RESUMO
BACKGROUND: The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. RESULTS: We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. CONCLUSIONS: Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Assuntos
Evolução Molecular , Processos de Determinação Sexual , Animais , Processos de Determinação Sexual/genética , Masculino , Feminino , Percas/genética , Filogenia , Receptores de Peptídeos/genética , Genoma , Receptores de Fatores de Crescimento Transformadores betaRESUMO
Exposure to high temperatures can lead to thermotolerance in fish, which is hypothesized to potentially improve post-release survival in species under restocking programs, like Atlantic sturgeon. The aim of this study was to determine whether Atlantic sturgeon juveniles exposed to a 4-week temperature treatment respond differently to a subsequent heat shock than juveniles exposed to heat shock for the first time (naive fish). Response to heat shock was assessed by mapping the liver transcriptome. In total, 838 unique contigs were differentially expressed between the trained and the control group (592 downregulated, 261 upregulated, and 15 down- or upregulated, depending on the condition), corresponding to genes involved in the response to heat, tissue damage, proteolysis, and metabolism. Temperature-trained fish showed 2-4-fold fewer dysregulated contigs than naive fish, indicating their ability to maintain and recover homeostasis faster. During heat shock, hspc1 was upregulated in both experimental groups, while hspa1 and dnaja4 were exclusively upregulated in the control. Overall, compensatory mechanisms were observed in addition to the heat shock response. Only two genes, fgg and apnl, were upregulated at nearly all timepoints in both groups. Peptidases were more strongly downregulated in control fish, which also showed a reduction in lipid metabolism during recovery. Keratins, pck1, gadd45ga, and gadd45gb were differentially expressed between trained and control fish, and due to their roles in tissue protection and ER stress reduction, they might be responsible for the maintenance of the transcriptional homeostasis observed in trained fish.
Assuntos
Adaptação Fisiológica , Peixes/fisiologia , Regulação da Expressão Gênica/fisiologia , Resposta ao Choque Térmico , Homeostase , AnimaisRESUMO
BACKGROUND: Innovations in fish nutrition act as drivers for the sustainable development of the rapidly expanding aquaculture sector. Probiotic dietary supplements are able to improve health and nutrition of livestock, but respective bacteria have mainly been isolated from terrestrial, warm-blooded hosts, limiting an efficient application in fish. Native probiotics adapted to the gastrointestinal tract of the respective fish species will establish within the original host more efficiently. RESULTS: Here, 248 autochthonous isolates were cultured from the digestive system of three temperate flatfish species. Upon 16S rRNA gene sequencing of 195 isolates, 89.7% (n = 175) Gram-negatives belonging to the Alpha- (1.0%), Beta- (4.1%) and Gammaproteobacteria (84.6%) were identified. Candidate probiotics were further characterized using in vitro assays addressing 1) inhibition of pathogens, 2) degradation of plant derived anti-nutrient (saponin) and 3) the content of essential fatty acids (FA) and their precursors. Twelve isolates revealed an inhibition towards the common fish pathogen Tenacibaculum maritimum, seven were able to metabolize saponin as sole carbon and energy source and two isolates 012 Psychrobacter sp. and 047 Paracoccus sp. revealed remarkably high contents of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Furthermore, a rapid and cost-effective method to coat feed pellets revealed high viability of the supplemented probiotics over 54 d of storage at 4°C. CONCLUSIONS: Here, a strategy for the isolation and characterization of native probiotic candidates is presented that can easily be adapted to other farmed fish species. The simple coating procedure assures viability of probiotics and can thus be applied for the evaluation of probiotic candidates in the future.
Assuntos
Bactérias/isolamento & purificação , Peixes/microbiologia , Probióticos/isolamento & purificação , Ração Animal/análise , Animais , Aquicultura , Bactérias/classificação , Bactérias/genética , Peixes/classificação , Peixes/crescimento & desenvolvimento , Trato Gastrointestinal/microbiologia , Probióticos/classificaçãoRESUMO
Inclusion of prebiotics in aqua feeds, though a costly strategy, has increased as a means to improve growth. Still, its effects on health improvement are not fully disclosed. Regarding their immunestimulatory properties, research has focused on carbohydrates such as fructooligosaccharides and xylooligosaccharides demonstrating their modulatory effects on immune defences in higher vertebrates but few studies have been done on their impact on fish immunity. Replacing fish meal (FM) by plant protein (PP) sources is a current practice in the aquaculture business but their content in antinutrients is still a drawback in terms of gut well-functioning. This work intends to evaluate the short-term effect (7 or 15 days feeding the experimental diets) on juvenile European seabass (Dicentrarchus labrax) immune status of dietary i) replacement of FM by PP sources; ii) prebiotics supplementation. Six isoproteic (46%) and isolipidic (15%) diets were tested including a FM control diet (FMCTRL), a PP control diet (PPCTRL, 30 FM:70 PP) and four other diets based on either FM or PP to which short-chain fructooligosaccharides (scFOS) or xylooligosaccharides (XOS) were added at 1% (FMFOS, PPFOS, FMXOS, PPXOS). The replacement of FM by PP in the diets induced nitric oxide (NO) and lysozyme production, while immunoglobulins (Ig), monocytes percentage and gut interleukin 10 (IL10) gene expression were inhibited. Dietary scFOS supplementation inhibited total bactericidal activity and neutrophils relative percentage regardless protein source and increased plasma NO and thrombocytes percentage in fish fed FM-based diets, while monocytes percentage was increased in PPFOS-fed fish. XOS supplementation down-regulated immune gene expression in the gut while it partly enhanced systemic response. Inconsistency among results regarding FM replacement by PP-based ingredients exposes the need for further research considering both local and systemic responses. Distinct outcomes of prebiotic supplementation were highlighted reflecting sight-specific effects with no clear interaction with protein source.
Assuntos
Bass/fisiologia , Dieta/veterinária , Suplementos Nutricionais , Trato Gastrointestinal/fisiologia , Imunidade Inata , Proteínas de Vegetais Comestíveis , Prebióticos , Ração Animal/análise , Animais , Bactérias/efeitos dos fármacos , Bass/imunologia , Trato Gastrointestinal/imunologia , Oligossacarídeos/imunologia , Proteínas de Vegetais Comestíveis/imunologiaRESUMO
European eels (Anguilla anguilla) undertake an impressive 5 000 km long migration from European fresh waters through the North Atlantic Ocean to the Sargasso Sea. Along with sexual maturation, the eel skeleton undergoes a remarkable morphological transformation during migration, where a hitherto completely obscure bone loss phenomenon occurs. To unravel mechanisms of the maturation-related decay of the skeleton, we performed a multiscale assessment of eels' bones at different life-cycle stages. Accordingly, the skeleton reflects extensive bone loss that is mediated via multinucleated bone-resorbing osteoclasts, while other resorption mechanisms such as osteocytic osteolysis or matrix demineralization were not observed. Preserving mechanical stability and releasing minerals for energy metabolism are two mutually exclusive functions of the skeleton that are orchestrated in eels through the presence of two spatially segregated hard tissues: cellular bone and acellular notochord. The cellular bone serves as a source of mineral release following osteoclastic resorption, whereas the mineralized notochord sheath, which is inaccessible for resorption processes due to an unmineralized cover layer, ensures sufficient mechanical stability as a part of the notochord sheath. Clearly, an eel's skeleton is structurally optimized to meet the metabolic challenge of fasting and simultaneous sexual development during an exhausting journey to spawning areas, while the function of the vertebral column is maintained to achieve this goal.
Assuntos
Anguilla/anatomia & histologia , Migração Animal , Reabsorção Óssea , Osso e Ossos/fisiologia , Estágios do Ciclo de Vida , Anguilla/fisiologia , Animais , Oceano Atlântico , Calcificação FisiológicaRESUMO
The catastrophic loss of aquatic life in the Central European Oder River in 2022, caused by a toxic bloom of the haptophyte microalga Prymnesium parvum (in a wide sense, s.l.), underscores the need to improve our understanding of the genomic basis of the toxin. Previous morphological, phylogenetic, and genomic studies have revealed cryptic diversity within P. parvum s.l. and uncovered three clade-specific (types A, B, and C) prymnesin toxins. Here, we used state-of-the-art long-read sequencing and assembled the first haplotype-resolved diploid genome of a P. parvum type B from the strain responsible for the Oder disaster. Comparative analyses with type A genomes uncovered a genome-size expansion driven by repetitive elements in type B. We also found conserved synteny but divergent evolution in several polyketide synthase (PKS) genes, which are known to underlie toxin production in combination with environmental cues. We identified an approximately 20-kbp deletion in the largest PKS gene of type B that we link to differences in the chemical structure of types A and B prymnesins. Flow cytometry and electron microscopy analyses confirmed diploidy in the Oder River strain and revealed differences to closely related strains in both ploidy and morphology. Our results provide unprecedented resolution of strain diversity in P. parvum s.l. and a better understanding of the genomic basis of toxin variability in haptophytes. The reference-quality genome will enable us to better understand changes in microbial diversity in the face of increasing environmental pressures and provides a basis for strain-level monitoring of invasive Prymnesium in the future.
Assuntos
Haptófitas , Haptófitas/genética , Haplótipos , Microalgas/genética , Toxinas Marinhas/genética , Animais , Filogenia , Peixes/genética , Policetídeo Sintases/genética , Policetídeo Sintases/metabolismoRESUMO
Carotenoids are determinants of reproductive fitness and egg quality. Here we studied the accumulation of astaxanthin (AX), canthaxanthin (CA) zeaxanthin (ZX), lutein (LU), retinol (RX) and dehydroretinol (DR) during vitellogenesis comparing previtellogenic and vitellogenic pikeperch (Sander lucioperca) eggs (n = 5 each), as well as selected tissues (liver, fat and muscles) in first süawning females (1176-1450 g). Futhermore, we compared egg batches with high (88-99% hatching rate, n = 5) or low (40-67% hatching rate, n= 5) egg quality. Vitellogenic follicles revealed higher concentrations of DR, RX, ZX and LU compared to previtellogenic follicles. Neither CA nor AX was detectable. In parallel, DR and RX were mobilized in the liver. In adipose and muscle tissue, comparing previtellogenic and vitellogenic females, no significant differences in carotenoid/retinoid content were observed. In high quality egg batches, both DR and RX were increased. LU was lower in high quality than in low quality eggs. In a conclusion, the amount of retinoids seems suboptimal in low quality egg batches and increased DR and RX are desirable in pikeperch. Since hypervitaminosis of retinoids can be problematic though, supplementation of the food with carotenoids, which can serve as precursors for retinoids, has to be carried out carefully.
RESUMO
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
RESUMO
The present study characterized changes in key parameters of reproduction in adult roach (Rutilus rutilus) from Lake Grosser Mueggelsee (Berlin, Germany) during natural gametogenesis. Fish of both sexes were sampled in monthly intervals between April and August in order to cover the onset of gametogenesis. Investigated parameters included gonad histology, plasma levels of 17ß-oestradiol (E2), testosterone (T), 11-ketotestosterone (11-KT), and 17,20ß-dihydroxy-4-pregnen-3-one (17,20ß-P) as well as the expression of gonadotropin subunits in the pituitary. Furthermore, the mRNA-expression of brain-type aromatase (cyp19a1b), androgen receptor (ar), and estrogen receptor isoforms was studied at the pituitary level. The onset of gametogenesis - as indicated by follicles with cortical alveoli in females and first spermatogonia B in males - was observed in July, accompanied by a significant up-regulation of follicle-stimulating hormone ß (fshß) mRNA in the pituitary in both sexes. On the other hand, luteinizing hormone ß (lhß) mRNA increased later on in August. In males, the increase of fshß mRNA in July coincided with a rise in plasma 11-KT concentrations. In females, E2 in plasma increased later, not until August, shortly before true vitellogenesis (late cortical alveoli stage). Expression of sex steroid receptors in the pituitary revealed only minor seasonal fluctuations. Most pronounced, ar mRNA displayed the highest level pre-spawning in both sexes. Interestingly, cyp19a1b mRNA-expression in the pituitary increased in parallel with fshß already before any changes in plasma E2 or T occurred. These data suggest an important role of pituitary FSH and aromatase at the onset of gametogenesis in the roach.
Assuntos
Aromatase/metabolismo , Gametogênese/fisiologia , Gonadotropinas/genética , Hipófise/enzimologia , Animais , Cyprinidae , Feminino , Gametogênese/genética , Masculino , RNA MensageiroRESUMO
The influence of changing composition and content of RNA on the results of expression profiling was studied in the group-synchronous ovaries of roach (Rutilus rutilus) over the course of their maturation. The highest yield of total RNA was detected in the primary growth and early cortical alveolus stages. The total RNA yield gradually decreased through the late cortical alveolus and late vitellogenic stages. In the primary growth and early cortical alveolus stages, total RNA was characterized by a low percentage of 18S and 28S rRNA and a high percentage of smaller-sized RNAs (tRNA, 5S and 5.8S rRNA), whereas 18S and 28S rRNA had increased by the late cortical alveolus stage and dominated by the late vitellogenic stage. The ratio of mRNA to total RNA was highest at the primary growth stage but decreased significantly in later ovarian stages. When total RNA was used for reverse transcription (RT), the shift in the mRNA/total RNA ratio influenced the results of qPCR expression profiling of several commonly used reference genes (ribosomal protein L8, elongation factor-1α, RNA polymerase-subunit B5, and ß2-microglobulin) and of two target genes, gonad-type aromatase (cyp19a1a) and follistatin (fst). We conclude that the expression of target genes should be related to the mRNA pool using the same input of either mRNA to RT or cDNA to qPCR. Furthermore, gene expression was related to tissue-specific RNA yield per body mass (RNA yield x ovary mass x body mass⻹) thereby reflecting the massive increase in the size and cellular composition of the ovary during the reproductive cycle.
Assuntos
Cyprinidae/genética , Perfilação da Expressão Gênica , Oogênese/genética , Ovário/crescimento & desenvolvimento , RNA/metabolismo , Animais , Aromatase/genética , Aromatase/metabolismo , Cyprinidae/crescimento & desenvolvimento , Feminino , Proteínas de Peixes/genética , Proteínas de Peixes/metabolismo , Folistatina/genética , Folistatina/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Ovário/anatomia & histologia , Fator 1 de Elongação de Peptídeos/genética , Fator 1 de Elongação de Peptídeos/metabolismo , RNA Mensageiro/metabolismo , RNA Ribossômico 18S/metabolismo , RNA Ribossômico 28S/metabolismo , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo , Transcrição Gênica , Microglobulina beta-2/genética , Microglobulina beta-2/metabolismoRESUMO
Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
Assuntos
Evolução Molecular , Peixes/genética , Genoma , Cromossomos Sexuais/genética , Processos de Determinação Sexual/genética , Animais , Feminino , FilogeniaRESUMO
Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGFß signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.
Assuntos
Peixes/genética , Peixes/fisiologia , Duplicação Gênica , Proteína 2 Inibidora de Diferenciação/genética , Proteína 2 Inibidora de Diferenciação/fisiologia , Cromossomos Sexuais , Animais , Mapeamento Cromossômico , Conservação dos Recursos Naturais , DNA/metabolismo , Evolução Molecular , Feminino , Pesqueiros , Marcadores Genéticos/genética , Genótipo , Masculino , Fenótipo , Filogenia , Reação em Cadeia da Polimerase , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Análise de Sequência de DNA , Cromossomo YRESUMO
Fish represent the most frequently used vertebrate class for the investigation of endocrine disruption (ED) in wildlife. However, field studies are complicated by exposure scenarios involving a variety of anthropogenic and natural influences interfering with the endocrine system. One natural aspect rarely considered in ecotoxicological studies is how parasites modulate host physiology. Therefore, investigations were carried out to characterise the impacts of the parasitic tapeworm Ligula intestinalis on plasma sex steroid levels and expression of key genes associated with the reproduction in roach (Rutilus rutilus), a sentinel species for wildlife ED research. Parasitisation by L. intestinalis suppressed gonadal development in both genders of roach and analysis of plasma sex steroids revealed substantially lower levels of 17beta-oestradiol (E2) and 11-ketotestosterone (11-KT) in infected females as well as E2, 11-KT, and testosterone in infected males. Consistently, in both, infected females and males, expression of the oestrogen dependent genes such as vitellogenin and brain-type aromatase in liver and brain was reduced. Furthermore, parasitisation differentially modulated mRNA expression of the oestrogen and androgen receptors in brain and liver. Most prominently, liver expression of oestrogen receptor 1 was reduced in infected females but not in males, whereas expression of oestrogen receptor 2a was up-regulated in both genders. Further, insulin-like growth factor 1 mRNA in the liver was increased in infected females but not in males. Despite severe impacts on plasma sex steroids and pituitary gonadotropin expression, brain mRNA levels of gonadotropin-releasing hormone (GnRH) precursors encoding GnRH2 and GnRH3 were not affected by L. intestinalis-infection. In summary, the present results provide basic knowledge of the endocrine system in L. intestinalis-infected roach and clearly demonstrate that parasites can cause ED in fish.
Assuntos
Infecções por Cestoides/veterinária , Cyprinidae/parasitologia , Doenças dos Peixes/parasitologia , Expressão Gênica/fisiologia , Hormônios Esteroides Gonadais/sangue , Reprodução/genética , Animais , Aromatase/genética , Encéfalo/metabolismo , Cestoides/fisiologia , Infecções por Cestoides/fisiopatologia , Cyprinidae/genética , Cyprinidae/fisiologia , Estradiol/sangue , Feminino , Doenças dos Peixes/fisiopatologia , Gônadas/crescimento & desenvolvimento , Fígado/metabolismo , Masculino , RNA Mensageiro/análise , Receptores Androgênicos/genética , Receptores de Estrogênio/genética , Caracteres Sexuais , Testosterona/análogos & derivados , Testosterona/sangue , Vitelogeninas/genéticaRESUMO
Diets containing Microcystis with considerable amounts of the cyanotoxin microcystin-LR (MC-LR) were fed to determine their impact on the physiological performance of the omnivorous Nile tilapia (Oreochromis niloticus) with regard to stress and growth performance. Four different diets were prepared based on a commercial diet (control, MC-5% [containing 5% dried Microcystis biomass], MC-20% [containing 20% dried Microcystis biomass], and Arthrospira-20% [containing 20% dried Arthrospira sp. biomass without toxin]) and fed to female Nile tilapia. Blood and tissue samples were taken after 1, 7, and 28 d, and MC-LR was quantified in gills, muscle, and liver by using high-performance liquid chromatography (HPLC). Only in the liver were moderate concentrations of MC-LR detected. The stress hormone cortisol and glucose were analyzed from plasma, suggesting that all modified diets caused only minor to moderate stress, which was confirmed by analyses of hepatic glycogen. In addition, the effects of the different diets on growth performance were investigated by determining gene expression of hypophyseal growth hormone (GH) and hepatic insulin-like growth factor-I (IGF-I). For all diets, quantitative reverse transcription-polymerase chain reaction (RT-qPCR) demonstrated no significant effect on gene expression of the major endocrine hormones of the growth axis, whereas classical growth data, including growth and feed conversion ratio, displayed slight inhibitory effects of all modified diets independent of their MC-LR content. However, no significant change was found in condition or hepatosomatic index among the various diets, so it seems feasible that dried cyanobacterial biomass might be even used as a component in fish diet for Nile tilapia, which requires further research in more detail.
Assuntos
Ciclídeos/crescimento & desenvolvimento , Microcistinas/toxicidade , Microbiologia da Água , Animais , Glicemia/análise , Ciclídeos/metabolismo , Dieta , Feminino , Hormônio do Crescimento/genética , Hidrocortisona/sangue , Glicogênio Hepático/análise , Toxinas Marinhas , RNA Mensageiro/análiseRESUMO
Nile tilapia (Oreochromis niloticus) were fed by diets supplemented with cyanobacteria containing in part the cyanotoxin microcystin-LR (MC-LR) to determine the potential impacts on detoxification. Four different diets were prepared based on a commercial diet: (1) control, (2) MC-5% (containing 5% dried Microcystis sp. biomass with 4.92 µg MC-LR g(-1) diet), (3) MC-20% (containing 20% dried Microcystis sp. biomass with 19.54 µg MC-LR g(-1) diet), and (4) Arthr-20% (containing 20% dried Arthrospira sp. biomass without MC-LR). Blood and liver samples were taken after one, 7, and 28 days and protein has been determined in plasma and liver. In the liver, impacts on detoxification were measured by glutathione-S-transferase (GST) activities and gene expression of multi drug resistance protein (MDRP). Plasma protein did not change between all four diets at any sampling time whereas liver protein was significantly elevated already after one day in Arthr-20% and after 28 days in both, MC-20% and Arthr-20%. Biochemical measurements of GST activities revealed no significant impact at any sampling time. In order to characterize the potential effect of MC-LR on MDRP, RT-qPCR method was established. However, as for GST activities no significant changes in MDRP gene expression have been observed. Thus, in summary, oral exposure of MC-LR containing cyanobacteria to Nile tilapia via feed ingestion did not impact significantly detoxification in liver concerning GST activities and MDRP expression despite biochemical composition concerning liver protein was significantly elevated by the diets containing 20% cyanobacteria biomass, regardless whether they contained MC-LR or not.
Assuntos
Ciclídeos/metabolismo , Microcistinas/metabolismo , Animais , Biomassa , Dieta , Expressão Gênica/efeitos dos fármacos , Inativação Metabólica , Fígado/química , Fígado/enzimologia , Fígado/metabolismo , Toxinas Marinhas , Microcistinas/sangue , Distribuição TecidualRESUMO
BACKGROUND: Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce. RESULT: Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads. CONCLUSIONS: CSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects.
Assuntos
Cromossomos/genética , Biologia Computacional/métodos , Genômica/métodos , Software , Vertebrados/metabolismo , Animais , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA , SinteniaRESUMO
Mandarin fishes (Sinipercidae) are piscivores that feed solely on live fry. Unlike higher vertebrates, teleosts exhibit feeding behavior driven mainly by genetic responses, with no modification by learning from parents. Mandarin fishes could serve as excellent model organisms for studying feeding behavior. We report a long-read, chromosomal-scale genome assembly for Siniperca chuatsi and genome assemblies for Siniperca kneri, Siniperca scherzeri and Coreoperca whiteheadi. Positive selection analysis revealed rapid adaptive evolution of genes related to predatory feeding/aggression, growth, pyloric caeca and euryhalinity. Very few gill rakers are observed in mandarin fishes; analogously, we found that zebrafish deficient in edar had a gill raker loss phenotype and a more predatory habit, with reduced intake of zooplankton but increased intake of prey fish. Higher expression of bmp4, which could inhibit edar expression and gill raker development through binding of a Xvent-1 site upstream of edar, may cause predatory feeding in Siniperca.
Assuntos
Comportamento Alimentar/fisiologia , Proteínas de Peixes/genética , Marcadores Genéticos , Genoma , Perciformes/genética , Comportamento Predatório/fisiologia , Animais , Evolução Molecular , Proteínas de Peixes/metabolismo , Perciformes/classificação , Perciformes/fisiologia , Filogenia , Análise de Sequência de DNARESUMO
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random.
Assuntos
Peixes/genética , Genoma , Animais , Cromossomos , Filogenia , PoliploidiaRESUMO
Elevated concentrations of carbon dioxide are a common stressor for fish and other aquatic animals. In particular, intensive aquaculture can impose prolonged periods of severe environmental hypercapnia, manifold exceeding CO2 concentrations of natural habitats. In order to cope with this stressor, gills are essential and constitute the primary organ in the acclimatization process. Yet, despite a general understanding of changes in ion regulation, not much is known with regard to other cellular mechanisms. In this study, we apply RT-qPCR to investigate changes in the expression of several genes associated with metabolism, stress and immunity within gills of juvenile turbot (Psetta maxima) after an eight-week exposure to different concentrations of CO2 (low = â¼3000 µatm, medium = â¼15,000 µatm and high = â¼25,000 µatm CO2). Histological examination of the gill tissue only found a significant increase of hypertrophied secondary lamella in the highest tested treatment level. gene expression results, on the other hand, implied both, mutual and dose-dependent transcriptional adjustments. Comparable up-regulation of IL-1ß, LMP7 and Grim19 at medium and high hypercapnia indicated an increase of reactive oxygen species (ROS) within gill cells. Simultaneous increase in Akirin and PRDX transcripts at medium CO2 indicated enhanced anti-oxidant activity and regulation of transcription, while reduced mRNA concentrations of COX, EF1α and STAT2 at high CO2 denoted suppressed protein synthesis and reduced metabolic capacity. In addition to upregulated DFAD and ApoE expression, implying compensating repair measures, gills exposed to the highest tested treatment level seemed to operate close to or even beyond their maximum capacity. Thus, fitting the model of capacity limitation, our results provide evidence for accretive intracellular hypoxia and oxidative stress in the gills of turbot, dependent on the level of environmental hypercapnia. Further, genes, such as COX, may be valuable biomarkers when attempting to discriminate between a successful and an overpowered stress response.
Assuntos
Dióxido de Carbono/toxicidade , Hipóxia Celular/efeitos dos fármacos , Exposição Ambiental , Linguados/fisiologia , Expressão Gênica/efeitos dos fármacos , Brânquias/efeitos dos fármacos , Estresse Oxidativo/efeitos dos fármacos , Animais , Aquicultura , Dióxido de Carbono/sangue , Linguados/genéticaRESUMO
We have sequenced the genome of the largest freshwater fish species of the world, the arapaima. Analysis of gene family dynamics and signatures of positive selection identified genes involved in the specific adaptations and unique features of this iconic species, in particular it's large size and fast growth. Genome sequences from both sexes combined with RAD-tag analyses from other males and females led to the isolation of male-specific scaffolds and supports an XY sex determination system in arapaima. Whole transcriptome sequencing showed that the product of the gland-like secretory organ on the head surface of males and females may not only provide nutritional fluid for sex-unbiased parental care, but that the organ itself has a more specific function in males, which engage more in parental care.