Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata)

Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Hypophthalmichthys nobilis) Early Development

The early development of fish is regulated through dynamic and complex mechanisms involving the regulation of various genes. Many genes are subjected to post-transcriptional regulation by microRNAs (miRNAs). In the Chinese aquaculture industry, the native species bighead carp (Hypophthalmichthys nobilis) is important. However, the genetic regulation related to the early development of bighead carp is unknown. Here, we generated developmental profiles by miRNA sequencing to study the dynamic regulation of miRNAs during bighead carp early development. This study identified 1 046 miRNAs, comprising 312 known miRNAs and 734 uncharacterized miRNAs. Changes in miRNA expression were identified in the six early development stages. An obviously increased expression trend was detected during the development process, with the main burst of activity occurring after the earliest stage (early blastula, DS1). Investigations revealed that several miRNAs were dominantly expressed during the development process, especially in the later stages (e.g., miR-10b-5p, miR-21, miR-92a-3p, miR-206-3p, and miR-430a-3p), suggesting that these miRNAs exerted important functions during embryonic development. The differentially expressed miRNAs (DEMs) and time-serial analysis (profiles) of DEMs were analyzed. A total of 372 miRNAs were identified as DEMs (fold-change >2, and false discovery rate <0.05), and three expression profiles of the DEMs were detected to have co-expression patterns (r > 0.7, and p < 0.05). The broad negative regulation of target genes by miRNAs was speculated, and many development-related biological processes and pathways were enriched for the targets of the DEMs, which might be associated with maternal genome degradation and embryogenesis processes. In conclusion, we revealed the repertoire of miRNAs that are active during early development of bighead carp. These findings will increase our understanding of the regulatory mechanisms of early development of fish.

Special features of neuroendocrine interactions between stress and reproduction in teleosts

Stress and reproduction are both essential functions for vertebrate survival, ensuring on one side adaptative responses to environmental changes and potential life threats, and on the other side production of progeny. With more than 25,000 species, teleosts constitute the largest group of extant vertebrates, and exhibit a large diversity of life cycles, environmental conditions and regulatory processes. Interactions between stress and reproduction are a growing concern both for conservation of fish biodiversity in the frame of global changes and for the development of sustainability of aquaculture including fish welfare. In teleosts, as in other vertebrates, adverse effects of stress on reproduction have been largely documented and will be shortly overviewed. Unexpectedly, stress notably via cortisol, may also facilitate reproductive function in some teleost species in relation to their peculiar life cyles and this review will provide some examples. Our review will then mainly address the neuroendocrine axes involved in the control of stress and reproduction, namely the corticotropic and gonadotropic axes, as well as their interactions. After reporting some anatomo-functional specificities of the neuroendocrine systems in teleosts, we will describe the major actors of the corticotropic and gonadotropic axes at the brain-pituitary-peripheral glands (interrenals and gonads) levels, with a special focus on the impact of teleost-specific whole genome duplication (3R) on the number of paralogs and their potential differential functions. We will finally review the current knowledge on the neuroendocrine mechanisms of the various interactions between stress and reproduction at different levels of the two axes in teleosts in a comparative and evolutionary perspective.

Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)

BACKGROUND

Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hypophthalmichthys nobilis). In the present study, we performed transcriptome analysis of six development stages in H. nobilis, aiming to understand the dynamic molecular regulation of early development in this fish.

RESULTS

A total of 76,573 unigenes were assembled from clean sequence reads, with an average length of 1768 base. Among which, 41,742 (54.54%) unigenes were annotated to public protein databases, and an additional 59,014 simple sequence repeat (SSR) loci were identified among the unigenes. Furthermore, 30,199 differentially expressed transcripts (DETs) (fold change > 4 or < 0.25, and the false discovery rate FDR < 0.01) were observed in comparisons between the adjacent developmental stages, and nine expression patterns (profiles) were simulated using series-cluster analysis across six developmental stages. The unigenes expression level markedly increased after the DS1 stage (early blastula), and the numbers of DETs gradually decreased during subsequent development. The largest transcriptomic change (up- or down-regulated) was detected during the period from DS1 to DS2 (6-somite stage), which was enriched for many biological processes and metabolic pathways related to maternal to zygotic transition (MZT). Distinctly protein-protein interaction (PPI) networks were plotted for DETs during the period from DS1 to DS2. The genes (or proteins) from the same pathways were integrated together, and showed with obvious co-regulation patterns. In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during H. nobilis development, and the strict co-expression of a hatching enzyme gene (hce1) with 33 other annotated genes was identified from this profile.

CONCLUSIONS

The results indicated that strict dynamic regulation occurs during the early development in H. nobilis, especially in embryogenesis before hatching. This study provides valuable new information and transcriptomic resources related to H. nobilis early development, and for certain events such as MZT and hatching.

Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)

Background

Coral reefs are major hotspots of diversity for marine fishes, yet there is still ongoing debate on the mechanisms that promote divergence in these rich ecosystems. Our understanding of how diversity originates in this environment could be enhanced by investigating the evolutionary dynamics of closely related fishes with overlapping ranges. Here, we focus on grunts of the genus Haemulon, a group of coral reef fishes with 15 species in the Western Atlantic, 11 of which are syntopic.

Methods

Wild fish samples from three sympatric species of the Caribbean: Haemulon flavolineatum, H. carbonarium and H. macrostomum, were collected while SCUBA diving. RNA was extracted from livers, and the transcriptomes were assembled and annotated to investigate positive selection (Pairwise d _N/d _S) and patterns of gene expression between the three species.

Results

Pairwise d _N/d _S analyses showed evidence of positive selection for genes associated with immune response, cranial morphology and formation of the anterior-posterior axis. Analyses of gene expression revealed that despite their sympatric distribution, H. macrostomum showed upregulation of oxidation-reduction machinery, while there was evidence for activation of immune response in H. carbonarium.

Discussion

Overall, our analyses suggest closely related grunts show important differences in genes associated with body shape and feeding morphology, a result in-line with previous morphological studies in the group. Further, despite their overlapping distribution they interact with their environment in distinct fashions. This is the largest compendium of genomic information for grunts thus far, representing a valuable resource for future studies in this unique group of coral reef fishes.

Characterization and Expression Dynamics of Key Genes Involved in the Gilthead Sea Bream (Sparus aurata) Cortisol Stress Response during Early Ontogeny

The present study identified and characterized six key genes involved in the hypothalamic-pituitary-interrenal (HPI) axis of gilthead sea bream (Sparus aurata), a commercially important European aquaculture species. The key genes involved in the HPI axis for which gene structure and synteny analysis was carried out, comprised of two functional forms of glucocorticoid receptors (GR), as well as three forms of pro-opiomelanocortin (POMC) genes and one form of mineralocorticoid receptor (MR) gene. To explore their functional roles during development but also in the stress response, the expression profiles of gr1, gr2, mr, pomc_aI, pomc_aII, and pomc_β were examined during early ontogeny and after an acute stress challenge. The acute stress challenge was applied at the stage of full formation of all fins, where whole body cortisol was also measured. Both the cortisol and the molecular data implied that sea bream larvae at the stage of the full formation of all fins at 45 dph are capable of a response to stress of a similar profile as observed in adult fish.

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish

Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.

Early life stress induces long-term changes in limbic areas of a teleost fish: the role of catecholamine systems in stress coping

Early life stress (ELS) shapes the way individuals cope with future situations. Animals use cognitive flexibility to cope with their ever-changing environment and this is mainly processed in forebrain areas. We investigated the performance of juvenile gilthead seabream, previously subjected to an ELS regime. ELS fish showed overall higher brain catecholaminergic (CA) signalling and lower brain derived neurotrophic factor (bdnf) and higher cfos expression in region-specific areas. All fish showed a normal cortisol and serotonergic response to acute stress. Brain dopaminergic activity and the expression of the α_2Α adrenergic receptor were overall higher in the fish homologue to the lateral septum (Vv), suggesting that the Vv is important in CA system regulation. Interestingly, ELS prevented post-acute stress downregulation of the α_2Α receptor in the amygdala homologue (Dm3). There was a lack of post-stress response in the β₂ adrenergic receptor expression and a downregulation in bdnf in the Dm3 of ELS fish, which together indicate an allostatic overload in their stress coping ability. ELS fish showed higher neuronal activity (cfos) post-acute stress in the hippocampus homologue (Dlv) and the Dm3. Our results show clear long-term effects on limbic systems of seabream that may compromise their future coping ability to environmental challenges.

Allostatic Load and Stress Physiology in European Seabass (Dicentrarchus labrax L.) and Gilthead Seabream (Sparus aurata L.)

The present study aimed to compare effects of increasing chronic stress load on the stress response of European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) to identify neuroendocrine functions that regulate this response. Fish were left undisturbed (controls) or exposed to three levels of chronic stress for 3 weeks and then subjected to an acute stress test (ACT). Chronic stress impeded growth and decreased feed consumption in seabass, not in seabream. In seabass basal cortisol levels are high and increase with stress load; the response to a subsequent ACT decreases with increasing (earlier) load. Basal cortisol levels in seabream increase with the stress load, whereas the ACT induced a similar response in all groups. In seabass and seabream plasma α-MSH levels and brain stem serotonergic activity and turnover were similar and not affected by chronic stress. Species-specific molecular neuro-regional differences were seen. In-situ hybridization analysis of the early immediate gene cfos in the preoptic area showed ACT-activation in seabream; in seabass the expression level was not affected by ACT and seems constitutively high. In seabream, expression levels of telencephalic crf, crfbp, gr1, and mr were downregulated; the seabass hypothalamic preoptic area showed increased expression of crf and gr1, and decreased expression of mr, and this increased the gr1/mr ratio considerably. We substantiate species-specific physiological differences to stress coping between seabream and seabass at an endocrine and neuroendocrine molecular level. Seabass appear less resilient to stress, which we conclude from high basal activities of stress-related parameters and poor, or absent, responses to ACT. This comparative study reveals important aquaculture, husbandry, and welfare implications for the rearing of these species.

A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)

Background

The impact of nutritional status and diet composition on mitochondrial oxidative phosphorylation (OXPHOS) in fish remains largely unknown. To identify biomarkers of interest in nutritional studies, herein we obtained a deep-coverage transcriptome by 454 pyrosequencing of liver and skeletal muscle cDNA normalised libraries from long-term starved gilthead sea bream (Sparus aurata) and fish fed different diets.

Results

After clean-up of high-throughput deep sequencing reads, 699,991 and 555,031 high-quality reads allowed de novo assembly of liver and skeletal muscle sequences, respectively (average length: 374 and 441 bp; total megabases: 262 and 245 Mbp). An additional incremental assembly was completed by integrating data from both tissues (hybrid assembly). Assembly of hybrid, liver and skeletal muscle transcriptomes yielded, respectively, 19,530, 11,545 and 10,599 isotigs (average length: 1330, 1208 and 1390 bp, respectively) that were grouped into 15,954, 10,033 and 9189 isogroups. Following annotation, hybrid transcriptomic data were used to construct an oligonucleotide microarray to analyse nutritional regulation of the expression of 129 genes involved in OXPHOS in S. aurata. Starvation upregulated cytochrome c oxidase components and other key OXPHOS genes in the liver, which exhibited higher sensitive to food deprivation than the skeletal muscle. However, diet composition affected OXPHOS in the skeletal muscle to a greater extent than in the liver: most of genes upregulated under starvation presented higher expression among fish fed a high carbohydrate/low protein diet.

Conclusions

Our findings indicate that the expression of coenzyme Q-binding protein (COQ10), cytochrome c oxidase subunit 6A2 (COX6A2) and ADP/ATP translocase 3 (SLC25A6) in the liver, and cytochrome c oxidase subunit 5B isoform 1 (COX5B1) in the liver and the skeletal muscle, are sensitive markers of the nutritional condition that may be relevant to assess the effect of changes in the feeding regime and diet composition on fish farming.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4148-x) contains supplementary material, which is available to authorized users.

The circadian transcriptome of marine fish (Sparus aurata) larvae reveals highly synchronized biological processes at the whole organism level

The regulation of circadian gene expression remains largely unknown in farmed fish larvae. In this study, a high-density oligonucleotide microarray was used to examine the daily expression of 13,939 unique genes in whole gilthead sea bream (Sparus aurata) larvae with fast growth potentiality. Up to 2,229 genes were differentially expressed, and the first two components of Principal Component Analysis explained more than 81% of the total variance. Clustering analysis of differentially expressed genes identified 4 major clusters that were triggered sequentially, with a maximum expression at 0 h, 3 h, 9–15 h and 18-21 h zeitgeber time. Various core clock genes (per1, per2, per3, bmal1, cry1, cry2, clock) were identified in clusters 1–3, and their expression was significantly correlated with several genes in each cluster. Functional analysis revealed a daily consecutive activation of canonical pathways related to phototransduction, intermediary metabolism, development, chromatin remodeling, and cell cycle regulation. This daily transcriptome of whole larvae resembles a cell cycle (G1/S, G2/M, and M/G1 transitions) in synchronization with multicellular processes, such as neuromuscular development. This study supports that the actively feeding fish larval transcriptome is temporally organized in a 24-h cycle, likely for maximizing growth and development.