Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca)
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ABSTRACT:
SUBMITTER: De los Rios-Perez L
PROVIDER: S-EPMC8801746 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The effects of 8 nutritional variables (Ca/P, Eicosapentaenoic acid (20:5n-3)?+?Docosahexaenoic acid (22:6n?-?3) (EPA?+?DHA), Arachidonic acid (20:4n?-?6) (ARA), Se, vitamins E, C, D and A) were investigated to identify their respective importance and interactions in pikeperch larval development. In this respect, two modalities (low and high levels) of each variable were tested through a fractional factorial experimental design allowing a reduction from 256 (28) to 16 (28?-?4) experimental units. Survival was significantly higher in larvae fed a high Ca/P diet while larval growth was significantly lower in larvae fed the same diet variant, associated with a higher incidence of kyphosis and pectoral anomalies in these larvae. Lordosis and scoliosis seemed to be mostly affected by dietary long chain polyunsaturated fatty acids (LC-PUFAs). A significant interaction was shown between n-3 LC-PUFA and vitamin C on jaw anomalies, while myocyte-specific enhancer factor 2C (mef2c) gene expression correlated positively with dietary vitamin C increment. Results also demonstrated an effect of the different nutrients and their interactions on the activity levels of digestive enzymatic activities. The results of the present study highlight the importance of the interactions between Ca/P, LC-PUFAs and vitamins C and E, suggesting their essential roles as key nutritional factors influencing pikeperch larval development.
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Project description:Sequencing raw reads for pikeperch genome including Illumina paired-end and mate-pairs reads, and PaCbio Sequel subreads.
| PRJEB34075 | ENA
Project description:The pikeperch (Sander lucioperca) is a species with a high potential for aquaculture and a valuable food with high market acceptance. The aim of the study was to evaluate the functional ontogeny of digestive enzyme of pikeperch from hatching to 45 days-post fertilization, 777 degree-day (DPF, dd) under culture condition. The average total length (TL) of larvae measured at hatching was 3.6 ± 0.4 mm (5 DPF; 67 dd) and at the end of experiment (45 DPF, 777 dd) was 27.1 ± 1.1 mm. The survival rate was 80-90% during the experiment period. Inhibition zimography reveals the presence of nine bands with proteolytic activity in the digestive tract of juvenile pikeperch. Zimography results during the ontogeny revealed that in larvae at 8 DPF (108 dd) and 13 DPF (189 dd), three bands were presented. The variations observed in the enzymatic activity reflected a high amount of total protease activity at 10 DPF (133.5 dd). Regarding pepsin, its activity was observed for the first time at 26 DPF (378.9 dd). Lipase activity remained constant from hatching to 26 DPF (378.9 dd). The highest amount of α-amylase activity was detected at 15 DPF (211.5 dd) and 45 DPF (777 dd). The low lipase enzyme activity suggested that live feeds with low lipid were more suitable than diets containing high lipid levels; larvae had also early capability to digest nutrient-dense diet that was high in protein. According to results the pikeperch larvae possess after the exogenous feeding, a functional digestive system with high activities that indicated the gradual development of the digestive system.
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Project description:Inadequate oxygen saturation can induce stress responses in fish and further affect their immunity. Pikeperch, recently introduced in intensive aquaculture, is suggested to be reared at nearly 100% DO (dissolved oxygen), yet this recommendation can be compromised by several factors including the water temperature, stocking densities or low circulation. Herein, we aimed to investigate the effect of low oxygen saturation of 40% DO (±3.2 mg/L) over 28 days on pikeperch farmed in recirculating aquaculture systems. The obtained data suggest that-although the standard blood and health parameters did not reveal any significant differences at any timepoint-the flow cytometric analysis identified a slightly decreased proportion of lymphocytes in the HK (head kidney) of fish exposed to hypoxia. This has been complemented by marginally downregulated expression of investigated immune and stress genes in HK and liver (including FTH1, HIF1A and NR3C1). Additionally, in the model of acute peritoneal inflammation induced with inactivated Aeromonas hydrophila, we observed a striking dichotomy in the sensitivity to the low DO between innate and adaptive immunity. Thus, while the mobilization of myeloid cells from HK to blood, spleen and peritoneal cavity, underlined by changes in the expression of key proinflammatory cytokines (including MPO, IL1B and TNF) was not influenced by the low DO, hypoxia impaired the influx of lymphocytes to the peritoneal niche in the later phases of the immune reaction. Taken together, our data suggest high robustness of pikeperch towards the low oxygen saturation and further encourage its introduction to the intensive aquaculture systems.
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Project description:Genetic selection for body size during domestication of animal species can inadvertently affect a number of physiological and behavioural traits. The pace-of-life syndrome (POLS) hypothesis predicts that domestication in an artificial environment lacking predators and providing abundant resources prefers proactive individuals with strong feeding motivation, high levels of aggression and risk taking, with low hypothalamus-pituitary-adrenal (HPA) axis responsiveness. In the present experiment we weaned fingerling pike-perch from live feed and habituated them to formulated feed. We recorded the number of weeks needed for the fish to accept pellets, their body length at the age of 100 days, their boldness in a novel object test and their HPI axis responsiveness. Individuals accepting the artificial feed within the first week grew larger than fish habituating later; therefore early weaners would be kept and bred in routine aquaculture procedures. Contrary to predictions of POLS hypothesis, fish weaning earlier and thus growing faster were less bold and had higher HPI axis responsiveness than fish accepting the pellets later or never. As live feed is preferred to artificial pellets, less competitive individuals may switch to pellets earlier. Inadvertent selection for stress sensitive fish may have an effect on production in aquaculture as well as on natural population after intensive restocking.
| S-EPMC5942806 | biostudies-literature
Project description:The development of three pikeperch (Sander lucioperca (L.)) populations in the northern Baltic Sea was monitored using standardized multimesh gillnets in 1995-2009. Declining trends in the abundances of pikeperch over 40 cm total length, low numbers of individuals older than 6 years, and high mortality rates were observed in all three populations. In the site with the largest commercial catches per unit area and a rapidly increased colony of great cormorants (Phalacrocorax carbo sinensis Blumenbach 1798), also the abundance of pikeperch below 40 cm total length and year-class strength showed declining trends. The adverse population level changes did not correlate with changes in water quality or eutrophication status. Together, the results suggest that in all study sites fisheries are harvesting a large proportion of the pikeperch soon after or even before reaching the maturity, and that predation from great cormorants may increase mortality of juveniles. Pikeperch is important not only for fisheries but also for ecosystem functioning, and our results point at the need for further management measures to ensure viable populations in the areas studied.
| S-EPMC3946125 | biostudies-literature
Project description:The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
| S-EPMC6770990 | biostudies-literature
Project description:Domestication of finfishes is a key element toward sustainable expansion of aquaculture sector. However, huge gap in knowledge on the mechanisms of adaptability of fish to the culture environment, being the first step toward successful domestication, exists. This affects the overall production capacity which is hindered, among others, by lowered reproductive capacity of domesticated stocks, including pikeperch – a highly valued commercial freshwater fish species. Transcriptomic profiling of embryos was found to be useful tool significantly contributing into understanding domestication process in aquaculture. Up to now there is no data on transcriptomic profiling of unfertilized eggs in any fish species as well as on pikeperch, in general. Using next generation sequencing the first complex transcriptome of pikeperch have been obtained (with 40,246 unique protein-coding genes). Next, specifically designed, pikeperch-specific microarrays (Agilent technologies) were developed (with 35,343 unique probes) and transcriptomic profiling of eggs coming from wild and domesticated populations (all characterized by high quality) was performed. From among 17,543 genes found to be expressed in eggs of pikeperch 710 were found to be differentially expressed. Functional, enrichment analysis revealed that the most enriched processes represented by the set of genes identified were developmental process, regulation of phosphorylation and nervous system development. The results of the present study provides a new insight into the processes being directly involved in the successful domestication of finfishes. It can be suggested that all the identified processes were pre-determined by the maternally derived set of genes contained already in the unfertilized eggs, what has never been reported to date. In addition to that, it has been shown for the first time that among the most important processes being affected by the domestication the post translation modifications of proteins along with development of the nervous system were identified. This allows to suggest that fish behavior should be considered as a very important trait for selection for aquaculture purposes in pikeperch.
2020-06-30 | GSE142412 | GEO
Project description:We studied life-history traits focusing on the growth and condition of the pikeperch Sander lucioperca to evaluate its phenotypic plasticity when introduced to new environments. Pikeperch is a non-native fish introduced to Iberian freshwater fauna in 1998 that quickly spread to other river basins through human-mediated activities, occupying now a wide variety of habitats along mainland Portugal. Condition (K and SMI), fork length at age, and length-weight relationships were studied for Portuguese populations. Pikeperch fork length for ages 1, 2, 3, and 4 was different between several populations. We applied generalized linear models (GLM) to study the influence of habitat type, latitude, altitude, time after first detection, and fish prey richness on pikeperch populations size at age 4 and condition. We observed higher condition values on populations from lower altitudes at lentic systems more recently introduced. But higher fork length at age 4 was found in populations from higher altitudes, on older populations with higher prey richness. Habitat type, time since first detection, and fish fauna composition are discussed as the main environmental factors explaining the observed phenotypic plasticity with concerns on predatory impact on native fauna.
| S-EPMC8131815 | biostudies-literature
Project description:Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.
| S-EPMC7749136 | biostudies-literature