Identification of hypoxia-regulated genes in the liver of common sole (Solea solea) fed different dietary lipid contents
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ABSTRACT:
ORGANISM(S): Solea solea
PROVIDER: GSE44579 | GEO | 2013/10/07
SECONDARY ACCESSION(S): PRJNA190091
REPOSITORIES: GEO
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Project description:Hepatic transcriptome of sole fed low and high lipid dietary content in the early response to hypoxic stress. Characterization of the hepatic transcriptome of S. solea in order to assess the molecular mechanisms underlying the effects of dietary lipid content on hypoxia tolerance in common sole. S. solea individuals (8 month post-hatching) were fed for two month with commercial diets containing either 11% lipids or 20% lipids. Before hypoxia challenge stress, 38 individuals (19 from each dietary group) were randomly pooled in a single tank (1 m3) and left undisturbed and unfed for 48 h. The hypoxia challenge consisted then in a decrease of water oxygenation from 100 % to 10 % within one hour, followed by a slower descent at 2 % hr-1 to 4%. As fish lost their equilibrium, they were removed and sampled. Thirty six individuals (18 from each dietary group) were also sampled in normoxic conditions, resulting in 4 experimental groups: Normoxia low-lipid, Normoxia high-lipid, Hypoxia low-lipid, Hypoxia high-lipid. The experimental design was therefore a 2-way full factorial design between two juvenile dietary lipid contents and two oxygen concentration conditions.
2013-10-07 | E-GEOD-44579 | biostudies-arrayexpress
Project description:A microarray platform for Solea solea was developed to study gene expression profiles of common sole developmental stages.
2013-09-20 | GSE41261 | GEO
Project description:A microarray platform for Solea solea was employed to study gene expression profiles of common sole developmental stages.
2017-02-14 | GSE81944 | GEO
Project description:A microarray platform for Solea solea was developed to study gene expression profiles of common sole developmental stages. Characterization of the transcriptome of S. solea, focusing on larval and juvenile stages. After transcriptome sequencing and annotation [TSA accession number GAAQ00000000], an oligo-DNA microarray for the detection of 12,836 unique transcripts was developed and applied to the study of gene expression profiles during larval-to-juvenile transition. For microarray experiments, pooled samples of 10–5 individuals (depending on larval age) were sampled and RNA extracted at 1, 4, 6, 11, 13, 18, 24 and 33 days post-hatching (dph). The number of biological replicates was four for each sampling point.
2013-09-20 | E-GEOD-41261 | biostudies-arrayexpress
Project description:BackgroundThe common sole (Solea solea) is a promising candidate for European aquaculture; however, the limited knowledge of the physiological mechanisms underlying larval development in this species has hampered the establishment of successful flatfish aquaculture. Although the fact that genomic tools and resources are available for some flatfish species, common sole genomics remains a mostly unexplored field. Here, we report, for the first time, the sequencing and characterisation of the transcriptome of S. solea and its application for the study of molecular mechanisms underlying physiological and morphological changes during larval-to-juvenile transition.ResultsThe S. solea transcriptome was generated from whole larvae and adult tissues using the Roche 454 platform. The assembly process produced a set of 22,223 Isotigs with an average size of 726 nt, 29 contigs and a total of 203,692 singletons. Of the assembled sequences, 75.2% were annotated with at least one known transcript/protein; these transcripts were then used to develop a custom oligo-DNA microarray. A total of 14,674 oligonucleotide probes (60 nt), representing 12,836 transcripts, were in situ synthesised onto the array using Agilent non-contact ink-jet technology. The microarray platform was used to investigate the gene expression profiles of sole larvae from hatching to the juvenile form. Genes involved in the ontogenesis of the visual system are up-regulated during the early stages of larval development, while muscle development and anaerobic energy pathways increase in expression over time. The gene expression profiles of key transcripts of the thyroid hormones (TH) cascade and the temporal regulation of the GH/IGF1 (growth hormone/insulin-like growth factor I) system suggest a pivotal role of these pathways in fish growth and initiation of metamorphosis. Pre-metamorphic larvae display a distinctive transcriptomic landscape compared to previous and later stages. Our findings highlighted the up-regulation of gene pathways involved in the development of the gastrointestinal system as well as biological processes related to folic acid and retinol metabolism. Additional evidence led to the formation of the hypothesis that molecular mechanisms of cell motility and ECM adhesion may play a role in tissue rearrangement during common sole metamorphosis.ConclusionsNext-generation sequencing provided a good representation of the sole transcriptome, and the combination of different approaches led to the annotation of a high number of transcripts. The construction of a microarray platform for the characterisation of the larval sole transcriptome permitted the definition of the main processes involved in organogenesis and larval growth.
| S-EPMC3659078 | biostudies-literature
Project description:The retinas of nonmammalian vertebrates have cone photoreceptor mosaics that are often organized as highly patterned lattice-like distributions. In fishes, the two main lattice-like patterns are composed of double cones and single cones that are either assembled as interdigitized squares or as alternating rows. The functional significance of such orderly patterning is unknown. Here, the cone mosaics in two species of Soleidae flatfishes, the common sole and the Senegalese sole, were characterized and compared to those from other fishes to explore variability in cone patterning and how it may relate to visual function. The cone mosaics of the common sole and the Senegalese sole consisted of single, double, and triple cones in formations that differed from the traditional square mosaic pattern reported for other flatfishes in that no evidence of higher order periodicity was present. Furthermore, mean regularity indices for single and double cones were conspicuously lower than those of other fishes with "typical" square and row mosaics, but comparable to those of goldfish, a species with lattice-like periodicity in its cone mosaic. Opsin transcripts detected by quantitative polymerase chain reaction (sws1, sws2, rh2.3, rh2.4, lws, and rh1) were uniformly expressed across the retina of the common sole but, in the Senegalese sole, sws2, rh2.4, and rh1 were more prevalent in the dorsal retina. Microspectrophotometry revealed five visual pigments in the retina of the common sole [S(472), M(523), M(536), L(559), and rod(511)] corresponding to the repertoire of transcripts quantified except for sws1. Overall, these results indicate a loss of cone mosaic patterning in species that are primarily nocturnal or dwell in low light environments as is the case for the common sole and the Senegalese sole. The corollary is that lattice-like patterning of the cone mosaic may improve visual acuity. Ecological and physiological correlates derived from observations across multiple fish taxa that live in low light environments and do not possess lattice-like cone mosaics are congruent with this claim.
| S-EPMC7392819 | biostudies-literature
Project description:Solea senegalensis breed:senegalese sole Genome sequencing
| PRJNA668895 | ENA
Project description: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.
| S-EPMC4232633 | biostudies-literature
Project description:In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding-activation of AMPA and NMDA receptors-long-term stimulation of postsynaptic potential-LTP (long term potentiation)-plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.
| S-EPMC8388432 | biostudies-literature
Project description:Larval dispersal and juvenile survival are crucial in determining variation in recruitment, stock size and adult distribution of commercially important fish. This study investigates the dispersal of early-life stages of common sole (Solea solea L.) in the southern North Sea, both empirically and through modeling. Age at different life-history events of juvenile flatfish sampled along the coasts of Belgium, the Netherlands and the United Kingdom in 2013, 2014 and 2016, was determined through the counting of daily growth rings in the otoliths. Juveniles captured between August and October were estimated to be on average 140 days old with an average pelagic larval duration of 34 days. The hatching period was estimated between early April and mid-May followed by arrival and settlement in the nurseries between May and mid-June. Growth rates were higher off the Belgian coast than in the other nursery areas, especially in 2013, possibly due to a post-settlement differentiation. Empirical pelagic larval duration and settlement distributions were compared with the Larvae&Co larval dispersal model, which combines local hydrodynamics in the North Sea with sole larval behavior. Yearly predicted and observed settlement matched partially, but the model estimated a longer pelagic phase. The observations fitted even better with the modelled average (1995-2015) distribution curves. Aberrant results for the small juvenile sole sampled along the UK coast in March 2016, led to the hypothesis of a winter disruption in the deposition of daily growth rings, potentially related to starvation and lower food availability. The similarities between measured and modelled distribution curves cross-validated both types of estimations and accredited daily ageing of juveniles as a useful method to calibrate biophysical models and to understand early-life history of fish, both important tools in support of efficient fisheries management strategies.
| S-EPMC8457496 | biostudies-literature