Full-Length Hybrid Transcriptome of the Olfactory Rosette in Senegalese Sole (Solea senegalensis): An Essential Genomic Resource for Improving Reproduction on Farms.

Use of probiotics intercropped with plant protein diets and their influence on the growth performance and immunological status of Senegalese sole (Solea senegalensis)

High levels of dietary lipids are incorporated in feeds for most teleost fish to promote growth and reduce nitrogen waste. However, in Senegalese sole (Solea senegalensis) previous studies revealed that increasing the level of dietary lipids above 8% negatively affect growth and nutrient utilization regardless of dietary protein content. It has been shown that glucose regulation and metabolism can be impaired by high dietary fat intake in mammals, but information in teleost fish is scarce. The aim of this study was to assess the possible effect of dietary lipids on glucose metabolism in Senegalese sole with special emphasis on the regulation of proteins involved in the muscle insulin-signalling pathway. Senegalese sole juveniles (29 g) were fed two isonitrogenous diets (53% dry matter) for 88 days. These two diets were one with a high lipid level (∼17%, HL) and a moderate starch content (∼14%, LC), and the other being devoid of fish oil (4% lipid, LL) and with high starch content (∼23%, HC). Surprisingly, feeding Senegalese sole the HL/LC diet resulted in prolonged hyperglycaemia, while fish fed on LL/HC diet restored basal glycaemia 2 h after feeding. The hyperglycaemic phenotype was associated with greater glucose-6-phosphatase activity (a key enzyme of hepatic glucose production) and lower citrate synthase activity in the liver, with significantly higher liver glycogen content. Sole fed on HL/LC diet also had significantly lower hexokinase activity in muscle, although hexokinase activity was low with both dietary treatments. The HL/LC diet was associated with significant reductions in muscle AKT, p70 ribosomal S6-K1 Kinase (S6K-1) and ribosomal protein S6 (S6) 2 h after feeding, suggesting down regulation of the AKT-mTOR nutrient signalling pathway in these fish. The results of this study show for the first time that high level of dietary lipids strongly affects glucose metabolism in Senegalese sole.

Ribosomal proteins (RPs) comprise a large set of highly evolutionarily conserved proteins that are often over-represented in complementary DNA libraries. They have become very useful markers in comparative genomics, genome evolution, and phylogenetic studies across taxa. In this study, we report the sequences of the complete set of 60S RPs in Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus), two commercially important flatfish species. Amino-acid sequence comparisons of the encoded proteins showed a high similarity both between these two flatfish species and with respect to other fish and human counterparts. Expressed sequence tag analysis revealed the existence of paralogous genes for RPL3, RPL7, RPL41, and RPLP2 in Atlantic halibut and RPL13a in Senegalese sole as well as RPL19 and RPL22 in both species. Phylogenetic analysis of paralogs revealed distinct evolutionary histories for each RP in agreement with three rounds of genome duplications and lineage-specific duplications during flatfish evolution. Steady-state transcript levels for RPL19 and RPL22 RPs were quantitated during larval development and in different tissues of sole and halibut using a real-time polymerase chain reaction approach. All paralogs were expressed ubiquitously although at different levels in different tissues. Most RP transcripts increased coordinately after larval first-feeding in both species but decreased progressively during the metamorphic process. In all cases, expression profiles and transcript levels of orthologous genes in Senegalese sole and Atlantic halibut were highly congruent. The genomic resources and knowledge developed in this survey will be useful for the study of Pleuronectiformes evolution.

The access to a wider variety of farmed fish species is an increasing consumer demand. Solea sp. are considered excellent candidates to diversify this demand, although some problems persist to farm this species in a commercial scale. Exploratory work in Senegalese sole ( Solea senegalensis) is being done in different farming areas and it is plausible that its cultivation in a commercial scale will be done in the near future. For this reason it is important to know how this farmed species maintain its quality during ice storage. Senegalese sole from two different areas in Spain and different size and rearing conditions were analysed up to 28 days of ice storage to establish the eating quality and storage life determined by a sensory panel by means of a quality test in the cooked fillets and a quality index (QI) applying the QI method (QIM), shear resistance of the raw and cooked muscle, color and microbiological counts. The batches were rejected by the sensory panel at 22 and 25 days of storage. The commercial period determined for Senegalese sole is longer than that for other commercial farmed species. The differences between the two batches may be due to differences in size and rearing conditions.

Simple SummaryEnrichment products for Artemia spp. metanauplii are commonly used to enhance the nutritional quality of this live prey offered to fish during conventional larval feeding. However, there are few reports on the influence of such enrichments on the development of skeletal anomalies in Senegalese sole, a major problem for this flatfish aquaculture. This study evaluated the frequency of vertebral anomalies in postlarvae and juvenile Senegalese sole fed with Artemia spp. metanauplii enriched with four commercial products (EA, EB, EC, and ED) in a fish farm. The results show a high percentage of individuals with skeletal anomalies in every dietary group. Some types of anomalies were very frequent in all diet-age groups, indicating the presence of a common trend or mainstay of vertebral deformities. Despite some variations in the frequency of anomalies among diets, it was not possible to establish a clear effect of the enrichment products on the development of vertebral deformities at both rearing stages, probably for the “masking effect” of other rearing conditions. The multivariate statistical technique, as the correspondence analysis, indicated a different anomaly pattern among ages, where bone adaptative responses may be implied.The high incidence of skeletal anomalies in Senegalese sole (Solea senegalensis) still constitutes a bottleneck constraining its production. There are diverse commercially available products for the enrichment of live preys, but few reports of their influence on skeletogenesis in Senegalese sole. This study evaluated the presence of vertebral anomalies in postlarvae and juvenile Senegalese sole fed with Artemia spp. metanauplii enriched with four commercial products (EA, EB, EC, and ED) in a fish farm. The most frequent alterations consisted of deformations of the neural/haemal arches and spines and fusions and deformations of hypurals, epural, or parhypural. The correspondence analysis ordered fish from each age in separated semiaxis, indicating the presence of different anomaly patterns for the two sampled stages. The results showed only very light changes in the frequency of vertebral abnormalities among tested enrichment products, i.e., individuals from EC and EA lots displayed less vertebral body anomalies and/or vertebral column deviations at 31 and 105 days after hatching, respectively. The existence of a large shared malformation pattern in all the experimental groups leads to impute to the rearing conditions as the main driving factor of the onset of such group of anomalies, probably masking some dietary effect.

The effect of dietary protein level and protein source on growth and proteolytic activity of juvenile Solea senegalensis was studied. In Experiment 1, fish were fed on four experimental diets containing increased protein levels (36, 46, 56 and 67%). In Experiment 2, Senegalese soles were fed on five diets with partial substitution of fish meal by soybean meal, soybean protein concentrate, soybean protein isolate, wheat gluten meal or pea protein concentrate. Results prove that growth and proteolytic activity in the distal intestine of fish were affected by the quantitative increase in dietary protein. The origin of protein source used in the elaboration of experimental diets affected both the amount and composition of the alkaline proteases secreted into the intestinal lumen; however, it did not decrease animal growth. Juvenile Senegalese sole showed capability to modulate digestive protease secretion when the concentration and/or source of dietary protein were modified. Quantity and quality of dietary protein affected protein hydrolysis in Senegalese sole intestine. This study establishes that 30% fish meal protein can be replaced by soybean derivatives without affecting intestinal proteases. Replacement with wheat gluten meal or pea protein concentrate should be taken cautiously, but further research is needed to establish whether growth performance and digestive enzyme physiology of Senegalese sole are affected by plant protein-supplemented diets in a long-term trial.

The efficacy of 2-phenoxyethanol, metomidate, clove oil and MS-222 as anaesthetic agents in the Senegalese sole ( Solea senegalensis Kaup 1858)

High rearing densities are typical conditions of both inland and onshore intensive aquaculture units. Despite obvious drawbacks, this strategy is nonetheless used to increase production profits. Such conditions inflict stress on fish, reducing their ability to cope with disease, bringing producers to adopt therapeutic strategies. In an attempt to overcome deleterious effects of chronic stress, Senegalese sole, Solea senegalensis, held at low (LD) or high density (HD) were fed tryptophan-supplemented diets with final tryptophan content at two (TRP2) or four times (TRP4) the requirement level, as well as a control and non-supplemented diet (CTRL) for 38 days. Fish were sampled at the end of the feeding trial for evaluation of their immune status, and mortalities were recorded following intra-peritoneal infection with Photobacterium damselae subsp. piscicida. Blood was collected for analysis of the hematological profile and innate immune parameters in plasma. Pituitary and hypothalamus were sampled for the assessment of neuro-endocrine-related gene expression. During the feeding trial, fish fed TRP4 and held at LD conditions presented higher mortalities, whereas fish kept at HD seemed to benefit from this dietary treatment, as disease resistance increased over that of CTRL-fed fish. In accordance, cortisol level tended to be higher in fish fed both supplemented diets at LD compared to fish fed CTRL, but was lower in fish fed TRP4 than in those fed TRP2 under HD condition. Together with lower mRNA levels of proopiomelanocortin observed with both supplementation levels, these results suggest that higher levels of tryptophan might counteract stress-induced cortisol production, thereby rendering fish better prepared to cope with disease. Data regarding sole immune status showed no clear effects of tryptophan on leucocyte numbers, but TRP4-fed fish displayed inhibited alternative complement activity (ACH50) when held at LD, as opposed to their HD counterparts whose ACH50 was higher than that of CTRL-fed fish. In conclusion, while dietary tryptophan supplementation might have harmful effects in control fish, it might prove to be a promising strategy to overcome chronic stress-induced disease susceptibility in farmed Senegalese sole.

This study aimed at investigating addition of microalgae in the rearing of marine fish larvae (green water technique). Addition of microalgae supernatant, or bacteria isolated from microalgae cultures, to the rearing tanks of larval Senegalese sole, Solea senegalensis, and gilthead seabream, Sparus aurata, had no significant (P < 0.05) influence on survival or growth of the larvae. Addition of four bacterial strains isolated from microalgae decreased however the numbers of presumptive Vibrio in gilthead seabream larvae and seawater were compared with the control treatment 7 d after hatching (P < 0.05). No such effects were shown on the numbers of presumptive Vibrio in the rearing of sole larvae. Addition of bacteria improved the digestive capacity of gilthead seabream larvae, as the total activity (U/larva) of trypsin, amylase, and alkaline phosphatase in the treatment with added bacteria were significantly higher (P < 0.05) than in larvae from the control treatment 10 d after hatching. No such effects were shown in the case of sole larvae. The present results indicated that bacteria associated with microalgae may play an important role for the inhibition of proliferation of Vibrio and improvement of digestive capacity during the first days of feeding of gilthead seabream larvae, but does not appear to be beneficial for larvae of Senegalese sole.

Habitat modelling requires incorporation of both biotic and abiotic information. For juvenile flatfish the factors that most influence growth are water temperature, food abundance and predatory pressure. This study focuses on the impact the predator, the shore crab,Carcinus maenas, has on the foraging activity of sole,Solea senegalensis. The results show that in the presence of both prey (ragworm,Nereis diversicolor) and predator, ≃10% decrease in foraging activity is observed when compared to the sole in the presence of only food. This suggests that when the shore crab is present, Senegalese soles are not only affected by direct predation but sub-optimal foraging is also found. Behaviours most correlated with foraging were crawling and tapping and these activities were also affected by the presence of the predator. This study also provides further support for visual recognition of predators and olfactory prey recognition in the Senegalese sole. Predator–prey encounters shape species behaviours profoundly and have to be looked at from different levels of ecology, behaviour and modelling.

The KISSPEPTIN-1 receptor (KISS1R) and its ligands (KISSPEPTINS) are implicated in the regulation of the onset of puberty. We report the coding region and genomic structure of the kiss1r gene of a modern teleost, the Senegalese sole (Ss). Ss kiss1r cDNA contained an opening frame of 1137 bp, which results in a predicted 378 amino acid protein. Searching genomic databases allowed the identification of kiss1r orthologues in six new species belonging to three vertebrate groups and established the evolutionary relationships of all KISS1R sequences available to date. Analysis of Ss kiss1r revealed for the first time in any vertebrate KISS1R gene the presence of features that are characteristic of a mechanism of alternative splicing. This was confirmed by the identification of two transcripts, Ss kiss1r_v1 and Ss kiss1r_v2. The latter, arising from intron III retention, contained a 27 codons insert in transmembrane region 4 with two stop codons, suggesting it may lead to a truncated protein. The mRNA of the two variants was differently expressed in several tissues. In the brain, levels of the Ss kiss1r_v1 were higher than those of Ss kiss1r_v2. In the gonads, the opposite was observed. Both isoforms exhibited changes depending on sex and maturity stage. The presence of two variants may help to explain some discrepancies observed in past studies regarding KISS1R expression during puberty. Thus, the existence of alternative splicing for the KISS1R gene may contribute to our understanding of the many physiological functions suspected to be mediated by KISSPEPTIN-KISS1R signaling.

Simple SummaryTo increase competitiveness, the aquaculture flatfish industry demands animals with optimal growth rates and a high shape quality. Genetic breeding is an essential tool to achieve these goals but it requires the estimation of the genetic components of these traits under industrial conditions. The current study provides phenotypic data and genetic parameters of eight traits related to growth and shape quality. The high heritabilities and correlations obtained support that genetic breeding programs can be successfully implemented in Senegalese sole to optimize production.Shape quality is very important in flatfish aquaculture due to the impact on commercialization. The Senegalese sole (Solea senegalensis) is a valuable flatfish with a highly elliptic body that slightly changes with age and size, and it is prone to accumulating malformations during the production cycle. The present study aims to investigate the genetic parameters of two growth traits (weight and standard length) and six shape quality predictors (ellipticity, three body heights (body height at the pectoral fin base [BHP], body maximum height [BMH] and caudal peduncle height [CPH]) and two ratios (BMH/BHP and BMH/CPH)). These traits were measured before the on-growing stage (age ~400 days (d)) and at harvest (~800 d). Phenotypic data, heritabilities and genetic and phenotypic correlations between the traits are presented and discussed. High or very high heritabilities (0.433–0.774) were found for growth traits, body heights and ellipticity and they were higher at 400 than 800 d. In contrast, the ratios of BMH/BHP and BMH/CPH were less heritable (0.144–0.306). Positive and very high (>0.95) correlations between growth traits and the three heights were found and decreased with age. In contrast, ellipticity had negative and medium-high genetic correlations with growth traits and heights, indicating fish selected for bigger size would also become rounder. The ratio of BMH/CPH showed low genetic correlations with all traits and provided complementary information to ellipticity for a better fitting to the expected lanceolate body morphology of sole. The genetic correlations for all traits at both ages were very high, indicating that selection before entering the growth-out stage in recirculation aquaculture systems is recommended to accelerate genetic gains.

Trace elements such as Cu, Fe, Mn and Zn are essential minerals in fish diets, especially important at early larval stages. The chemical speciation of these elements directly influences their uptake efficiency and metabolic utilization. In order to optimize the form of trace elements incorporated into larval feed, two experiments were conducted using two commercial fish species, European seabass (Dicentrarchus labrax) and Senegalese sole (Solea senegalensis), and two chemical forms (inorganic and glycinate chelates). Several fish performance parameters were measured, as well as bone status parameters to assess which form of mineral results in optimal fish biological performance. European seabass and Senegalese sole post-larvae were unresponsive (P > 0.05) to dietary treatments in terms of dry weight (DW), standard length (SL), relative growth rate (RGR) or feed conversion rates (FCR) when fed diets supplemented with chelated over inorganic trace minerals. This study suggests that replacing dietary inorganic mineral supplementation by their organic glycinate-chelated forms brings no beneficial effects on somatic growth and bone development in Senegalese sole and European seabass post-larvae fed high-quality commercial microdiets. Additionally, we show that mineral leaching from diets can be significant, but the use of chelated minerals can potentially mitigate this leaching phenomenon. Therefore, the selection of the dietary mineral form should take into account not only their economic value, but also their biological effect and environmental impact. Data generated in this trial provides new knowledge in trace mineral nutrition of early-stage marine fish.

Increasing water CO2, aquatic hypercapnia, leads to higher physiological pCO2 levels in fish, resulting in an acidosis and compensatory acid-base regulatory response. Senegalese sole is currently farmed in super-intensive recirculating water systems where significant accumulation of CO2 in the water may occur. Moreover, anthropogenic releases of CO2 into the atmosphere are linked to ocean acidification. The present study was designed to assess the effects of acute (4 and 24 h) and prolonged exposure (4 weeks) to CO2 driven acidification (i.e., pH 7.9, 7.6, and 7.3) from normocapnic seawater (pH 8.1) on the innate immune status, gill acid-base ion transporter expression and metabolic rate of juvenile Senegalese sole. The acute exposure to severe hypercapnia clearly affected gill physiology as observed by an increase of NHE3b positive ionocytes and a decrease of cell shape factor. Nonetheless only small physiological adjustments were observed at the systemic level with (1) a modulation of both plasma and skin humoral parameters and (2) an increased expression of HIF-1 expression pointing to an adjustment to the acidic environment even after a short period (i.e., hours). On the other hand, upon prolonged exposure, the expression of several pro-inflammatory and stress related genes was amplified and gill cell shape factor was aggravated with the continued increase of NHE3b positive ionocytes, ultimately impacting fish growth. While these findings indicate limited effects on energy use, deteriorating immune system conditions suggest that Senegalese sole is vulnerable to changes in CO2 and may be affected in aquaculture where a pH drop is more prominent. Further studies are required to investigate how larval and adult Senegalese sole are affected by changes in CO2.

BackgroundBlueberries (Vaccinium sp.) are native to North America and breeding efforts to improve blueberry fruit quality are focused on improving traits such as increased firmness, enhanced flavor and greater shelf-life. Such efforts require additional genomic resources, especially in southern highbush and rabbiteye blueberries.ResultsWe generated the first full-length fruit transcriptome for the southern highbush and rabbiteye blueberry using the cultivars, Suziblue and Powderblue, respectively. The transcriptome was generated using the Pacific Biosciences single-molecule long-read isoform sequencing platform with cDNA pooled from seven stages during fruit development and postharvest storage. Raw reads were processed through the Isoseq pipeline and full-length transcripts were mapped to the ‘Draper’ genome with unmapped reads collapsed using Cogent. Finally, we identified 16,299 and 15,882 non-redundant transcripts in ‘Suziblue’ and ‘Powderblue’ respectively by combining the reads mapped to Northern Highbush blueberry ‘Draper’ genome and Cogent analysis. In both cultivars, > 80% of sequences were longer than 1,000 nt, with the median transcript length around 1,700 nt. Functionally annotated transcripts using Blast2GO were > 92% in both ‘Suziblue’ and ‘Powderblue’ with overall equal distribution of gene ontology (GO) terms in the two cultivars. Analyses of alternative splicing events indicated that around 40% non-redundant sequences exhibited more than one isoform. Additionally, long non-coding RNAs were predicted to represent 5.6% and 7% of the transcriptomes in ‘Suziblue’ and ‘Powderblue’, respectively. Fruit ripening is regulated by several hormone-related genes and transcription factors. Among transcripts associated with phytohormone metabolism/signaling, the highest number of transcripts were related to abscisic acid (ABA) and auxin metabolism followed by those for brassinosteroid, jasmonic acid and ethylene metabolism. Among transcription factor-associated transcripts, those belonging to ripening-related APETALA2/ethylene-responsive element-binding factor (AP2/ERF), NAC (NAM, ATAF1/2 and CUC2), leucine zipper (HB-zip), basic helix-loop-helix (bHLH), MYB (v-MYB, discovered in avian myeloblastosis virus genome) and MADS-Box gene families, were abundant.Further we measured three fruit ripening quality traits and indicators [ABA, and anthocyanin concentration, and texture] during fruit development and ripening. ABA concentration increased during the initial stages of fruit ripening and then declined at the Ripe stage, whereas anthocyanin content increased during the final stages of fruit ripening in both cultivars. Fruit firmness declined during ripening in ‘Powderblue’. Genes associated with the above parameters were identified using the full-length transcriptome. Transcript abundance patterns of these genes were consistent with changes in the fruit ripening and quality-related characteristics.ConclusionsA full-length, well-annotated fruit transcriptome was generated for two blueberry species commonly cultivated in the southeastern United States. The robustness of the transcriptome was verified by the identification and expression analyses of multiple fruit ripening and quality–regulating genes. The full-length transcriptome is a valuable addition to the blueberry genomic resources and will aid in further improving the annotation. It will also provide a useful resource for the investigation of molecular aspects of ripening and postharvest processes.