Somite formation and expression ofMyoD,myogeninandmyosinin Atlantic halibut (Hippoglossus hippoglossusL.)embryos incubated at different temperatures: transient asymmetric expression ofMyoD

Effects of dietary leucine on growth, antioxidant capacity, immune response, and inflammation in juvenile yellow catfish Pelteobagrus fulvidraco

The experiment was conducted to investigate the effects of dietary leucine on growth, antioxidant capacity, immune response, and inflammation in juvenile yellow catfish. Five diets were formulated to contain five dietary leucine levels: 12.00 (control), 19.00, 26.00, 33.00, and 40.00 g kg-1. Each diet was randomly assigned to triplicate groups of 30 juvenile fish (5.02 ± 0.15 g) twice daily to apparent satiation for 56 days. Weight gain rate, specific growth rate, and activities of liver superoxide dismutase, glutathione peroxidase, and serum lysozyme, as well as immunoglobulin M content, significantly increased with increase in dietary leucine levels up to 26.00 g kg-1, but those values decreased significantly with a further increase in dietary leucine. On the contrary, the lowest malondialdehyde content was found in 26.00 and 33.00 g kg-1 leucine groups. The expression levels of IGF 1 and MYF 5 genes in muscle were significantly upregulated with increase in dietary leucine levels up to 26.00 g kg-1, but the expression of MSTN level showed the opposite trend. The lowest expression levels of IL 8 and TNFɑ genes in the liver were found in 26.00 g kg-1 leucine groups. The quadratic regression analysis on weight gain, specific growth rate, and feed conversion ratio against dietary leucine levels indicated that the optimal dietary leucine requirement was estimated to be 26.84-27.00 g kg-1of the dry diet.

Functional analysis of two MyoDs revealed their role in the activation of myomixer expression in yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782)

Myoblast determination protein (MyoD), a muscle-specific basic helix-loop-helix (bHLH) transcription factor, plays a pivotal role in regulating skeletal muscle growth and development. However, the regulation mechanism of MyoD has not been determined in marine fishes. In the present study, we isolated the MyoD1 (AlMyoD1) and MyoD2 (AlMyoD2) genomic sequences and analyzed the expression patterns in different tissues of yellowfin seabream (Acanthopagrus latus). The open reading frame (ORF) sequences of AlMyoD1 and AlMyoD2 encoded 297 and 271 amino acids possessing three common characteristic domains, respectively, containing a myogenic basic domain, a bHLH domain, and a ser-rich region (helix III). Phylogenetic and genome structure analyses exhibited classic phylogeny and highly conserved exon/intron architecture. Furthermore, the AlMyoD1 and AlMyoD2 transcription levels were higher in white muscle than in the other tissues. In order to further study AlMyoD function in muscle, promoter sequence analysis found that several E-box binding sites were present. Additionally, binding sites of Almyomixer involved in mammal myoblast fusion, which expression was also the highest in white muscle, were found in the promoter of AlMyoD. Pomoter activity assays further confirmed that both AlMyoD1 and AlMyoD2 can dramatically activate Almyomixer expression, and the AlMyoD1 M2 and AlMyoD2 M5 E-box binding sites were functionally important for Almyomixer transcription based on mutation analysis and electrophoretic mobile shift assays (EMSA). In summary, two MyoDs play a core role in Almyomixer regulation and may promote myofibre formation during muscle development and growth by regulating Almyomixer expression.

Delta-Notch signalling in segmentation

Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor. Here, we discuss vertebrate segmentation with particular emphasis on the role of the Notch intercellular signalling pathway. We introduce vertebrate segmentation and Notch signalling, pointing out historical milestones, then describe existing models for the Notch pathway in the synchronization of noisy neighbouring oscillators, and a new role in the modulation of gene expression wave patterns. We ask what functions Notch signalling may have in arthropod segmentation and explore the relationship between Notch-mediated lateral inhibition and synchronization. Finally, we propose open questions and technical challenges to guide future investigations into Notch signalling in segmentation.

Embryonic development of the grass pufferfish (Takifugu niphobles): From egg to larvae

Tetraodontidae (pufferfish) family members carry the smallest genomes among vertebrates, and these pocket-sized genomes have directly contributed to our understanding of the structure and evolution of higher animals. The grass pufferfish (Takifugu niphobles) could be considered a potential new model organism for comparative genomics and development due to the potential access to embryos, and availability of sequence data for two similar genomes: that of spotted green pufferfish (Tetraodon nigroviridis) and Fugu (Takifugu rubripes). In this study, we provide the first description of the normal embryonic development of T. niphobles, by drawing comparisons with the closely related species cited above. Embryos were obtained by in vitro fertilization of eggs, and subsequent development was monitored at a constant temperature consistent with natural conditions. T. niphobles development was divided into seven periods of embryogenesis: the zygote, cleavage, blastula, gastrula, segmentation, pharyngula, and hatching periods; and stages subdividing these periods are defined based on morphological characteristics. The developmental stage series described in this study aims to provide the utilization of T. niphobles as an experimental model organism for comparative developmental studies.

Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality

BACKGROUND

Commercial Atlantic halibut (Hippoglossus hippoglossus) farming is restricted by variable oocyte quality, slow growth, and early maturation of male fish. Maternally transferred components regulate early developmental processes; therefore, they have an effect on the future viability of the embryo. Using a newly developed Agilent 10 k custom-made oligonucleotide array, we profiled components of the transcriptome involved in immune defence as well as germline and muscle development during early developmental stages: 8-cell embryos (8CS), germ ring stage (GR), 10-somite stage (10SS), and hatched embryos (HT). In addition, we identified differentially expressed transcripts in low (≤9 ± 3% hatching) and high (≥86 ± 3°% hatching) quality eggs at 8CS to identify potential maternal markers for embryo quality.

RESULTS

Out of 2066 differentially expressed transcripts, 160 were identified as maternal transcripts being specifically expressed at 8CS only. Twenty transcripts were differentially expressed in 8-cell embryos between low and high quality egg groups. Several immune-related transcripts were identified as promising molecular markers of hatching success including interferon regulatory factor 7 and mhc class 2A chain. Differential expression was positively validated with quantitative real-time PCR.

CONCLUSIONS

We have demonstrated maternal transfer of innate and adaptive immune system transcripts into Atlantic halibut embryos and their relation with future embryo developmental potential. We identified several transcripts as potential molecular markers of embryo quality. The developed microarray represents a useful resource for improving the commercial production of Atlantic halibut.

Molecular characterization and expression patterns of myogenin in compensatory growth of Megalobrama amblycephala

Myogenin (myog) is a muscle-specific basic helix-loop-helix (bHLH) transcription factor that plays an essential role in regulating skeletal muscle development and growth. To investigate molecular characterization of myog and the effect of starvation/refeeding on the gene expression, we isolated the myog cDNA sequence and analyzed the expression patterns using quantitative real-time polymerase chain reaction in Megalobrama amblycephala. Sequence analysis indicated that M. amblycephala myog shared an analogous structure with the highly conserved His/Cys-rich, bHLH and C-terminal helix III domains with other vertebrates. Sequence alignment and phylogenetic tree showed that M. amblycephala myog had the highest identity with the homologues of Ctenopharyngodon idella and Cyprinus carpio. Spatio-temporal expression patterns revealed that myog mRNA levels at the segmentation period and 12 h post-hatching (hph) were significantly higher than at other development stages (P<0.05). Furthermore, the highest myog expression level was predominantly observed in white muscle compared with the other types of muscle. Fish body weight continuously decreased during 21-day starvation and then significantly increased after 7days of refeeding and reached the similar level to the control at 21days of refeeding, indicating that the pattern of complete compensatory growth possibly occurred in M. amblycephala; meanwhile, the relative somatic growth rate after refeeding was also dramatically higher than the control group. In addition, the myog expression decreased during 21days of starvation and then exhibited a strong rebound effect after 7days of refeeding and subsequently declined gradually to the control level by 21days of refeeding.

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development

BACKGROUND

MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Developmental profiles of miRNAs have been reported in few fish species only and, to our knowledge, differential expressions of isomiRs have not yet been shown during fish development. Atlantic halibut, Hippoglossus hippoglossus L., undergoes dramatic metamorphosis during early development from symmetrical pelagic larval stage to unsymmetrical flatfish. No data exist on role of miRNAs in halibut metamorphosis.

RESULTS

miRNA profiling using SOLiD deep sequencing technology revealed a total of 199 conserved, one novel antisense, and one miRNA* mature form. Digital expression profiles of selected miRNAs were validated using reverse transcription quantitative PCR. We found developmental transition-specific miRNA expression. Expression of some miRNA* exceeded the guide strand miRNA. We revealed that nucleotide truncations and/or additions at the 3' end of mature miRNAs resulted in size variants showing differential expression patterns during the development in a number of miRNA families. We confirmed the presence of isomiRs by cloning and Sanger sequencing. Also, we found inverse relationship between expression levels of sense/antisense miRNAs during halibut development.

CONCLUSION

Developmental transitions during early development of Atlantic halibut are associated with expression of certain miRNA types. IsomiRs are abundant and often show differential expression during the development.

Maternal gene expression in Atlantic halibut (Hippoglossus hippoglossus L.) and its relation to egg quality

BACKGROUND

The commercial production of Atlantic halibut (Hippoglossus hippoglossus L.) suffers from a major bottleneck due to the low success of producing juveniles for on-growing. Atlantic halibut females are routinely hand-stripped and incorrect timing of stripping can result in low quality eggs due to post-ovulatory aging. Post-ovulatory aging leads to compositional changes in eggs that include maternally provided proteins and RNAs. There have been few studies of the maternally provided mRNA transcripts that control early development in commercially important fish species. The present study aimed to study maternal gene expression in Atlantic halibut and its relation to egg quality parameters including blastomere symmetry and hatching success.

RESULTS

A maternal EST library containing 2341 sequences was constructed by suppressive subtractive hybridisation. Thirty genes were selected for expression studies; 23 novel genes and 7 genes with documented roles in early development. The expressions of twenty-one selected genes were measured by qPCR from fertilization to the 10-somite stage. Three genes were identified as strictly maternal genes that were expressed until the start of gastrulation; askopos (kop), si:dkey-30j22.9 (Tudor family member), and Tudor 5 protein (Tdrd5). The expressions of 18 genes at the 8-cell stage were correlated with egg quality parameters. The majority of genes showed either no or very minor correlations with egg quality parameter. However, two genes correlated positively with hatching success (r> 0.50, HHC00353: r = 0.58, p < 0.01; HHC01517: r = 0.56, p < 0.01) and one gene (HHC00255) was negatively correlated with the percentage of normal blastomeres (r = -0.62, p < 0.05).

CONCLUSIONS

During this study we have related maternal levels of gene expression to hatching success in fish. Poor hatching success was not correlated with a general decrease in transcript abundance but with low transcript levels of some specific genes. Thus, the molecular mechanisms leading to low Atlantic halibut egg quality cannot be entirely explained by post-ovulatory aging.

Differential spatio-temporal expression and functional diversification of the myogenic regulatory factors MyoD1 and MyoD2 in Atlantic halibut (Hippoglossus hippoglossus)

Development of the vertebrate skeletal muscle is orchestrated by the myogenic regulatory factors MyoD, Myf5, myogenin and MRF4, which likely arose from the duplications of a single ancestral gene early in vertebrate evolution. We have isolated two myod genes from Atlantic halibut and examined their differential expression during embryogenesis using quantitative PCR and in situ hybridization to address their functional roles in this asymmetrically organized flatfish. myod1 was initially maternally expressed, while myod2 mRNA was first detectable during gastrulation. The myod1 mRNA levels predominated throughout somitogenesis, and both slow and fast muscle precursor cells displayed the bilateral symmetric myod1 signal during the formation of the symmetric somite pairs. In contrast, myod2 was left-right asymmetrically expressed in the fast muscle precursors. The random expression of myod2 was not associated with the right-sided eye migration and the development of thicker fast skeletal muscle on the eyed side than on the blind side. The nucleotide substitution analysis indicated that the teleost MyoDs essentially have evolved under purifying selection, but a subset of amino acid sites under strong positive selection were identified in the MyoD2 branch. Altogether, halibut MyoD1 seems to have retained the central role of MyoD in driving skeletal myogenesis, whereas the function of MyoD2 is uncertain in this flatfish species.

Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens

Background

The turbot (Scophthalmus maximus; Scophthalmidae; Pleuronectiformes) is a flatfish species of great relevance for marine aquaculture in Europe. In contrast to other cultured flatfish, very few genomic resources are available in this species. Aeromonas salmonicida and Philasterides dicentrarchi are two pathogens that affect turbot culture causing serious economic losses to the turbot industry. Little is known about the molecular mechanisms for disease resistance and host-pathogen interactions in this species. In this work, thousands of ESTs for functional genomic studies and potential markers linked to ESTs for mapping (microsatellites and single nucleotide polymorphisms (SNPs)) are provided. This information enabled us to obtain a preliminary view of regulated genes in response to these pathogens and it constitutes the basis for subsequent and more accurate microarray analysis.

Results

A total of 12584 cDNAs partially sequenced from three different cDNA libraries of turbot (Scophthalmus maximus) infected with Aeromonas salmonicida, Philasterides dicentrarchi and from healthy fish were analyzed. Three immune-relevant tissues (liver, spleen and head kidney) were sampled at several time points in the infection process for library construction. The sequences were processed into 9256 high-quality sequences, which constituted the source for the turbot EST database. Clustering and assembly of these sequences, revealed 3482 different putative transcripts, 1073 contigs and 2409 singletons. BLAST searches with public databases detected significant similarity (e-value ≤ 1e-5) in 1766 (50.7%) sequences and 816 of them (23.4%) could be functionally annotated. Two hundred three of these genes (24.9%), encoding for defence/immune-related proteins, were mostly identified for the first time in turbot. Some ESTs showed significant differences in the number of transcripts when comparing the three libraries, suggesting regulation in response to these pathogens. A total of 191 microsatellites, with 104 having sufficient flanking sequences for primer design, and 1158 putative SNPs were identified from these EST resources in turbot.

Conclusion

A collection of 9256 high-quality ESTs was generated representing 3482 unique turbot sequences. A large proportion of defence/immune-related genes were identified, many of them regulated in response to specific pathogens. Putative microsatellites and SNPs were identified. These genome resources constitute the basis to develop a microarray for functional genomics studies and marker validation for genetic linkage and QTL analysis in turbot.

The gonadotropin receptors FSH-R and LH-R of Atlantic halibut (Hippoglossus hippoglossus)--2. Differential follicle expression and asynchronous oogenesis

The biological activity and spatio-temporal expression patterns of the gonadotropin receptors FSH-R and LH-R were examined in the repetitive spawner Atlantic halibut to elucidate the gonadotropic regulation of the asynchronous follicle development. The cloned receptors were expressed in mammalian COS-7 cells, and stimulation with sea bass FSH and LH increased the cAMP production. The halibut FSH-R and LH-R genes were shown to be highly expressed in the gonads of sexually mature fish, but the transcripts were also found in extra-gonadal tissues such as pituitary and brain. Different expression patterns of FSH-R and LH-R in the developing follicles were documented by semi-quantitative RT-PCR. Abundant FSH-R mRNA was found in the small follicles during primary growth and vitellogenesis, and the signals were localized to the granulosa cells by in situ hybridization. In contrast, follicular LH-R mRNA was hardly detectable during the early stages. Conversely, in follicles during final maturation FSH-R mRNA levels tended to decrease, while the expression of LH-R was highly upregulated. Whereas the pituitary FSH and LH are asynchronously expressed in annual spawners, both gonadotropins were expressed in the female halibut pituitary throughout the reproductive cycle, except in the prespawning females. Hence, the sequential gonadotropic activation of ovarian follicle growth and maturation in repetitive spawners is probably regulated by modulating the temporal expression of FSH-R and LH-R in the follicle membrane.

Selection of suitable reference genes for real-time PCR studies of Atlantic halibut development

Gene expression studies are fundamental to understand the molecular basis of severe malformations in fish development, particularly under aquaculture conditions. Real-time PCR (qPCR) is the most accurate method of quantifying gene expression, provided that suitable endogenous controls are used to normalize the data. To date, no reference genes have been validated for developmental gene expression studies in Atlantic halibut (Hippoglossus hippoglossus). We have determined the expression profiles of 6 candidate reference genes (Actb, Eef2, Fau, Gapdh, Tubb2 and 18S rRNA) in 6 embryonic and 5 larval stages of Atlantic halibut development. There were significant changes in expression levels throughout development, which stress the importance and complexity of finding appropriate reference genes. The three software applications (BestKeeper, geNorm and NormFinder) used to evaluate the stability of potential reference genes produced comparable results. Tubb2 and Actb were the most stable genes across the different developmental stages, whereas 18S rRNA and Gapdh were the most variable genes and thus inappropriate to use as reference genes. According to geNorm and NormFinder, the best two-gene normalization factors corresponded to the geometric average of Tubb2/Actb and Tbb2/Fau, respectively. We believe that either of these normalization factors can be used for future developmental gene expression studies in Atlantic halibut.

Comprehensive EST analysis of Atlantic halibut (Hippoglossus hippoglossus), a commercially relevant aquaculture species

Background

An essential first step in the genomic characterisation of a new species, in this case Atlantic halibut (Hippoglossus hippoglossus), is the generation of EST information. This forms the basis for subsequent microarray design, SNP detection and the placement of novel markers on genetic linkage maps.

Results

Normalised directional cDNA libraries were constructed from five different larval stages (hatching, mouth-opening, midway to metamorphosis, premetamorphosis, and post-metamorphosis) and eight different adult tissues (testis, ovary, liver, head kidney, spleen, skin, gill, and intestine). Recombination efficiency of the libraries ranged from 91–98% and insert size averaged 1.4 kb. Approximately 1000 clones were sequenced from the 5'-end of each library and after trimming, 12675 good sequences were obtained. Redundancy within each library was very low and assembly of the entire EST collection into contigs resulted in 7738 unique sequences of which 6722 (87%) had matches in Genbank. Removal of ESTs and contigs that originated from bacteria or food organisms resulted in a total of 7710 unique halibut sequences.

Conclusion

A Unigene collection of 7710 functionally annotated ESTs has been assembled from Atlantic halibut. These have been incorporated into a publicly available, searchable database and form the basis for an oligonucleotide microarray that can be used as a tool to study gene expression in this economically important aquacultured fish.