Transcriptomic responses of early developmental larval stages exposed to a hypoosmotic environment in the flatfish Senegalese solea
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ABSTRACT:
ORGANISM(S): Solea senegalensis
PROVIDER: GSE57173 | GEO | 2016/04/24
SECONDARY ACCESSION(S): PRJNA245827
REPOSITORIES: GEO
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Project description:Introduction: A major economic impediment to the aquaculture of marine finfish in land-based recirculating systems is maintaining the system salinity at a range for optimal growth. Florida Pompano (Trachinotus carolinus) are warm water, euryhaline, marine finfish shown to be a suitable candidate for low-salinity culture. Due to its popularity among sport and commercial fishers, high market value, and ability to readily consume pelleted feeds, the Florida Pompano has become a renewed target for commercialized aquaculture. Although the Florida Pompano has been successfully grown at various salinities, its optimal growth salinity has not yet been established. Studies have shown culturing at different salinities has an effect on digestion rates, feed utilization, and lipid biosynthesis. Identifying the optimal salinity for growth would result in decreased energy expenditure on maintaining homeostasis, since osmoregulation is a highly demanding process. This would allow for energy to be spent on the efficient use of nutrients. Methods: Our study was designed to determine how Florida Pompano larviculture at various salinities affects fish health with transcriptomics (RNA-seq) and fatty acid analysis. RNA-seq was used to identify genes actively transcribed and expressed at the time of sampling. After hatching in a salinity of ~ 30 ppt, larvae were reared in 345 L tanks at one of three salinities (10, 20, 30 ppt) in triplicate. Larvae samples for RNA-seq and fatty acid analysis were collected every three days until weaning. Samples for fatty acid composition were analyzed using a gas chromatography-mass spectrometry (GC/MS). RNA was extracted from homogenized whole-body samples using the Qiagen RNeasy Mini kit. Total RNA was sequenced on the Illumina HiSeq 4000 System. Raw sequences were filtered for low-quality sequences, aligned to the S. dumerili reference genome (NCBI Genome: 12614), and quantified. Each sampling day was compared across salinities to establish the differentially expressed genes (DEGs) between salinities. Results & Discussion: The numbers of DEGS in pooled samples was minimal (less than 15 total in each comparison) and the number of DEGS at each dph was variable. There were no significant differences between pooled samples or at each dph according to PERMANOVA analysis, but each dph was statistically different on pairwise analysis. Gene set enrichment analysis revealed that there was a downregulation of immune related genes in lower salinities versus higher salinities suggesting larvae may be dealing with less stress at lower salinities. Most osmoregulation, fatty acid, and immune related genes tested were not significantly different across salinities. This is likely be cause the Florida pompano is euryhaline and has a tolerance to the salinities selected. There was an increase in the expression levels of several immune related genes that may indicate an increase exposure to pathogens at later days post hatch likely related to feeding schedule. There was also an increase in fatty acid biosynthesis genes that corresponded with levels of fatty acids indicating a possible synthesis of essential fatty acids from precursors. Conclusions: From a transcriptomics perspective, the larvae did not show a negative response to lower salinities in comparison to higher salinities, which in fact showed upregulation of immune related genes. Further exploration of Florida pompano’s ability to biosynthesize essential fatty acids is necessary. This study will help enable the optimization of Florida Pompano larviculture using information on the optimal salinity and fatty acid content for growth and facilitate more cost-effective rearing methods.
2022-12-01 | GSE190968 | GEO
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:The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis.
| S-EPMC8242048 | biostudies-literature
Project description:Flatfish species seem to require dietary taurine for normal growth and development. Although dietary taurine supplementation has been recommended for flatfish, little is known about the mechanisms of taurine absorption in the digestive tract of flatfish throughout ontogeny. This study described the cloning and ontogenetic expression of the taurine transporter (TauT) in the flatfish Senegalese sole (Solea senegalensis). Results showed a high similarity between TauT in Senegalese sole and other vertebrates, but a change in TauT amino acid sequences indicates that taurine transport may differ between mammals and fish, reptiles or birds. Moreover, results showed that Senegalese sole metamorphosis is an important developmental trigger to promote taurine transport in larvae, especially in muscle tissues, which may be important for larval growth. Results also indicated that the capacity to uptake dietary taurine in the digestive tract is already established in larvae at the onset of metamorphosis. In Senegalese sole juveniles, TauT expression was highest in brain, heart and eye. These are organs where taurine is usually found in high concentrations and is believed to play important biological roles. In the digestive tract of juveniles, TauT was more expressed in stomach and hindgut, indicating that dietary taurine is quickly absorbed when digestion begins and taurine endogenously used for bile salt conjugation may be recycled at the posterior end of the digestive tract. Therefore, these results suggest an enterohepatic recycling pathway for taurine in Senegalese sole, a process that may be important for maintenance of the taurine body levels in flatfish species.
| S-EPMC3296012 | biostudies-literature
Project description:Dominance is defined as the preferential access to limited resources. The present study aimed to characterise dominance in a non-aggressive flatfish species, the Senegalese sole (Solea senegalensis) by 1) identifying dominance categories and associated behaviours and 2) linking dominance categories (dominant and subordinate) with the abundance of selected mRNA transcripts in the brain. Early juveniles (n = 74, 37 pairs) were subjected to a dyadic dominance test, related to feeding, and once behavioural phenotypes had been described the abundance of ten selected mRNAs related to dominance and aggressiveness was measured in the brain. Late juveniles were subjected to two dyadic dominance tests (n = 34, 17 pairs), related to feeding and territoriality and one group test (n = 24, 4 groups of 6 fish). Sole feeding first were categorized as dominant and sole feeding second or not feeding as subordinate. Three social behaviours (i. "Resting the head" on another fish, ii. "Approaching" another fish, iii. "Swimming above another" fish) were associated with dominance of feeding. Two other variables (i. Total time occupying the preferred area during the last 2 hours of the 24 h test, ii. Organisms occupying the preferred area when the test ended) were representative of dominance in the place preference test. In all tests, dominant fish compared to subordinate fish displayed a significantly higher number of the behaviours "Rest the head" and "Approaches". Moreover, dominant sole dominated the sand at the end of the test, and in the group test dominated the area close to the feed delivery point before feed was delivered. The mRNA abundance of the selected mRNAs related to neurogenesis (nrd2) and neuroplasticity (c-fos) in dominant sole compared to subordinate were significantly different. This is the first study to characterise dominance categories with associated behaviours and mRNA abundance in Senegalese sole and provides tools to study dominance related problems in feeding and reproduction in aquaculture.
| S-EPMC5587333 | biostudies-literature
Project description:To understand the sensitivity of larval lice to changing environmental parameters we applied a 38K oligo microarray and characterized transcriptome responses after 24 hour exposures to reduced salinity (30-10 parts per thousand (ppt)) or varied temperature (16-4M-BM-:C). To further characterize the effects of salinity, we profiled expression changes over a range of seawater with single increment differences (30-25 ppt). Three separate projects. Low resolution salinity (aka wide range or LR_SAL) contains 2 duplicate experiments, each with pools of lice (~500 copepodid lice per beaker; n=3 beakers per condition), incubated for 24 hr at 10M-BM-:C diluted to 30, 25, 20, or 10 parts per thousand (ppt). Temperature study conducted as above, but with a constant salinity of 30 ppt and changed temperature of 4, 10, or 16M-BM-:C. High resolution salinity conducted as above, but with no experiment replication, but with biological repication of n=6 beakers per condition, and with a range of 25, 26, 27, 28, 29, 30 ppt salinity. Please note that each experiment was normalized separately.
2012-05-18 | E-GEOD-37976 | biostudies-arrayexpress
Project description:Seawater (SW)-acclimated Nile tilapia, Oreochromis niloticus, can tolerate up to 30-ppt SW but rarely produce offspring. The embryos of SW-acclimated O. niloticus survived equally well from 0- to 10-ppt environment but not under 20 ppt. However, when the embryos were incubated under 10 ppt during days 0-3 and then the salinity was suddenly shifted to and maintained at 20 ppt during days 4-6, their survival rate was comparable to those incubated under 0 and 10 ppt. To elucidate a molecular adaptation of the embryos that survived different salinity environment, the proteomic profiles of the newly hatched embryos, or early larvae, hatched under 0 ppt, 10 ppt, and those being incubated at 10 ppt during days 0-3 followed by at 20 ppt during days 4-6 were compared.
2024-10-02 | PXD045852 | JPOST Repository
Project description:To understand the sensitivity of larval lice to changing environmental parameters we applied a 38K oligo microarray and characterized transcriptome responses after 24 hour exposures to reduced salinity (30-10 parts per thousand (ppt)) or varied temperature (16-4ºC). To further characterize the effects of salinity, we profiled expression changes over a range of seawater with single increment differences (30-25 ppt).
2012-05-19 | GSE37976 | GEO
Project description:BACKGROUND: The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species. RESULTS: Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data. CONCLUSION: New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.
| S-EPMC2612027 | biostudies-literature
Project description:The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom that naturally tolerates a broad range of salinities, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling at 8 time points across 10 hours. We found substantial remodeling of the transcriptome, with over half of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in functions related to cell growth and osmolyte production, and strong induction of genes implicated in stress defense such as scavenging reactive oxygen species and maintaining osmotic balance. Notably, transcripts largely returned to baseline levels within 4–10 hours, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a study of expression profiling following months-long acclimation of C. cryptica to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.
2022-06-23 | GSE206725 | GEO