus, we identified a duplication of the anti-Müllerian hormone receptor type II gene (amhr2), which was further characterized as being sex-linked in males and expressed only in testicular samples. These first results point to a male-specific duplication on the Y chromosome (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Short-read genome sequencing and reference-guided assembly of 11 additional Pangasiid species, along with sex-linkage studies, revealed that this truncated amhr2by duplication is also conserved as a male-specific gene in many Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication / insertion event at the root of the Siluroidei radiation that is dated around 100 million years ago. Altogether these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiid catfishes, a finding that highlights the recurrent usage of the transforming growth factor β pathway in teleost sex determination and brings another empirical case towards the understanding of the dynamics or stability of sex determination systems.

International audience; Chub mackerel Scomber japonicus and blue mackerel S. australasicus have become important aquaculture target species in Japan. For an efficient and stable aquaculture production of mackerels, it is desirable to work with a female-biased broodstock and thus to be able to manage precisely their sex ratio. As these two mackerel species do not have any external sexual dimorphism, direct biopsy of the gonads or measurement of sex hormone plasma levels is used in research to determine their phenotypic sex. However, these methods are associated with handling stress that results in gonadal atresia. Besides, it is difficult to identify sex using these methods in immature individuals. Therefore, genetic sexing would be desirable in these species to overcome these problems. In this study, we developed molecular sex identification tools for both chub and blue mackerels using sex-specific single-nucleotide variations (SNVs) identified by pool-sequencing (pool-seq) analyses. Genomic DNA was isolated from 30 males and females, in each species, and sequenced as pooled samples. Results of these pool-seq analyses identified a clear XX/XY male heterogametic sex-determination system in blue mackerel and a ZZ/ZW female heterogametic system in chub mackerel. Using this pool-seq information, we designed primer sets for genetic sex identification in both species. Results demonstrated that these primer sets are robust and accurate in assessing the genotypic sex of both blue and chub mackerels (accuracy > 99.5% in the chub, and > 94.5% in the blue mackerel) in various geographical samples of different ages. This method can now be applied for the efficient management of sex ratios in both mackerel aquaculture populations and wild-caught animals for fisheries management.

International audience; Trophic support of species-rich tropical fish communities remains uncertain in small forest streams where dense and constant canopy cover strongly limits the solar radiation available to aquatic producers. We sampled >1300 fish from 80 species in 14 remote headwater streams during the dry season in French Guiana. Carbon and nitrogen stable isotope analyses and mixing models were run to estimate the trophic position (TP) of each species and its dependence on terrestrial organic carbon sources. Matching patterns were found between nitrogen stable isotope ratios and the literature on diets of species at the base and top of the food web. Nearly 60% of the species fed exclusively on animal prey (mean TP >3), including piscivorous and parasitic fish species. Phylogenetic analysis revealed that TP were distributed broadly along the phylogeny and changed gradually within lineages. Carbon stable isotope ratios differed strongly between herbivores that fed on aquatic primary producers and those that fed on terrestrial plants along banksides. Terrestrial carbon was dominant in nearly 90% of species, and most of them depended more or less exclusively on terrestrial carbon. Ancestral state reconstructions indicated that only a few lineages showed local changes toward the consumption of algal carbon. We conclude that fish in neotropical headwater streams shaded by a dense tree canopy depend strongly on terrestrial subsidies. Changes in this aquatic-terrestrial linkage would have major consequences for the remarkable fish biodiversity in these streams.; La contribution majoritaire du carbone algal aux réseaux trophiques d'eau douce a été démontrée, même dans la partie amont des bassins versants où les apports de carbone terrestre sont substantiels. Ces apports terrestres proviennent principalement de lignocellulose, une source de nourriture que les consommateurs n'assimilent pas bien sous les climats tempérés, contrairement aux algues de haute qualité nutritive. La prédominance de l'apport algal reste en questionnement dans les petits cours d'eau en forêt tropicale, qui diffèrent entre autre par un couvert forestier dense et constant limitant fortement le rayonnement solaire disponible pour les producteurs aquatiques, par les essences végétales elles même, et par les caractéristiques physicochimiques du sol et de l'eau. Nous avons étudié l'écologie trophique de 80 espèces de poissons (> 1300 individus) issues de 14 ruisseaux pauvres en nutriments dans un contexte de forêt tropicale préservée en Guyane Française. Nous avons rassemblé des informations sur leur alimentation, puis combiné ces connaissances avec l'analyse des isotopes stables C et N dans leur muscle et dans une variété d'aliments potentiels, aquatiques et terrestres. Nous avons calculé leur position trophique et leur dépendance vis‐à‐vis des sources de C terrestres ou aquatiques. Nos résultats montrent des profils trophiques concomitants entre les isotopes stables de l'azote et la littérature sur les régimes alimentaires des espèces à la base et au sommet du réseau trophique, validant la pertinence d'une telle approche combinée pour ces communautés de poissons. Nous constatons qu'une majorité des espèces (60%) se nourrit de proies animales, y compris des poissons strictement piscivores. Une grande majorité (près de 90%) dépend principalement de sources alimentaires terrestres (>50% de C terrestre dans leurs tissus), et 65% en dépendrait plus ou moins exclusivement (>75% de C terrestre). Leurs niveaux trophiques sont très variables, depuis l'herbivorie (Myloplus ternetzi) jusqu’à l'ichtyoparasitisme (Ituglanis nebulosus). Seules 9 espèces sont plus fortement liées aux sources de C aquatique, et elles ont majoritairement un niveau trophique bas (Farlowella reticulata, Cyphocharax helleri, Ancistrus temminckii, Ancistrus aff. hoplogenys, Satanoperca rhynchitis and Ancistrus cf. leucostictus). Ces traits trophiques ont été utilisés dans une analyse phylogénétique pour tester leur pertinence évolutive. Ceci révèle que les positions trophiques sont largement réparties le long de la phylogénie et changent progressivement au sein des lignées. Les reconstructions d'états ancestraux indiquent toutefois que quelques lignées montrent des changements ponctuels vers la consommation de carbone algal. Nous concluons que les poissons des petits cours d'eau néotropicaux ombragés par un couvert forestier dense dépendent très fortement des apports nutritifs terrestres. Des changements dans ce lien aquatique‐terrestre auraient des conséquences majeures sur la remarquable biodiversité des poissons de ces cours d'eau. Ces connaissances aideront les gestionnaires de l'environnement à mieux appréhender les impacts potentiels des projets d'exploitation des ressources naturelles, et à proposer des solutions de remédiations plus pertinentes dans les cas de réhabilitation de sites en fin d'exploitation.

MicroRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole-genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the teleost genome duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than nonclustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3′-complementary regions, compared with minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multispecies analysis of the mechanisms influencing metazoan miRNA evolution after whole-genome duplication.

Pikeperch, Sander lucioperca, is a species of high interest to the aquaculture. The expansion of its production can only be achieved by furthering domestication level. However, the mechanisms driving the domestication process in finfishes are poorly understood. Transcriptome profiling of eggs was found to be a useful tool allowing understanding of the domestication process in teleosts. In this study, using next-generation sequencing, the first pikeperch transcriptome has been generated as well as pikeperch-specific microarray comprising 35,343 unique probes. Next, we performed transcriptome profiling of eggs obtained from wild and domesticated populations. We found 710 differentially expressed genes that were linked mostly to nervous system development. These results provide new insights into processes that are directly involved in the domestication of finfishes. It can be suggested that all the identified processes were predetermined by the maternally derived set of genes contained in the unfertilized eggs. This allows us to suggest that fish behavior, along with many other processes, can be predetermined at the cellular level and may have significant implications on the adaptation of cultured fish to the natural environment. This also allows to suggest that fish behavior should be considered as a very important pikeperch aquaculture selection trait.

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression involved in countless biological processes and are widely studied across metazoans. Although miRNA research continues to grow, the large community of fish miRNA researchers lacks exhaustive resources consistent among species. To fill this gap, we developed FishmiRNA, an evolutionarily supported miRNA annotation and expression database for ray-finned fishes: www.fishmirna.org. The self-explanatory database contains detailed, manually curated miRNA annotations with orthology relationships rigorously established by sequence similarity and conserved syntenies, and expression data provided for each detected mature miRNA. In just few clicks, users can download the annotation and expression database in several convenient formats either in its entirety or a subset. Simple filters and Blast search options also permit the simultaneous exploration and visual comparison of expression data for up to any ten mature miRNAs across species and organs. FishmiRNA was specifically designed for ease of use to reach a wide audience.

Simple Summary The Atlantic bluefin tuna Thunnus thynnus is a species characterized by complex trans-oceanic migrations linked to size, which rely on the delicate trade-off between somatic growth and reproduction before and during the migratory movements to reach spawning grounds. Therefore, understanding the processes that drive reproduction and elucidating its age-related regulation is essential in the context of sustainable fishery management. In this study, carried out in the Mediterranean Sea, older bluefin tuna females were found to have greater reproductive performances than younger females according to a molecular biology approach (i.e., gene expression), a result that likely mirrors a better physical condition, different habitat usage or migratory behaviour. This result highlights the importance of preserving large females for their major reproductive contribution at a stock level. Furthermore, the gonad-specific mir-202, which belongs to a class of non-coding RNA, called miRNA, that regulate the post-transcription of protein-coding genes, was identified as a potential candidate to play a role in egg quality and quantity (i.e., fecundity) during ovarian maturation through age- or stage-dependent reproductive processes. Overall, the present study contributes to improve the sustainability of the Atlantic bluefin tuna fishery in the Mediterranean Sea. Abstract In the Mediterranean Sea, a demographic substructure of the Atlantic bluefin tuna Thunnus thynnus has emerged over the last decade, with old and young individuals exhibiting different horizontal movements and spatial–temporal patterns of gonad maturation. In the present study, histology and molecular reproductive markers were integrated with the gonad-specific mir-202 gene expression and ovarian localization to provide a comprehensive picture of the reproductive performances in young and old females and investigate the role played by the mir-202 during gonadal maturation. During the reproductive period, old females (>100 kg; 194.6 ± 33.9 cm straight fork length; 11.3 ± 2.7 years old) were found to have greater reproductive performances than younger females (

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu., この研究のプレスリリース版はこちら: http://id.nii.ac.jp/1342/00002272/

Several steps of sturgeon somatic cell nuclear transfer (SCNT) have been recently established, but improvements are needed to make it a feasible tool to preserve the natural populations of this group of endangered species. The donor cell position inside the recipient egg seems to be crucial for its reprogramming; therefore by injecting multiple donor somatic cells instead of a single cell with a single manipulation, we increased the potential for embryo development. Using the Russian sturgeon Acipenser gueldenstaedtii as a multiple cell donor and sterlet Acipenser ruthenus as the non-enucleated egg recipient, we obtained higher proportion of eggs developing into embryos than previously reported with single-SCNT. Molecular data showed the production of a specimen (0.8%) contained only the donor genome with no contribution from the recipient, while two specimens (1.6%) showed both recipient and donor genome. These findings are the first report of donor DNA integration into a sturgeon embryo after interspecific cloning. In all, we provide evidence that cloning with the multiple donor somatic cells can be feasible in the future. Despite the fact that the sturgeon cloning faces limitations, to date it is the most promising technique for their preservation.

International audience; CRISPR-Cas9 technology is a very efficient functional analysis tool and has been developed in several insects to edit their genome through injection of eggs with guideRNAs targeting coding sequences of genes of interest. However, its implementation in aphids is more challenging. Aphids are major pests of crops worldwide thatalternate during their life cycle between clonality and sexual reproduction. The production of eggs after mating of sexual individuals is a single yearly event and isnecessarily triggered by a photoperiod decrease. Fertilized eggs then experience an obligate 3-month diapause period before hatching as new clonal colonies. Takinginto consideration these particularities, we developed in the pea aphid Acyrthosiphon pisum a step-by-step protocol of targeted mutagenesis based on the microinjectionwithin fertilized eggs of CRISPR-Cas9 components designed for the editing of a cuticular protein gene (stylin-01). This protocol includes the following steps:i) the photoperiod-triggered induction of sexual morphs (2 months), ii) the mating and egg collection step (2 weeks), iii) egg microinjection and melanization, iv) the3-month obligate diapause, v) the hatching of new lineages from injected eggs (2 weeks) and vi) the maintenance of stable lineages (2 weeks). Overall, this 7-monthlong procedure was applied to three different crosses in order to estimate the impact of the choice of the genetic combination on egg production dynamics by femalesas well as hatching rates after diapause. Mutation rates within eggs before diapause were estimated at 70–80%. The hatching rate of injected eggs following diapauseranged from 1 to 11% depending on the cross and finally a total of 17 stable lineages were obtained and maintained clonally. Out of these, 6 lineages were mutated atthe defined sgRNAs target sites within stylin-01 coding sequence, either at the two alleles (2 lineages) or at one allele (4 lineages). The final germline transmission rateof the mutations was thus around 35%. Our protocol of an efficient targeted mutagenesis opens the avenue for functional studies through genome editing in aphids.

Reprogramming of cultured cells using Xenopus egg extract involves controlling four major steps: plasma membrane permeabilization, egg factors import into the nucleus, membrane resealing, and cell proliferation. Using propidium iodide to assess plasma membrane permeability, we established that 90% of the cultured fin cells were permeabilized by digitonin without any cell losses. We showed that egg extract at metaphase II stage was essential to maintain nuclear import function in the permeabilized cells, as assessed with a fusion GFP protein carrying the nuclear import signal NLS. Moreover, the Xenopus-egg-specific Lamin B3 was detected in 87% of the cell nuclei, suggesting that other egg extract reprogramming factors of similar size could successfully enter the nucleus. Lamin B3 labelling was maintained in most cells recovered 24 h after membrane resealing with calcium, and cells successfully resumed cell cycle in culture. In contrast, permeabilized cells that were not treated with egg extract failed to proliferate in culture and died, implying that egg extract provided factor essential to the survival of those cells. To conclude, fish fin cells were successfully primed for treatment with reprogramming factors, and egg extract was shown to play a major role in their survival and recovery after permeabilization.

Sustainable aquaculture production requires a greater reduction in the use of marine-derived ingredients, and one of the most promising solutions today is the augmentation in the proportion of digestible carbohydrates in aquafeed. This challenge is particularly difficult for high trophic level teleost fish as they are considered to be glucose-intolerant (growth delay and persistent postprandial hyperglycemia observed in juveniles fed a diet containing more than 20% of carbohydrates). It was previously suggested that broodstock could potentially use carbohydrates more efficiently than juveniles, probably due to important metabolic changes that occur during gametogenesis. To investigate this hypothesis, 2-year old male and female rainbow trout (Oncorhynchus mykiss) were either fed a diet containing no carbohydrates (NC) or a 35%-carbohydrate diet (HC) for an entire reproductive cycle. Zootechnical parameters as well as the activities of enzymes involved in carbohydrate metabolism were measured in livers and gonads. Fish were then reproduced to investigate the effects of such a diet on reproductive performance. Broodstock consumed the HC diet, and in contrast to what is commonly observed in juveniles, they were able to grow normally and they did not display postprandial hyperglycemia. The modulation of their hepatic metabolism, with an augmentation of the glycogenesis, the pentose phosphate pathway and a possible better regulation of gluconeogenesis, may explain their improved ability to use dietary carbohydrates. Although the HC diet did induce precocious maturation, the reproductive performance of fish was not affected, confirming that broodstock are able to reproduce when fed a low-protein high-carbohydrate diet. In conclusion, this exploratory work has Frontiers in Physiology | www.frontiersin.org 1 May 2020 | Volume 11 | Article 303 Callet et al. Carbohydrate Utilization in Trout Broodstock shown that broodstock are able to use a diet containing digestible carbohydrates as high as 35% and can then grow and reproduce normally over an entire reproductive cycle for females and at least at the beginning of the cycle for males. These results are highly promising and suggest that dietary carbohydrates can at least partially replace proteins in broodstock aquafeed.

For the sustainable development of aquaculture, vegetable ingredients have been used to replace the traditional ingredients fishmeal and fish oil in aquafeeds. On the other hand, selective breeding has also been implemented at research level to obtain strains that are adapted to feeding on the plant-based diet. To better understand the underlying mechanisms prompting the adaptation to plant-based diets in fish, we investigated the hepatic expression of several microRNAs (miRNAs) that are involved in the post-transcriptional regulation of cholesterol and lipid metabolism at 8 h and 16 h after the last meal in two lines of rainbow trout: one selected for better adaptation to plant-based diets and the corresponding control line. Both groups were fed either a fishmeal and fish oil based diet or a 100% plant-based diet. Results showed that the expression of miR-33a in liver was greatly elevated in trout fed the plant-based diet, while the expression of miR-122 and miR-128 was much higher in the selected line at 8 h after the last meal regardless of the diet. Furthermore, our results indicated that some genes involved in immune processes (caspase 6 apoptosis-related cysteine peptidase like 2, casp6l2) and cAMP signal transduction (phosphodiesterase 4B cAMP-specific a, pde4ba) were also potentially regulated by miRNAs. They were newly identified as putative direct targets of miRNAs and affected in trout fed the plant-based diet. Though further investigations are still needed to establish a valid relationship between miRNAs and their target genes, our study found miR-33a, miR-122 and miR-128 as potential candidates for further study and provided new perspectives to understand the role of miRNAs in the selective breeding for adaptation to the plant-based diets.

Deciphering mechanisms of oocyte development in the fish ovary still remain challenging, and a comprehensive overview of this process at the level of the organ is still needed. The recent development of optical tissue clearing methods has tremendously boosted the three-dimensional (3D) imaging of large size biological samples that are naturally opaque. However, no attempt of clearing on fish ovary that accumulates extremely high concentration of lipids within oocytes has been reported to date. To face with this ovarian-specific challenge, we combined two existing clearing methods, the nontoxic solvent-based ethyl cinnamate (ECi) method for efficient clearing and the Clear Unobstructed Brain Imaging Cocktails and Computational (CUBIC) method to enhance lipid removal and reduce nonspecific staining. The methyl green fluorescent dye was used to stain nuclei and delineate the follicular structures that include oocytes. Using this procedure (named CUBIC-ECi [C-ECi]), ovaries of both medaka and trout could be imaged in 3D and follicles analyzed. To our knowledge, this is the first procedure elaborated for clearing and imaging fish ovary in 3D. The C-ECi method thus provides an interesting tool for getting precise quantitative data on follicular content in fish ovary and promises to be useful for further developmental and morphological studies.

International audience; The present study aimed to investigate whether environmental enrichment had significant effects on rainbow trout's welfare through nature-, functions- and feeling-based approaches. Fish group behavior was analyzed during the rearing phase, as well as growth performance and health status. We assessed individual's emotional reactivity through a novel-tank test by measuring fear-related behaviors and stress-related physiological responses. Fish boldness and neophobia were then evaluated towards a novel object. We showed that more complex environments decreased aggression levels and improved growth, without impacting fish immune status. Enriched fish were also found less fearful when isolated in a novel tank and bolder when facing a novel object. We concluded that complexifying the environment through the addition of physical structures which stimulate and encourage fish to explore promotes rainbow trout's welfare in farming conditions, according to the three different welfare approaches.

International audience; Pacific oyster Crassostrea gigas is one major species for aquaculture, and the development of breeding programs and the need for preservation of wild stock genetic resources prompted the need for larvae cryopreservation. The objective of the present study was to choose the most reliable protocol from several existing publications, to test its biological and practical limitations, and to adapt it to hatchery conditions. The selected protocol was characterized by a very slow freezing rate without seeding, and by the use of ethylene glycol and sucrose as cryoprotectant. The best survivals after thawing and rearing up to 48 h post fertilization (hpf) were obtained with larvae that were frozen at late trochophore (20 hpf) and early-D (24 hpf) stages. Increasing the larvae concentration in the straws and using high throughput straw filling and freezing devices did not alter the cryopreservation outcome. The whole procedure was applied to cryopreservation in a commercial hatchery (Satmar, France), and the thawed larvae yielded 9.4 ± 4.5% survivals at 12 days post fertilization. The overall success was dampened by some variability in the larvae survival that is likely due to the physiological status of the larvae. In all, the proposed procedure is robust and reliable and can be used for cryobanking of oyster genetic resources.

International audience; In fish, the presence of predator cues in the parental or juvenile environment engenders plasticity in the expression of fear-related behaviours. Whether these cues may engender developmental plasticity when they are present in the environment of embryos remains unexplored. Here, we tested in rainbow trout, Oncorhynchus mykiss: (1) whether exposure to alarm cues during embryonic stages engendered developmental plasticity; and (2) whether an abiotic stressor could also orient the behavioural development of fry. We divided fertilized eggs into three groups: a control nonstressed group (Control), a group of embryos exposed to a conspecific alarm pheromone (e.g. predator-related cue stressor, PS), and a group of embryos that were chronically air exposed for 1 min (e.g. abiotic stressor, AS). Stressors were applied once a day, 3 times per week from 19 days postfertilization (dpf) until 52 dpf. Between 57 and 143 dpf, and for each individual, we assessed the propensity to express fear responses in different contexts and learning performances. When exposed to a novel environment or a novel object, PS fish showed significantly less fear-related behaviour, less freezing and higher activity levels than Control fish. PS fish also showed slower acquisition of a learning task than controls. AS fish did not differ from controls in any test situation. Our results show that in ovo exposure to a natural but not an abiotic signal is a prominent inducer of rainbow trout behavioural plasticity across a number of contexts. Our study provides evidence that the expression of neophobia by fish fry may be modulated by the level of risk perceived by embryos in the environment.

Whole genome duplications (WGD) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however remains incomplete. Teleost fish experienced a common WGD (teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest lineage of teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and teleostean fish species, including spotted gar, zebrafish and medaka (the PhyloFish project), offered a unique opportunity to study the evolution of gene expression following TGD in teleosts. We show that most TGD duplicates gained their current status (loss of one duplicate gene or retention of both duplicates) relatively rapidly after TGD (i.e. prior to the divergence of medaka and zebrafish lineages). The loss of one duplicate is the most common fate after TGD with a probability of approximately 80%. In addition, the fate of duplicate genes after TGD, including subfunctionalization, neofunctionalization, or retention of two ‘similar’ copies occurred not only before, but also after the radiation of species tested, in consistency with a role of the TGD in speciation and/or evolution of gene function. Finally, we report novel cases of TGD ohnolog subfunctionalization and neofunctionalization that further illustrate the importance of these processes.

Background Glucose-6-phosphate (G6pc) is a key enzyme involved in the regulation of the glucose homeostasis. The present study aims at revisiting and clarifying the evolutionary history of g6pc genes in vertebrates. Results g6pc duplications happened by successive rounds of whole genome duplication that occurred during vertebrate evolution. g6pc duplicated before or around Osteichthyes/Chondrichthyes radiation, giving rise to g6pca and g6pcb as a consequence of the second vertebrate whole genome duplication. g6pca was lost after this duplication in Sarcopterygii whereas both g6pca and g6pcb then duplicated as a consequence of the teleost-specific whole genome duplication. One g6pca duplicate was lost after this duplication in teleosts. Similarly one g6pcb2 duplicate was lost at least in the ancestor of percomorpha. The analysis of the evolution of spatial expression patterns of g6pc genes in vertebrates showed that all g6pc were mainly expressed in intestine and liver whereas teleost-specific g6pcb2 genes were mainly and surprisingly expressed in brain and heart. g6pcb2b, one gene previously hypothesised to be involved in the glucose intolerant phenotype in trout, was unexpectedly up-regulated (as it was in liver) by carbohydrates in trout telencephalon without showing significant changes in other brain regions. This up-regulation is in striking contrast with expected glucosensing mechanisms suggesting that its positive response to glucose relates to specific unknown processes in this brain area. Conclusions Our results suggested that the fixation and the divergence of g6pc duplicated genes during vertebrates’ evolution may lead to adaptive novelty and probably to the emergence of novel phenotypes related to glucose homeostasis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3727-1) contains supplementary material, which is available to authorized users.

Dmrt1 is a highly conserved transcription factor, which is critically involved in regulation of gonad development of vertebrates. In medaka, a duplicate of dmrt1—acting as master sex-determining gene—has a tightly timely and spatially controlled gonadal expression pattern. In addition to transcriptional regulation, a sequence motif in the 3′ UTR (D3U-box) mediates transcript stability of dmrt1 mRNAs from medaka and other vertebrates. We show here that in medaka, two RNA-binding proteins with antagonizing properties target this D3U-box, promoting either RNA stabilization in germ cells or degradation in the soma. The D3U-box is also conserved in other germ-cell transcripts, making them responsive to the same RNA binding proteins. The evolutionary conservation of the D3U-box motif within dmrt1 genes of metazoans—together with preserved expression patterns of the targeting RNA binding proteins in subsets of germ cells—suggest that this new mechanism for controlling RNA stability is not restricted to fishes but might also apply to other vertebrates., In medaka a duplicate of dmrt1 acts as master sex-determining gene, with tightly controlled expression pattern in the gonads. This study shows that two RNA-binding proteins with antagonistic properties target a sequence motif in the 3’-UTR (D3U-box), promoting either RNA stabilization in germ cells or degradation in the soma., Author summary The development of the gonads in vertebrates is mainly regulated by dmrt1, a master sex-determining gene that has a timely and spatially controlled gonadal expression pattern. In addition to transcriptional regulation, a sequence motif located in the 3′ UTR (D3U-box) mediates transcript stability of dmrt1 mRNAs. However, this regulation is complex, and the mechanisms are barely understood. Here, we analyse further dmrt1 regulation in the fish model medaka and show that two RNA-binding proteins with antagonizing properties target the D3U-box and promote either RNA stabilization in germ cells or degradation in the soma. The evolutionary conservation of the D3U-box motif within metazoan dmrt1 genes—together with preserved expression patterns of the targeting RNA binding proteins in subsets of germ cells—suggest that this new mechanism for controlling RNA stability is not restricted to fishes but might also apply to other vertebrates.

The WFIKKN (WAP, Follistatin/kazal, Immunoglobulin, Kunitz and Netrin domain-containing) protein family is composed of two multidomain proteins: WFIKKN1 and WFIKKN2. They were formed by domain shuffling and are likely present in deuterostoms. The WFIKKN (also called GASP) proteins are well known for their function in muscle and skeletal tissues, namely, inhibition of certain members of the transforming growth factor beta (TGFB) superfamily such as myostatin (MSTN) and growth and differentiation factor 11 (GDF11). However, the role of the WFIKKN proteins in other tissues is still poorly understood in spite of evidence suggesting possible action in the inner ear, brain and reproduction. Further, several recent studies based on next generation technologies revealed differential expression of WFIKKN1 and WFIKKN2 in various tissues suggesting that their function is not limited to MSTN and GDF11 inhibition in musculoskeletal tissue. In this review, we summarize current knowledge about the WFIKKN proteins and propose that they are “companion” proteins for various growth factors by providing localized and sustained presentation of TGFB proteins to their respective receptors, thus regulating the balance between the activation of Smad and non-Smad pathways by TGFB.

Introduction to the special issue on recent advances in fish gamete and embryo research

Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis. In fish, as in other vertebrates, these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity. The role of small non-coding RNAs in the regulation of animal reproduction remains however largely unknown and poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in male and female gonads in several vertebrate species. We studied its expression in the medaka ovary and generated a mutant line (using CRISPR/Cas9 genome editing) to determine its importance for reproductive success with special interest for egg production. Our results show that miR-202-5p is the most abundant mature form of the miRNA and that it is expressed in granulosa cells and in the unfertilized egg. The knock out (KO) of mir-202 gene resulted in a strong phenotype both in terms of number and quality of eggs produced. Mutant females exhibited either no egg production or produced a dramatically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. We quantified the size distribution of the oocytes in the ovary of KO females and performed a large-scale transcriptomic analysis approach to identified dysregulated molecular pathways. Together, cellular and molecular analyses indicate that the lack of miR-202 impairs the early steps of oogenesis/folliculogenesis and decreases the number of large (i.e. vitellogenic) follicles, ultimately leading to dramatically reduced female fecundity. This study sheds new light on the regulatory mechanisms that control the early steps of follicular development, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction., Author summary The role of small non-coding RNAs in the regulation of animal reproduction remains poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in gonads in vertebrate. We studied its expression in the medaka ovary and knocked out the mir-202 gene to study its importance for reproductive success. We showed that the lack of miR-202 results in the sterility of both females and males. In particular, it led to a drastic reduction of both the number and the quality of eggs produced by females. Mutant females exhibited either no egg production or produced a drastically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. Quantitative histological and molecular analyses indicated that mir-202 KO impairs oocyte development and is also associated with the dysregulation of many genes that are critical for reproduction. This study sheds new light on the regulatory mechanisms that control oogenesis, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction.

Foxl2 is a member of the large family of Forkhead Box (Fox) domain transcription factors. It emerged during the last 15 years as a key player in ovarian differentiation and oogenesis in vertebrates and especially mammals. This review focuses on Foxl2 genes in light of recent findings on their evolution, expression, and implication in sex differentiation in animals in general. Homologs of Foxl2 and its paralog Foxl3 are found in all metazoans, but their gene evolution is complex, with multiple gains and losses following successive whole genome duplication events in vertebrates. This review aims to decipher the evolutionary forces that drove Foxl2/3 gene specialization through sub- and neo-functionalization during evolution. Expression data in metazoans suggests that Foxl2/3 progressively acquired a role in both somatic and germ cell gonad differentiation and that a certain degree of sub-functionalization occurred after its duplication in vertebrates. This generated a scenario where Foxl2 is predominantly expressed in ovarian somatic cells and Foxl3 in male germ cells. To support this hypothesis, we provide original results showing that in the pea aphid (insects) foxl2/3 is predominantly expressed in sexual females and showing that in bovine ovaries FOXL2 is specifically expressed in granulosa cells. Overall, current results suggest that Foxl2 and Foxl3 are evolutionarily conserved players involved in somatic and germinal differentiation of gonadal sex.

Bioassays are particularly useful tools to link the chemical and ecological assessments in water quality monitoring. Different methods cover a broad range of toxicity mechanisms in diverse organisms, and account for risks posed by non-target compounds and mixtures. Many tests are already applied in chemical and waste assessments, and stakeholders from the science-police interface have recommended their integration in regulatory water quality monitoring. Still, there is a need to address bioassay suitability to evaluate water samples containing emerging pollutants, which are a current priority in water quality monitoring. The presented interlaboratory study (ILS) verified whether a battery of miniaturized bioassays, conducted in 11 different laboratories following their own protocols, would produce comparable results when applied to evaluate blinded samples consisting of a pristine water extract spiked with four emerging pollutants as single chemicals or mixtures, i.e. triclosan, acridine, 17 alpha-ethinylestradiol (EE2) and 3-nitrobenzanthrone (3-NBA). Assays evaluated effects on aquatic organisms from three different trophic levels (algae, daphnids, zebrafish embryos) and mechanism-specific effects using in vitro estrogenicity (ER-Luc, YES) and mutagenicity (Ames fluctuation) assays. The test battery presented complementary sensitivity and specificity to evaluate the different blinded water extract spikes. Aquatic organisms differed in terms of sensitivity to triclosan (algae > daphnids > fish) and acridine (fish > daphnids > algae) spikes, confirming the complementary role of the three taxa for water quality assessment. Estrogenicity and mutagenicity assays identified with high precision the respective mechanism-specific effects of spikes even when non-specific toxicity occurred in mixture. For estrogenicity, although differences were observed between assays and models, EE2 spike relative induction EC50 values were comparable to the literature, and E2/EE2 equivalency factors reliably reflected the sample content. In the Ames, strong revertant induction occurred following 3-NBA spike incubation with the TA98 strain, which was of lower magnitude after metabolic transformation and when compared to TA100. Differences in experimental protocols, model organisms, and data analysis can be sources of variation, indicating that respective harmonized standard procedures should be followed when implementing bioassays in water monitoring. Together with other ongoing activities for the validation of a basic bioassay battery, the present study is an important step towards the implementation of bioanalytical monitoring tools in water quality assessment and monitoring. (C) 2016 Elsevier Ltd. All rights reserved.

Sexual dimorphism is one of the most pervasive and diverse features of animal morphology, physiology, and behavior. Despite the generality of the phenomenon itself, the mechanisms controlling how sex is determined differ considerably among various organismic groups, have evolved repeatedly and independently, and the underlying molecular pathways can change quickly during evolution. Even within closely related groups of organisms for which the development of gonads on the morphological, histological, and cell biological level is undistinguishable, the molecular control and the regulation of the factors involved in sex determination and gonad differentiation can be substantially different. The biological meaning of the high molecular plasticity of an otherwise common developmental program is unknown. While comparative studies suggest that the downstream effectors of sex-determining pathways tend to be more stable than the triggering mechanisms at the top, it is still unclear how conserved the downstream networks are and how all components work together. After many years of stasis, when the molecular basis of sex determination was amenable only in the few classical model organisms (fly, worm, mouse), recently, sex-determining genes from several animal species have been identified and new studies have elucidated some novel regulatory interactions and biological functions of the downstream network, particularly in vertebrates. These data have considerably changed our classical perception of a simple linear developmental cascade that makes the decision for the embryo to develop as male or female, and how it evolves.

Robustness is a complex trait difficult to characterize and phenotype. In the present study, two features of robustness in rainbow trout were investigated: sensitivity and resilience to an acute stressor. For that purpose, oxygen consumption, cortisol release, group dispersion and group activity of two isogenic lines of juvenile rainbow trout were followed before and after an environmental challenge. The effect of a 4h confinement protocol (~140kg/m(3)), which is generally considered as a highly stressful challenge, was investigated. Temporal patterns produced by this experiment were analyzed using multivariate statistics on curve characteristics to describe physiological and behavioral adaptive systems for each isogenic line. The two isogenic lines were found to be highly divergent in their corticosteroid reactivity. However, no correlation between physiological and behavioral sensitivity or resilience was observed. Furthermore, the multivariate analysis results indicated two separate and independent fish group coping strategies, i.e. by favoring either behavioral or physiological responses. In addition, considerable intra-line variabilities were observed, suggesting the importance of micro-environment effects on perturbation sensitivities. In this context, cortisol release rate variability was found to be related to the pre-stress social environment, with a strong correlation between pre-stress aggressiveness and cortisol release rate amplitude. Overall, this approach allowed us to extract important characteristics from dynamic data in physiology and behavior to describe components of robustness in two isogenic lines of rainbow trout.

Adaptive phenotypic plasticity is a key component of the ability of organisms to cope with changing environmental conditions. Fish have been shown to exhibit a substantial level of phenotypic plasticity in response to abiotic and biotic factors. In the present study, we investigate the link between environmental sensitivity assessed globally (revealed by phenotypic variation in body weight) and more targeted physiological and behavioral indicators that are generally used to assess the sensitivity of a fish to environmental stressors. We took advantage of original biological material, the rainbow trout isogenic lines, which allowed the disentangling of the genetic and environmental parts of the phenotypic variance. Ten lines were characterized for the changes of body weight variability (weight measurements taken every month during 18 months), the plasma cortisol response to confinement stress (3 challenges) and a set of selected behavioral indicators. This study unambiguously demonstrated the existence of genetic determinism of environmental sensitivity, with some lines being particularly sensitive to environmental fluctuations and others rather insensitive. Correlations between coefficient of variation (CV) for body weight and behavioral and physiological traits were observed. This confirmed that CV for body weight could be used as an indicator of environmental sensitivity. As the relationship between indicators (CV weight, risk-taking, exploration and cortisol) was shown to be likely depending on the nature and intensity of the stressor, the joint use of several indicators should help to investigate the biological complexity of environmental sensitivity.

Monitoring fish shoal behaviour is a growing concern for scientists studying fish stress and welfare. This study presents an algorithm developed to calculate, from videos taken from above aquaria, two indexes characterizing fish shoal behaviour. These two indexes quantify the dispersion and the swimming activity of the fish shoal in the aquaria. The reliability of these indexes was tested on fish shoal simulations following the rules of Reynolds' model on flocks, herds and schools. Since coordinates of each simulated fish in the shoal was known, these simulations provided true values of dispersion and swimming speed of each fish in the shoal, which were compared to values calculated using the presented algorithm. Further, the two indexes were tested on videos of rainbow trout in aquaria. Behavioural variations of the shoal were estimated before and after food distribution in one test, and before and after a four hours confinement stress in a second test. Data resulting from simulations indicate that the two indexes are sensitive to the simulated changes in the cohesion or the swimming speed of the group. Thus, indexes faithfully translated true values in simulations, with a minimum of 94% of the total variation in true values explained by indexes. Furthermore, the two indexes were sensitive to shoal behaviour modifications observed in the two case studies. Indeed, as expected, a strong group dispersion decrease associated with an important swimming activity increase could be detected just after food distribution using our method. Similarly, our indexes were sensitive to a group behaviour change observed after the four hours confinement stress. Finally, our method was compared to Israeli's, and was found to be more sensitive and more accurate in our conditions. This method provides therefore a sensitive, non-invasive, simple and widely applicable tool to quantify behavioural changes associated with various challenges in aquacultural conditions.

A natural sediment spiked with three individual polycyclic aromatic hydrocarbons (PAHs; pyrene, phenanthrene and benzo[a]pyrene) was used to expose zebrafish embryos and larvae during 4 days. The total PAH concentration was 4.4 μg g(-1) which is in the range found in sediment from contaminated areas. Quantification of metabolites in the larvae after exposure confirmed the actual contamination of the larvae and indicated an active metabolism especially for pyrene and benzo[a]pyrene. After a transfer in a clean medium, the larvae were reared to adulthood and evaluated for survival, growth, reproduction, and behavior. Measured endpoints revealed a late disruption of growth (appearing at 5 months) and a trend toward a lower reproductive ability. Adults of embryos exposed to sediment spiked with PAHs displayed lethargic and/or anxiety-like behaviors. This latter behavior was also identified in offspring at larval stage. All together, these effects could have detrimental consequences on fish performances and contribution to recruitment.

The release of polycyclic aromatic hydrocarbons (PAHs) into the environment has increased very substantially over the last decades leading to high concentrations in sediments of contaminated areas. To evaluate the consequences of long-term chronic exposure to PAHs, zebrafish were exposed, from their first meal at 5 days post fertilisation until they became reproducing adults, to diets spiked with three PAH fractions at three environmentally relevant concentrations with the medium concentration being in the range of 4.6-6.7 μg g(-1) for total quantified PAHs including the 16 US-EPA indicator PAHs and alkylated derivatives. The fractions used were representative of PAHs of pyrolytic (PY) origin or of two different oils of differing compositions, a heavy fuel (HO) and a light crude oil (LO). Fish growth was inhibited by all PAH fractions and the effects were sex specific: as determined with 9-month-old adults, exposure to the highest PY inhibited growth of females; exposure to the highest HO and LO inhibited growth of males; also, the highest HO dramatically reduced survival. Morphological analysis indicated a disruption of jaw growth in larvae and malformations in adults. Intestinal and pancreatic enzyme activities were abnormal in 2-month-old exposed fish. These effects may contribute to poor growth. Finally, our results indicate that PAH mixtures of different compositions, representative of situations encountered in the wild, can promote lethal and sublethal effects which are likely to be detrimental for fish recruitment.

Most persistent organic pollutants, due to their hydrophobic properties, accumulate in aquatic sediments and represent a high risk for sediment quality. To assess the toxicity of hydrophobic pollutants, a novel approach was recently proposed as an alternative to replace, refine and reduce animal experimentation: the medaka embryo-larval sediment contact assay (MELAc). This assay is performed with Japanese medaka embryos incubated on a natural sediment spiked with the compound being tested. With the aim of improving this assay, our study developed a reference exposure protocol with an artificial sediment specifically designed to limit natural sediment composition uncertainties and preparation variability. The optimum composition of the new artificial sediment was tested using a model polycyclic aromatic hydrocarbon (PAH), fluoranthene. The sediment was then validated with two other model PAHs, benz[a]anthracene and benzo[a]pyrene. Various developmental end points were recorded, including survival, embryonic heartbeat, hatching delay, hatching success, larval biometry and abnormalities. The final artificial sediment composition was set at 2.5 % dry weight (dw) Sphagnum peat, 5 % dw kaolin clay and 92.5 % dw silica of 0.2- to 0.5-mm grain size. In contrast with natural sediments, the chemical components of this artificial matrix are fully defined and readily identifiable. It is totally safe for fish embryos and presents relatively high sorption capacities for hydrophobic compounds. Studies with other hydrophobic and metallic contaminants and mixtures should be performed to further validate this artificial sediment.

Genetic control of male or female gonad development displays between different groups of organisms a remarkable diversity of “master sex-determining genes” at the top of the genetic hierarchies, whereas downstream components surprisingly appear to be evolutionarily more conserved. Without much further studies, conservation of sequence has been equalized to conservation of function. We have used the medaka fish to investigate the generality of this paradigm. In medaka, the master male sex-determining gene is dmrt1bY, a highly conserved downstream regulator of sex determination in vertebrates. To understand its function in orchestrating the complex gene regulatory network, we have identified targets genes and regulated pathways of Dmrt1bY. Monitoring gene expression and interactions by transgenic fluorescent reporter fish lines, in vivo tissue-chromatin immunoprecipitation and in vitro gene regulation assays revealed concordance but also major discrepancies between mammals and medaka, notably amongst spatial, temporal expression patterns and regulations of the canonical Hedgehog and R-spondin/Wnt/Follistatin signaling pathways. Examination of Foxl2 protein distribution in the medaka ovary defined a new subpopulation of theca cells, where ovarian-type aromatase transcriptional regulation appears to be independent of Foxl2. In summary, these data show that the regulation of the downstream regulatory network of sex determination is less conserved than previously thought.

[Departement_IRSTEA]Ecotechnologies [TR1_IRSTEA]SPEE; International audience; The potentiality of MRI to quantify fat content in flesh and subcutaneous fat in fish cutlets was investigated. Low measurement time was aimed at in a view to handling large number of samples needed in selective breeding programs for example. Results on fresh and frozen-thawed cutlets were compared to assess this way of conservation. As MRI generates unwanted spatial variations of the signal, a correction method was developed enabling the measurement on several cutlets simultaneously in less than 3 min per sample. For subcutaneous fat, the results were compared with vision measurements. High correlations between both techniques were found (R2 = 0.77 and 0.87 for the ventral and dorsal part). Fat in flesh was validated vs NMR measurements. No statistical difference was found between fresh and frozen-thawed cutlets. RMSE was respectively 0.8% and 0.89%. These results confirmed the potentiality of MRI for fat measurement in fish particularly for a large number of samples.

In vertebrates, one of the first recognizable sex differences in embryos is the onset of meiosis, known to be regulated by retinoic acid (RA) in mammals. We investigated in medaka a possible meiotic function of RA during the embryonic sex determination (SD) period and in mature gonads. We found RA mediated transcriptional activation in germ cells of both sexes much earlier than the SD stage, however, no such activity during the critical stages of SD. In adults, expression of the RA metabolizing enzymes indicates sexually dimorphic RA levels. In testis, RA acts directly in Sertoli, Leydig and pre-meiotic germ cells. In ovaries, RA transcriptional activity is highest in meiotic oocytes. Our results show that RA plays an important role in meiosis induction and gametogenesis in adult medaka but contrary to common expectations, not for initiating the first meiosis in female germ cells at the SD stage.

The Nme gene family, also known as Nm23 or NDPK, is a very ancient gene family that can be found in all kingdoms of life. In the late eighties, a gene of the Nme family, NME1, was identified as the first metastatic suppressor gene, resulting in a major interest for this family. Due to the complexity of the family, the need for a unified and evolutionary-supported gene nomenclature was recently stressed by the scientific community. Based on a complete evolutionary history study of the gene family in metazoans and vertebrates, a unified nomenclature was recently proposed and accepted by gene nomenclature consortia. In addition to its well-documented role in tumor metastasis, members of the Nme family are also involved in a wide variety of cellular and physiological processes. Available data in non-mammalian species remain, however, scarce with the noticeable exception of Drosophila in which a major role in development was reported. In fish, very few studies have specifically investigated the role of nme genes. Several transcriptomic and proteomic studies have, however, revealed the expression of nme genes in various fish organs and tissues, in mature oocytes, and during embryonic development. Altogether, interest for the Nme gene family in fish is growing and new functions/roles in fish biology are expected to be discovered in the forthcoming years. Here, we briefly review the current knowledge of the Nme family in fish.

The nanog gene plays a major role in vertebrate development and was only recently discovered in teleosts. In order to gain new insight into its regulation in gametes and early embryo in teleost fish, the present study aimed at characterizing nanog upstream sequence features and DNA methylation, as well as early embryonic expression pattern in a Cyprinid fish, the goldfish. Using an in silico approach, we were able to demonstrate that despite the existence of conserved regulatory motifs in the promoter region of the nanog gene, specific features known to play a major role in the regulation of Nanog in mammals were missing in teleosts. The analysis of CpG sites in the upstream region of the nanog genes in goldfish revealed a significant DNA methylation state in oocytes while a hypomethylated state was observed in sperm. Using both quantitative PCR and whole mount in situ hybridization, we were able to clearly demonstrate the maternal inheritance of the nanog transcript in goldfish. Corresponding mRNA levels subsequently decreased during early gastrulation. Together, our results reveal striking differences in expression and DNA methylation patterns in gametes and during early development and in upstream region features between teleosts and mammals that are consistent with the hypothesis of a rapid evolution of the Nanog gene in vertebrates, at least in some lineages. (C) 2011 Elsevier B.V. All rights reserved.

Chantier qualité GA; All salmonid species investigated to date have been characterized with a male heterogametic sex-determination system. However, as these species do not share any Y-chromosome conserved synteny, there remains a debate on whether they share a common master sex-determining gene. In this study, we investigated the extent of conservation and evolution of the rainbow trout (Oncorhynchus mykiss) master sex-determining gene, sdY (sexually dimorphic on the Y-chromosome), in 15 different species of salmonids. We found that the sdY sequence is highly conserved in all salmonids and that sdY is a male-specific Y-chromosome gene in the majority of these species. These findings demonstrate that most salmonids share a conserved sex-determining locus and also strongly suggest that sdY may be this conserved master sex-determining gene. However, in two whitefish species (subfamily Coregoninae), sdY was found both in males and females, suggesting that alternative sex-determination systems may have also evolved in this family. Based on the wide conservation of sdY as a male-specific Y-chromosome gene, efficient and easy molecular sexing techniques can now be developed that will be of great interest for studying these economically and environmentally important species.

Several environmental chemicals disrupt thyroid function, a key regulator of normal development involved in many physiological processes in fish. We studied the effects of such chemicals in vivo using transient transgenic zebrafish (Danio rerio), expressing Green Fluorescent Protein (GFP) under the control of a TH/bZIP promoter from Xenopus laevis. Exposure to thyroid hormone (T3) at 10(-8) M increased GFP fluorescence in F0 embryos and larvae. Transient transgenic embryos were exposed to a T3 signaling agonist (TRIAC) or antagonists (NH(3) or NaClO(4)), or to the endocrine disruptor Bisphenol A (BPA). When tested alone, TRIAC increased fluorescence, confirming the specificity of our model. Exposure to NH3 or NaClO(4) decreased fluorescence, reflecting inhibition of thyroid function. When tested alone, BPA did not modify fluorescence, but when tested with T3, it significantly reduced T3-induced fluorescence, suggesting disruption of the thyroid function by BPA. The expression of genes involved in the TH axis (TR-alpha, TR-beta, TSH) and the corticoid axis (GR and MR) was followed by q-PCR after T3 or BPA exposure (24 or 48 h) and at different developmental stages (0, 1, or 5 days post-fertilization). Expression of TR-alpha, TR-beta, and TSH genes increased after 48 h T3 exposure in 1-day-old larvae. When tested alone, BPA only slightly affected gene expression. When applied with T3, BPA decreased expression of all candidate genes in 1-day-old embryos compared to the T3 treated group, in agreement with data obtained with the TH/bZIP-eGFP zebrafish model. Finally, we show that T3 exposure leads to up-regulation of MR and GR genes. This study provides a new rapid diagnostic tool for characterizing the disrupting effects of toxicants on thyroid function and suggests possible crosstalk between the TR and Corticoid Signaling system. (C) 2011 Elsevier B.V. All rights reserved.

41 p., 3 figures, 2 tables and references, The aim of the present work was to investigate the transcriptome response of gilthead sea bream (Sparus aurata) after challenge with the myxosporean Enteromyxum leei, a wide-spread enteric parasite causing heavy economic losses in Mediterranean sparid farms. This parasite causes severe desquamative enteritis which usually leads to death of the fish, and there are no preventative or curative treatments for this enteromyxosis. After 113 days of exposure to parasite-contaminated effluent, fish were classified into three cohorts: control fish not exposed to parasite, those that were exposed and infected, and those that were exposed but not infected. In order to detect target genes that may be candidates for infective status or resistance, a cDNA microarray containing 18,490 cDNA clones enriched in genes differentially expressed after infection was hybridised with head kidney and intestine samples. In infected fish, 371 and 373 genes were differentially regulated at the >1.5-fold level in intestine and head kidney respectively, whereas in non-infected fish 175 and 501 genes were differentially regulated in these tissues, respectively. A global marked gene down-regulation was evident in infected fish, mainly in genes involved in the immune and acute phase response particularly complement and mannose binding lectin. Microarray analysis demonstrated a complex interplay between host and/or parasite derived proteases and protease inhibitors, apoptosis, cell proliferation and antioxidant defence genes in exposed fish. In the head kidney of non-infected fish a marked depression of genes involved in the acute phase response was evident. By contrast, in the intestine of non-infected fish, interferon-stimulated and MHC class II genes involved in antigen processing and presentation were up-regulated, possibly indicating that an active immune response at the local level is important to avoid infection with or proliferation of the parasite. © 2011 Elsevier Ltd.

Tbx1 is a member of the T-box transcription factor gene family involved in embryogenesis and organogenesis. Recently, within a pan-genomic screen using rainbow trout (Oncorhynchus mykiss) cDNA microarrays, we identified a tbx1 homolog with testicular over-expression during sex differentiation. Here, we characterized two very similar rainbow trout tbx1 paralogs, tbx1a and tbx1b. In adult tissues, tbx1a expression is restricted to the gonads, with high expression in the testis, while tbx1b is more widely expressed in gonads, gills, brains, muscle, and skin. During gonadal differentiation, both genes are differentially expressed in favor of testis formation shortly after hatching. These genes are expressed in somatic cells surrounding germ cells of the differentiating testis, while no or only weak expression was observed in the differentiating ovary. tbx1a and tbx1b were also both down-regulated in the differentiating testis during feminization with estrogens and up-regulated in the differentiating ovary during masculinization with an aromatase inhibitor. These results suggest that tbx1a and tbx1b are probably involved in the regulation of testicular differentiation in rainbow trout. Since Tbx1 is known to interact with the retinoic acid (RA) signaling pathway, we also examined the effect of RA on the rainbow trout tbx1 expression pattern. Expression of tbx1a and tbx1b was down-regulated in RA-treated male gonads, suggesting that tbx1 interacts with the RA signaling pathway and thus could be involved in the control of rainbow trout gonadal differentiation.

When different ages of juvenile allis shad Alosa alosa (18-74 days post-fertilization) were exposed for 48 h to elevated salinity (25 or 30), all ages could tolerate moderates salinity (25) whereas only the older stages could tolerate the higher salinity. In 88 days post-fertilization allis shad, acclimatation to full-strength sea water for 2 weeks did not lead to significant changes in total water content and gill Na+/K+-ATPase activity whereas total Na+ content increased within 5 days to values which remained stable thereafter. Together, these data suggest that juvenile allis shad develop a limited euryhalinity, which allows them to fully adapt to hyperosmotic environment immediately after transfer.

International audience; In many organisms, the sex chromosome pair can be recognized due to heteromorphy; the Y and W chromosomes have often lost many genes due to the absence of recombination during meiosis and are frequently heterochromatic. Repetitive sequences are found at a high proportion on such heterochromatic sex chromosomes and the evolution and emergence of sex chromosomes has been connected to the dynamics of repeats and transposable elements. With an amazing plasticity of sex determination mechanisms and numerous instances of independent emergence of novel sex chromosomes, fish represent an excellent lineage to investigate the early stages of sex chromosome differentiation, where sex chromosomes often are homomorphic and not heterochromatic. We have analyzed the composition, distribution, and relative age of TEs from available sex chromosome sequences of seven teleost fish. We observed recent bursts of TEs and simple repeat accumulations around young sex determination loci. More strikingly, we detected transposable element (TE) amplifications not only on the sex determination regions of the Y and W sex chromosomes, but also on the corresponding regions of the X and Z chromosomes. In one species, we also clearly demonstrated that the observed TE-rich sex determination locus originated from a TE-poor genomic region, strengthening the link between TE accumulation and emergence of the sex determination locus. Altogether, our results highlight the role of TEs in the initial steps of differentiation and evolution of sex chromosomes.

Skeletal muscles are composed of different fiber types, largely defined by differential expression of protein isoforms involved in myofibrillogenesis or metabolism. To learn more about the gene activations that underlie the differentiation and the diversification of embryonic fish myotomal fibers, we investigated the developmental expression of 25 muscle genes in trout embryos by in situ hybridization of muscle-specific transcripts. The earliest event of muscle differentiation, at approximately the 25-somite stage, was the expression of a variety of muscle-specific genes, including slow-twitch and fast-twitch muscle isoforms. The activation of these muscle genes started in the deep somitic domain, where the slow muscle precursors (the adaxial cells) were initially located, and progressively spread laterally throughout the width of the myotome. This mediolateral progression of gene expression was coordinated with the lateral migration of slow adaxial cells, which specifically expressed the slow myosin light chain 1 and the SLIM1/FHL1 genes. Subsequently, the fast and slow skeletal muscle isoforms precociously expressed in the course of the mediolateral wave of muscle gene activation became down-regulated in the superficial slow fibers and the deep fast fibers, respectively. Finally, several muscle-specific genes, including troponins, a slow myosin-binding protein C, tropomodulins, and parvalbumin started their transcription only in late embryos. Taken together, these findings show in fish embryos that a common myogenic program is triggered in a mediolateral progression in all muscle cells. The acquisition of the slow phenotype involves the additional activation of several slow-specific genes in migrating adaxial muscle cells. These events are followed by sequential gene activations and repressions in fast and slow muscle cells.

The interactive effects of an aryl hydrocarbon receptor (AhR) agonist and of a xenoestrogen on biomarker responses were studied in the liver of male mosquitofish (Gambusia holbrooki). Hepatic 7-ethoxyresorufin O-deethylase (EROD) enzymatic activity was measured as a biomarker of exposure to the model AhR agonist beta-naphthoflavone (bNF). Hepatic proteins indicating the exposure of males to the synthetic oestrogen 17alpha-ethynylestradiol (EE2) were monitored by Western blot analysis using immunoserum prepared for this study. After a semi-static exposure only to waterborne EE2, Western blot analysis of liver homogenate revealed the induction of two protein bands (a double band at 205 kDa and a single band at 125 kDa). The interaction between bNF and EE2 was investigated by analysing, on the one hand, EROD activity and, on the other hand, immunoreactivity corresponding to the two oestrogen-dependent protein bands in the liver of fish exposed to different concentrations of bNF for 2 days, then to the same concentrations of bNF plus 0.1 microg l(-1) EE2 for 5 days. EE2 changed neither the basal activity of EROD nor its rate of induction with 1.0 and 4.0 microg l(-1) bNF. On the other hand, the induction of oestrogen-dependent proteins with 0.1 microg l(-1) EE2 was inhibited by exposure to 4.0 microg l(-1) bNF. These results together with literature data suggest that field monitoring of xenoestrogen contamination through the analysis of oestrogen-dependent protein in male fish as a biomarker should take into account the possible negative interference of AhR agonists.

Sex steroids play a key role in triggering sex differentiation in fish, the use of exogenous hormone treatment leading to partial or complete sex reversal. This phenomenon has attracted attention since the discovery that even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development) and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find out mechanisms of actions (MOA) and identify biomarkers related to the toxic action of a compound. However, high throughput data interpretation relies on statistical analysis, species genomic resources, and bioinformatics tools. The goals of this study are to improve the knowledge of feminisation in fish, by the analysis of molecular responses in the gonads of rainbow trout fry after chronic exposure to several doses (0.01, 0.1, 1 and 10 μg/L) of ethynylestradiol (EE2) and to offer target genes as potential biomarkers of ovotestis development. We successfully adapted a bioinformatics microarray analysis workflow elaborated on human data to a toxicogenomic study using rainbow trout, a fish species lacking accurate functional annotation and genomic resources. The workflow allowed to obtain lists of genes supposed to be enriched in true positive differentially expressed genes (DEGs), which were subjected to over-representation analysis methods (ORA). Several pathways and ontologies, mostly related to cell division and metabolism, sexual reproduction and steroid production, were found significantly enriched in our analyses. Moreover, two sets of potential ovotestis biomarkers were selected using several criteria. The first group displayed specific potential biomarkers belonging to pathways/ontologies highlighted in the experiment. Among them, the early ovarian differentiation gene foxl2a was overexpressed. The second group, which was highly sensitive but not specific, included the DEGs presenting the highest fold change and lowest p-value of the statistical workflow output. The methodology can be generalized to other (non-model) species and various types of microarray platforms.

International audience

Sexual reproduction is one of the most highly conserved processes in evolution. However, the genetic and cellular mechanisms making the decision of whether the undifferentiated gonad of animal embryos develops either towards male or female are manifold and quite diverse. In vertebrates, sex-determining mechanisms range from environmental to simple or complex genetic mechanisms and different mechanisms have evolved repeatedly and independently. In species with simple genetic sex-determination, master sex-determining genes lying on sex chromosomes drive the gonadal differentiation process by switching on a developmental program, which ultimately leads to testicular or ovarian differentiation. So far, very few sex-determining genes have been identified in vertebrates and apart from mammals and birds, these genes are apparently not conserved over a larger number of related orders, families, genera, or even species. To fill this knowledge gap and to better explore genetic sex-determination, we propose a strategy (RAD-Sex) that makes use of next-generation sequencing technology to identify genetic markers that define sex-specific segments of the male or female genome.; La reproduction sexuée est une des fonctions biologiques les plus conservées au cours de l’évolution. Cependant, les mécanismes génétiques et cellulaires qui gouvernent la différenciation d’une gonade embryonnaire indifférenciée vers le sexe mâle (testicules) ou femelle (ovaires) sont très variables. Les déterminismes du sexe ont évolué à plusieurs reprises et de façon indépendante dans les différents groupes de vertébrés, et ils sont, soit contrôlés par l’environnement, soit basés sur des systèmes génétiques plus ou moins complexes. Chez les espèces qui possèdent des systèmes génétiques simples de détermination du sexe, les déterminants majeurs du sexe localisés sur les chromosomes sexuels vont enclencher le processus de différenciation des gonades, qui conduira in fine à la différenciation de testicules ou d’ovaires. Jusqu’à présent, très peu de gènes déterminants majeurs du sexe ont été identifiés chez les vertébrés et, en dehors des mammifères et des oiseaux, ces gènes ne sont apparemment pas conservés en dehors de groupes taxonomiques restreints, voire même au sein de la même espèce. Pour combler ce peu de connaissances et pour obtenir une vision plus large de l’évolution de ces déterminants majeurs du sexe, nous proposons une stratégie (RAD-Sex) basée sur l’utilisation d’une technologie de séquençage moderne pour identifier, chez de nombreuses espèces, des marqueurs génétiques associés au sexe mâle ou femelle.

Background Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution. Results A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB. Conclusions Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-952) contains supplementary material, which is available to authorized users.