Genomic and Transcriptional Profiles of Kelch-like (klhl) Gene Family in Polyploid Carassius Complex

Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.

Comparative genomics studies on the stk gene family in vertebrates: From the bighead carp (Hypophthalmichthys nobilis) genome

The mammalian sterile 20-like (MST) family belongs to the serine/threonine protein kinase (STK) superfamily and participates in a variety of biological processes, such as cell apoptosis, polarity, migration, immune regulation, inflammatory responses, and cancer. In the economically important bighead carp (Hypophthalmichthys nobilis), the STK gene family and immune-related biological functions may be helpful in increasing its economic yield. However, the comprehensive role of STKs in the bighead carp remains unclear. In this study, the five stk sequences from the bighead carp were divided into two classes: stk3/4 and stk24/25/26. Gene structure and motif prediction analyses confirmed that stk is conserved in the bighead carp. Compared to 26 other vertebrate species, teleosts (including bighead carp) possess more stk members because of teleost-specific whole-genome duplication. Synteny analysis revealed that stk3, stk24, stk25, and stk26 have been relatively conserved in bighead carp during evolution. Meanwhile, stk4 was lost in most Cyprinid species, including bighead carp, during evolution. RNA-seq data revealed that STK expression was associated with various pathogens, and the expression of these STKs (Hnstk3, Hnstk24a, Hnstk24b, Hnstk25, and Hnstk26) was different in seven tissues of bighead carp. In addition, we showed that STK expression levels were dramatically altered in the head kidney and that stk24 was involved in defense against Aeromonas hydrophila. This study provides a molecular basis for the analysis of stk function in bighead carp, and can be used as a reference for further phylogenomics.

Effects of Curcumin on Oxidative Stress and Ferroptosis in Acute Ammonia Stress-Induced Liver Injury in Gibel Carp (Carassius gibelio)

This study investigated the potential role of curcumin (CUR) in preventing oxidative stress and ferroptosis induced by ammonia exposure in gibel carp. Experimental fish (initial weight: 11.22 ± 0.10 g, n = 150) were fed diets supplemented with or without 0.5% CUR for 56 days, followed by a 24 h ammonia (32.5 mg/L) exposure. Liver damages (aspartate aminotransferase (AST), alanine aminotransferase (ALT), adenosine deaminase (ADA), and alkaline phosphatase (ALP)) and oxidative stress enzyme activities (reactive oxygen species (ROS), malondialdehyde (MDA); and the content of antioxidant capacity (T-AOC), superoxide dismutase (SOD), and glutathione peroxidase (GPx)) were induced by ammonia stress. The antioxidant capacity was decreased, as indicated by inhibited gene expression of nuclear factor erythroid 2-related factor 2 (nrf2), heme oxygenase-1 (ho-1), catalase (cat), and sod. Ferroptosis was induced by ammonia stress, as suggested by upregulated mRNA levels of nuclear receptor coactivator 4 (ncoa4), transferrin receptor 1 (tfr1), and iron-responsive element-binding protein 2 (ireb2), and downregulated expression of glutathione peroxidase 4 (gpx4), ferroportin (fpn), and ferritin heavy chain 1 (fth1). In addition, both mRNA and protein levels of ferroptosis markers acyl-CoA synthetase long-chain family member 4 (ACSL4) and prostaglandin-endoperoxide synthase 2 (PTGS2) were upregulated, while cystine/glutamate antiporter (SLC7A11) was downregulated. However, liver injury and ferroptosis in fish induced by ammonia could be attenuated by CUR. Collectively, these findings demonstrate that CUR ameliorates oxidative stress and attenuates ammonia stress-induced ferroptosis. This study provides a new perspective on potential preventive strategies against ammonia stress in gibel carp by dietary CUR.

REVIVE: A feasibility assessment tool for freshwater fish conservation translocations in Mediterranean rivers

Conservation translocation is a management action applied for population recovery of threatened freshwater fishes, often however with partially successful outcome, mainly due to inadequate feasibility assessment prior to the translocation. Up to date, feasibility assessments have been mainly focused on economically important species (e.g., salmonids) inhabiting perennial rivers, while little attention has been given to fish translocations in rivers in Mediterranean climate areas. In this study, we developed a robust feasibility assessment tool for freshwater fish translocations in Mediterranean-type riverine ecosystems within an interdisciplinary, multispecies approach. The REVIVE tool integrates quantitative and semi-quantitative data, incorporates uncertainty and consists of two main components. The first component is the evaluation of the potential release water bodies (R-WBs) for their suitability for the planned translocation, incorporating a number of essential criteria for Mediterranean rivers, with emphasis on flow regime and habitat quantity. Additional criteria include the current and historical presence of the target species, water and biological quality, habitat suitability in terms of the ecological requirements of the target species, alien invasive species' pressure, and hydromorphological pressures, including their mitigation potential. The second component is the evaluation of the potential source water bodies (S-WBs) in terms of genetic compatibility and provision of a sufficient number of propagules. A trial application in a Mediterranean basin (Vassilopotamos River, Southern Greece) for the potential translocation of two threatened cyprinids in five R-WBs indicated the robustness of the tool. This integrative, flexible tool combines several elements identified as essential in reintroduction biology and can have wider applications, for a multitude of freshwater fish taxa and riverine systems, maximizing the success of planned translocation actions by natural resources' managers. Modifications to enable its transferability to other river types or fish taxa are also discussed.

Effects of 17α-Methyltestosterone on the Transcriptome and Sex Hormones in the Brain of Gobiocypris rarus

17α-Methyltestosterone (MT), a synthetic environmental endocrine disruptor with androgenic effects, has been shown to disrupt the reproductive system and inhibit germ cell maturation in Gobiocypris rarus. To further investigate the regulation of gonadal development by MT through the hypothalamic-pituitary-gonadal (HPG) axis, G. rarus were exposed to 0, 25, 50, and 100 ng/L of MT for 7, 14, and 21 days. We analyzed its biological indicators, gonadotropin-releasing hormone (GnRH), gonadotropins, reproduction-related gene expression, and brain tissue transcriptome profiles. We found a significant decrease in the gonadosomatic index (GSI) in G. rarus males exposed to MT for 21 days compared to the control group. GnRH, follicle-stimulating hormone (FSH), and luteinizing hormone (LH) levels, as well as the expressions of the gnrh3, gnrhr1, gnrhr3, fshβ, and cyp19a1b genes, were significantly reduced in the brains of both male and female fish when exposed to 100 ng/L MT for 14 days compared to the controls. Therefore, we further constructed four RNA-seq libraries from 100 ng/L MT-treated groups of male and female fish, obtaining 2412 and 2509 DEGs in male and female brain tissue, respectively. Three common pathways were observed to be affected in both sexes after exposure to MT, namely, nicotinate and nicotinamide metabolism, focal adhesion, and cell adhesion molecules. Furthermore, we found that MT affected the PI3K/Akt/FoxO3a signaling pathway through the upregulation of foxo3 and ccnd2, and the downregulation of pik3c3 and ccnd1. Therefore, we hypothesize that MT interferes with the levels of gonadotropin-releasing hormone (GnRH, FSH, and LH) in G. rarus brains through the PI3K/Akt/FoxO3a signaling pathway, and affects the expression of key genes in the hormone production pathway (gnrh3, gnrhr1 and cyp19a1b) to interfere with the stability of the HPG axis, thus leading to abnormal gonadal development. This study provides a multidimensional perspective on the damaging effects of MT on fish and confirms that G. rarus is a suitable model animal for aquatic toxicology.

"Fishcide" effect of the fungicide difenoconazole in freshwater fish (Labeo rohita): A multi-endpoint approach

Difenoconazole is widely used to protect crops, fruits, and vegetables. However, this fungicide can enter aquatic environments and cause harmful effects to non-target organisms and induce little-known biological disorders. Thus, aiming to expand our knowledge about the ecotoxicity of difenoconazole on freshwater ichthyofauna, we aimed to determine the median lethal concentration (LC₅₀) of difenoconazole and evaluate its possible impacts from different toxicity biomarkers, using freshwater fish Labeo rohita as a model system. Using the probit analysis method, the 96 h LC₅₀ value of difenoconazole in the fish was calculated as 4.5 mg L^-1. Posteriorly, fish were exposed to two sublethal concentrations (0.45 mg L^-1 1/10th and 0.9 mg L^-1 1/5th LC₅₀ value) for 21 days. A significant reduction of superoxide dismutase (SOD) and catalase (CAT) activity was noted in the gill, liver, and kidneys of fish compared to the control groups. The level of glutathione-S-transferase (GST) and lipid peroxidation (LPO) activity was higher in all vital tissues of difenoconazole-treated fish. Histological alterations in the gill include epithelial lifting, lamellar fusion, hypertrophy, and epithelial necrosis. At the same time, the liver showed pyknotic nucleus, vacuolation, cellular edema and tubular necrosis, shrinkage of glomeruli, vacuolation, and pyknotic nuclei in the kidney. DNA damage was increased significantly with tail formation based on the concentration and time-dependent manner. Therefore, our study confirms that the exposure of L. rohita to difenoconazole induces negative biological consequences and sheds light on the danger of this fungicide for freshwater fish species. We believe that studies like ours can support actions and strategies for the remediation/mitigation of aquatic pollution by difenoconazole and for the conservation of freshwater ichthyofauna.

Genome-wide identification and expression of the peroxisome proliferator-activated receptor gene family in the Tibetan highland fish Gymnocypris przewalskii

Peroxisome proliferator-activated receptor (PPAR) plays an important role in the regulation of lipid metabolism and has been widely identified in diverse species. Gymnocypris przewalskii is a native fish of the Qinghai Tibetan Plateau that survives in a chronically cold environment. In the current study, we conducted genome-wide identification of PPAR genes, revealing the existence of seven PPARs in the G. przewalskii genome. Collinearity was observed between two copies of PPARαb and PPARγ in G. przewalskii, suggesting that the additional copy might be gained through whole genome duplication. Both phylogenetic and multiple sequence alignment analyses indicated that PPARs in G. przewalskii were conserved with teleosts. The cold treatment (10 °C and 4 °C) led to the developmental delay of G. przewalskii embryos. Continuous expression of PPARs was observed during the embryonic development of G. przewalskii under normal and cold conditions, with significantly different transcriptional patterns. These results indicated that PPARs participated in the embryonic development of G. przewalskii, and were involved in the cold response during development. The current study proposed a potential role of PPARs in the cold response in the embryonic development of G. przewalskii, which shed light on understanding cold adaptation in Tibetan highland fish.

Genome-Wide Association Study Reveals SNPs and Candidate Genes Related to Growth and Body Shape in Bighead Carp (Hypophthalmichthys nobilis)

Growth is an economically important trait in bighead carp and other aquaculture species that affects production efficiency. Interestingly, the head of the bighead carp has a high market value in China; therefore, it is important to study the genetic bases of both growth and body shape traits. A genome-wide association study was performed based on 2b-RAD sequencing of 776 individuals to identify SNPs associated with growth and body shape traits, including body weight, body length, body height, and deheaded body length. In total, 26 significant and 19 suggestive SNPs were identified, and more than half of these significant SNPs were clustered in LG16. Two LGs (LG16 and LG21) contained QTLs associated with body weight. Fourteen SNPs of LG16 and two LG21 SNPs were found to be associated with body length. For body height, 12 significantly associated SNPs were identified in LG16. Additionally, 12 SNPs of LG16 and 3 SNPs of LG21 were found to be associated with deheaded body length. Forty-three genes were significantly or suggestively associated with body shape/growth traits based on GWAS results, 18 of which were candidate genes for all BW, BL, BH, and DBL traits. One of these genes, fndc5b, was selected for further analyses. Association analysis revealed that one SNP (g.245 C > T) in the introns of fndc5b was significantly associated with growth-related traits in growth-extreme samples. The mRNA levels of fndc5b in the brains of the lightweight group were significantly higher than those of the heavy-weight group. This study helps to reveal the genetic structure of growth and body development in fish and provides candidate genes for future molecular marker-assisted selection for fast growth and better body conformation in bighead carp.

Capoeta ekmekciae Turan, Kottelat, Kirankaya & Engin, 2006, a junior synonym of Capoeta capoeta (Güldenstädt, 1773) (Teleostei: Cyprinidae)

Some recent works have proposed that Capoeta ekmekciae from the Çoruh River and C. capoeta from the Kura-Aras River system are synonyms based on molecular data, which prompted this study to compare their morphometric, meristic and molecular data to investigate this hypothesis. Based on the results, the C. ekmekciae form displays morphometric and meristic traits quite similar to the C. capoeta form. Since there are no diagnostic traits to distinguish these two allopatric species from each other and they share identical cytb gene, we treat C. ekmekciae as a junior synonym of C. capoeta.

Environmentally relevant concentrations of Triclosan cause transcriptomic and biomolecular alterations in the hatchlings of Labeo rohita

Suppression (p ≤ 0.05) of antioxidative/detoxification (except GPx and CYP3a) and cytoskeletal (except DHPR) genes but induction of metabolic (except for AST and TRY) and heat shock (except HSP60) genes of Labeo rohita hatchlings after 14 days of exposure to environmentally relevant concentrations of Triclosan (0.0063, 0.0126, 0.0252 and 0.06 mg/L) was followed by an increase (p ≤ 0.05) for most of the genes after 10 days recovery period. After recovery, LDH, ALT, CK, CHY, PA, HSP47 and DHPR declined, while SOD, CAT, GST, GR, GPx, CYP1a, CYP3a, AST, AChE, TRY, HSP60, HSP70, HSc71, HSP90 MLP-3, α-tropomyosin, desmin b and lamin b1 increased over exposure. Peak area of biomolecules (except 3290-3296, 2924-2925 and 2852-2855 cm^-1) declined (p ≤ 0.01) more after recovery [except for an increase (p ≤ 0.01) at 1398-1401 cm^-1]. CYP3a, CK, HSP90, MLP-3 and secondary structure of amide A are the most sensitive markers for the environmentally relevant concentrations of Triclosan.

A new set of microsatellite markers for Phoxinus lumaireul senso lato, Phoxinus marsilii and Phoxinus krkae for population and molecular taxonomic studies

Minnows of the genus Phoxinus are common and an often highly abundant fish species in Palearctic freshwater habitats. Phoxinus species have a complex evolutionary history, phylogenetic relationships are not well understood and there are a number of unresolved taxonomic problems. There are currently 23 different mitochondrial genetic lineages identified in the genus Phoxinus, 13 of which are recognized as valid species. The taxonomic status of these lineages requires resolution, including the degree to which they can interbreed. Suitable nuclear molecular markers for studies of population divergence and interbreeding between morphotypes and mitochondrial lineages are lacking for Phoxinus species. Therefore, the authors developed a set of microsatellite markers using genomic information from Phoxinus lumaireul and tested their suitability for this and two related species, Phoxinus krkae and Phoxinus marsilii. Out of 16 microsatellite candidate loci isolated, 12 were found to be in Hardy-Weinberg equilibrium when tested on two P. lumaireul senso lato populations. Seven loci amplified across the three species, enabling the study of intraspecific genetic diversity and population structure within P. marsilii and P. krkae. The markers were able to clearly resolve differences among the three tested species, including the recently described P. krkae, and are therefore suitable for the detection of introgression and hybridization among populations consisting of mixtures of two or more of P. lumaireul s. l., P. marsilii and P. krkae.

Establishment of a cell line derived from the gills of Gymnocypris przewalskii, an endemic Schizothoracine fish from Qinghai Lake of Tibet Plateau

Gymnocypris przewalskii (Naked carp), a native teleost, plays an important role in maintaining the ecological balance of Lake Qinghai (altitude, 3.2 km), the largest saline lake in China. In this study, a new gill cell line from G. przewalskii was developed using the explant technique and named as GPG. This cell line was maintained in Dulbecco's Modified Eagle Medium (DMEM) (high glucose), supplemented with 15% fetal bovine serum (FBS), and was successfully subcultured up to 32 passages. Meanwhile, this cell line was also authenticated by sequencing the mitochondrial cytochrome C oxidase subunit I (COI) and 16S rRNA genes and by chromosome analysis. With the Cytomegalovirus (CMV) promoter, the GPG cell line could express green fluorescent protein (GFP) at about 5% transfection efficiency. MTT test showed that Clostridium botulinum toxin (BTX) was toxic to the cell line. After cryopreservation with 10% dimethyl sulfoxide (DMSO), this cell line could be successfully revived at an efficiency over 70%. This study revealed that the GPG cell line could be used as materials for physio-chemical investigation of G. przewalskii and also provided a tool for gene function study and toxicological reaction in vitro.

Computational analysis and functional characterisation of Tor putitora toll-like receptor 4 with the elucidation of its binding sites for microbial mimicking ligands

In the current study, full-length Toll-like receptor 4 (TLR4) cDNA was cloned and characterised in Tor putitora, an important fish inhibiting Himalayan rivers. The complete coding sequence of TpTLR4 is 2457 bp with nine key structural domains, including six leucine-rich repeats (LRRs). The phylogenetic tree revealed that TpTLR4 showed the closest relationship with TLR4 of Cyprinus carpio (96%), Labeo rohita (91%) and Megalobrama amblycephala (88%), all belonging to the Cyprinidae family. CELLO2GO tool revealed that TpTLR4 protein is highly localised in the plasma (67.7%), and the protein has a strong association with myeloid differentiation primary response 88 (MYD88) followed by Tumor necrosis factor receptor-associated factor (TRAF) family. In the toll-interleukin-1 receptor (TIR) domain of TpTLR4, the proline is replaced by the alanine amino acid, thus may give plasticity to the receptor to recognise both bacterial and viral ligands. Molecular docking has revealed that TpTLR4 showed the strongest affinity towards poly (I:C) with the binding energy of -6.1 kcal/mol and five hydrogen bonds among all ligands. Based on our molecular docking results, it can be presumed that TpTLR4 can sense bacterial, fungal and viral molecular patterns with binding sites mainly present in the TpTLR4 LRR9 motif, which spans between 515 and 602 amino acids. Tor putiora TLR4 transcript was ubiquitously expressed in all the tested fish tissues. Although, transcript level was found to be highest in blood and spleen followed by the kidney. The TpTLR4 transcripts showed peak expression in spleen and kidney at 12 h post-injection (hpi) (p < 0.05) of poly (I:C). The constitutive expression of TpTLR4 in various tissues, up-regulation in different tissues and strong binding affinities with poly (I:C) indicate that TpTLR4 may play an essential role in sensing pathogen-associated molecular patterns (PAMPs), particularly of viral origin.

RNA-seq reveals potential gene biomarkers in fathead minnows (Pimephales promelas) for exposure to treated wastewater effluent

Discharged wastewater treatment plant (WWTP) effluent greatly contributes to the generation of complex mixtures of contaminants of emerging concern (CECs) in aquatic environments which often contain neuropharmaceuticals and other emerging contaminants that may impact neurological function. However, there is a paucity of knowledge on the neurological impacts of these exposures to aquatic organisms. In this study, caged fathead minnows (Pimephales promelas) were exposed in situ in a temperate-region effluent-dominated stream (i.e., Muddy Creek) in Coralville, Iowa, USA upstream and downstream of a WWTP effluent outfall. The pharmaceutical composition of Muddy Creek was recently characterized by our team and revealed many compounds there were at a low microgram to high nanogram per liter concentration. Total RNA sequencing analysis on brain tissues revealed 280 gene isoforms that were significantly differentially expressed in male fish and 293 gene isoforms in female fish between the upstream and downstream site. Only 66 (13%) of such gene isoforms overlapped amongst male and female fish, demonstrating sex-dependent impacts on neuronal gene expression. By using a systems biology approach paired with functional enrichment analyses, we identified several potential novel gene biomarkers for treated effluent exposure that could be used to expand monitoring of environmental effects with respect to complex CEC mixtures. Lastly, when comparing the results of this study to those that relied on a single-compound approach, there was relatively little overlap in terms of gene-specific effects. This discovery brings into question the application of single-compound exposures in accurately characterizing environmental risks of complex mixtures and for gene biomarker identification.

Natural selection drives the evolution of mitogenomes in Acrossocheilus

The mitochondrial genome plays a crucial role in the balance of energy and heat production in organisms and, thus, may be under natural selection due to its potential role in adaptive divergence and speciation. Here, we studied natural selection on the mitogenome of Acrossocheilus (Cypriniformes: Cyprinidae), a genus of fish that inhabits a broad latitudinal distribution ranging from the tropics and subtropics through temperate regions. Specifically, we used 25 published mitogenome sequences of Acrossocheilus species to investigate phylogenetic relationships in this genus and detected signals of positive selection on 13 protein-coding, mitochondrial genes. We found that relaxed purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, we also found evidence of diversifying selection on some codons, indicating episodes of positive selection. Additionally, we analyzed the mitogenomic data within an environmental modeling framework and found that the Ka/Ks ratio of ATP6 may correlated with a mean diurnal temperature range (p = 0.0449), while the Ka/Ks ratio of COX2 may correlated with precipitation during the driest month (p = 0.00761). These results suggest that the mitogenomes of Acrossocheilus species may be involved in evolutionary adaptations to different habitats. Based on this, we believe that our study provides a new insight into the role of the mitochondrial genome of Acrossocheilus species in adaptation to different environments. During our study, we also discovered several cases of paraphyly and polyphyly among accessions of species and their putative synonyms. Thus, our study suggests that a careful reassessment of the taxonomy of Acrossocheilus is using high-quality molecular data merited.

Evolutionary convergence in body shape obscures taxonomic diversity in species of the African Labeo forskalii group: Case study of L. parvus Boulenger 1902 and L. ogunensis Boulenger 1910

Labeo is the third most diverse genus of African cyprinids and is widely distributed across the continent. Labeo parvus, a small species originally described from the Congo basin, has been considered the only species of the L. forskalii group distributed across five African ichthyofaunal provinces (Nilo-Sudan, Congo, Cuanza, and Upper and Lower Guinea). However, morphological similarity between L. parvus and numerous congeners remains a central cause of taxonomic confusion within the genus. Here we employed a phylogenetic comparative approach to assess phenotypic convergence among species of the L. forskalii group, investigate the taxonomic status of L. parvus sensu lato (sl) in west Africa, and reevaluate the composition and distribution of L. parvus sensu stricto (ss). Our phylogenetic analysis provides no support for a sister relationship between L. parvus ss and any of the west African Labeo parvus-like species. Geometric morphometric and molecular phylogenetic data indicate that L. parvus ss is a Congo basin endemic, and seemingly ecologically equivalent species found in west Africa are L. ogunensis, L. obscurus and other undescribed or previously synonymized species. We discuss our findings in terms of convergent evolution using phylomorphospace and tests for phylogenetic signal.

Molecular cloning, expression analysis of interleukin 17D (cysteine knot cytokine) from Amphiprion clarkii and their functional characterization and NFκB pathway activation using FHM cells

Interleukin 17D (IL-17D), a pro-inflammatory cytokine, is a signature cytokine of T helper 17 (Th17) cells. However, studies characterizing the functions of IL-17D in teleost are scarce. Therefore, we aimed to characterize the properties of IL-17D in Amphiprion clarkii. We performed spatial and temporal expression, AcIL-17D-mediated antibacterial and inflammatory gene expression, NFκB pathway-related gene expression analyses, and bacterial colony counting and cell protection assays. We found that AcIL-17D contains a 630 bp coding sequence and encodes 210 amino acids. The spatial expression analysis of AcIL-17D in 12 tissues showed ubiquitous expression, with the highest expression in the brain, followed by blood and skin. Temporal expression analysis of AcIL-17D in blood showed upregulated expression at 6 and 24 h (polyinosinic: polycytidylic acid and lipopolysaccharide), 12 h (all stimulants), and 48 h (polyinosinic: polycytidylic acid and Vibrio harveyi). AcIL-17D expression in the blood gradually decreased at later hours in response to all the stimulants. After treatment of fathead minnow (FHM) cells with different recombinant AcIL-17D concentrations, the downstream gene expression analysis showed increased expression of antimicrobial genes in the FHM cells, namely [NK-Lysin (NKL), Hepcidin antimicrobial peptide-1 (HAMP-1), Defensin-β (DEFB1)] and some inflammatory genes such as IL-1β, TNF-α, IL-11, and STAT3. Further nuclear factor κB (NFκB) subunits (NFκB1, NFκB2, RelA, and Rel-B) showed upregulated gene expression at 12 and 24 h. The bacterial colony counting assay using FHM cells showed lower bacterial colony counts in rAcIL-17D-treated cells than in control. Furthermore, the Water-Soluble Tetrazolium Salt (WST -1) assay confirmed the ability of rAcIL-17D in the protection of FHM cells from bacterial infection and conducted the Hoechst 33342 staining upon treatment with rAcIL-17D and rMBP. Therefore, our findings provide important insights into the activation of IL-17D pathway genes in FHM cells, the protective role of AcIL-17D against bacterial infection, and host defense mechanisms in teleost.

Testicular miRNAs and tsRNAs provide insight into gene regulation during overwintering and reproduction of Onychostoma macrolepis

The late overwintering period and breeding period are two important developmental stages of testis in Onychostoma macrolepis. Small non-coding RNAs (sncRNAs) are well-known regulators of biological processes associated with numerous biological processes. This study aimed to elucidate the roles of four sncRNA classes (microRNAs [miRNAs], Piwi-interacting RNAs [piRNAs], tRNA-derived small RNAs [tsRNAs], and rRNA-derived small RNAs [rsRNAs]) across testes in the late overwintering period (in March) and breeding period (in June) by high-throughput sequencing. The testis of O. macrolepis displayed the highest levels of piRNAs and lowest levels of rsRNAs. Compared with miRNAs and tsRNAs in June, tsRNAs in March had a higher abundance, while miRNAs in March had a much lower abundance. Bioinformatics analysis identified 1,362 and 1,340 differentially expressed miRNAs and tsRNAs, respectively. Further analysis showed that miR-200-1, miR-143-1, tRFi-Lys-CTT-1, and tRFi-Glu-CTC-1 could play critical roles during the overwintering and breeding periods. Our findings provided an unprecedented insight to reveal the epigenetic mechanism underlying the overwintering and reproduction process of male O. macrolepis.

A comprehensive overview of ovarian small non-coding RNAs in the late overwintering and breeding periods of Onychostoma macrolepis

The development of the ovary of Onychostoma macrolepis undergoes distinct annual cyclic changes in which small non-coding RNAs (sncRNAs) could play vital roles. In this study, four sncRNA classes in the ovary, including miRNA, piRNAs, tsRNA, and rsRNAs, were systematically profiled by high-throughput sequencing. In adult ovaries of O. macrolepis, 247 miRNAs and 235 tsRNAs were identified as differentially expressing in the late overwintering period (in March) and breeding period (in June). Some up-regulated sncRNAs in March, such as miR-125-1 and tRFi-Lys-CTT-1, could be involved in inhibiting biomolecule metabolism and enhancing stress tolerance during the overwintering period. Compared with the level expression of sncRNAs in March, some sncRNAs were up-regulated in June, such as miR-146-1 and tRFi-Gly-GCC-1, and could be involved in influencing molecular synthesis and metabolism, enhancing oocyte proliferation and maturation, accelerating ovarian development, and increasing fertilization of oocytes by regulating related target mRNAs. The results suggested that sncRNAs in the ovary of Onychostoma macrolepis not only reflect characteristics of the fish's physiology at different developmental periods, but also directly affect ovarian development and oocyte maturation during the breeding period. In conclusion, these results significantly advance our understanding of the roles of sncRNA during overwintering and reproduction periods, and provide a novel perspective for uncovering characteristics of the special overwintering ecology and reproductive physiology of an atypical cavefish.

Characterization of EPO H131S as a key mutation site in the hypoxia-adaptive evolution of Gymnocypris dobula

Erythropoietin (EPO) is a glycoprotein hormone involved in proerythropoiesis, antioxidation, and antiapoptosis. It also contributes to cellular immune function in high-altitude species, such as the schizothoracine fish Gymnocypris dobula. Six mutation sites previously identified in EPO from G. dobula (GD-EPO) were injected into zebrafish embryos, and their effects were compared with EPO from the low-altitude schizothoracine Schizothorax prenanti. The key mutation site in GD-EPO was identified as H131S. Under hypoxic conditions, the levels of superoxide dismutase and malondialdehyde were decreased, whereas that of nitric oxide was increased in zebrafish injected with GD-EPO compared with those injected with S. prenanti-EPO (SP-EPO). The results suggest that EPO in high-altitude schizothoracine species is both antioxidative and antiapoptotic, driven by the H131S mutation site. Thus, this enhanced the ability of this species to adapt to the high-altitude hypoxic environment. These results provide a basis for investigating further the hypoxia adaptation mechanisms of teleosts.

An improved hybrid bream derived from a hybrid lineage of Megalobrama amblycephala (♀)×Culter alburnus (♂)

Distant hybridization is an important technique in fish genetic breeding. In this study, based on the establishment of an allodiploid fish lineage (BT, 2n=48, F₁-F₆) derived from distant hybridization between female Megalobrama amblycephala (BSB, 2n=48) and male Culter alburnus (TC, 2n=48), and the backcross progeny (BTB, 2n=48) derived by backcrossing female F₁ of BT to male BSB, an improved hybrid bream (BTBB, 2n=48) was obtained by backcrossing BTB (♀) to BSB (♂). Moreover, the morphological and genetic characteristics of BTBB individuals were investigated; BTBB was similar to BSB in appearance but had a higher body height than BSB. The study results regarding chromosome numbers and DNA content indicated that BTBB is a diploid hybrid fish. The 5S rDNA and Hox gene of BTBB were inherited from the original parents. Gonadal development in BTBB was normal. On the other hand, BTBB had a faster growth rate, higher muscle protein level, and lower muscle carbohydrate level than BSB. Hence, bisexual fertile BTBB is promoted and can be applied as a high-quality fish, and it can also be used as a new fish germplasm resource to develop high-quality fish further. Thus, this study is of great significance for fish genetic breeding.

Molecular characterization of farnesoid X receptor alpha in Megalobrama amblycephala and its potential roles in high-carbohydrate diet-induced alterations of bile acid metabolism

Farnesoid X receptorα (FXRα) plays a central role in maintaining the bile acid homeostasis in mammals, while relevant processes are still poorly interpreted in aquatic species. This study was conducted to characterize the fxrα gene in a cyprinidae species: blunt snout bream (Megalobrama amblycephala), and investigate its potential roles in bile acid metabolism. The Fxrα protein contains one DNA binding domain, one ligand binding domain, one His-Try "switch" and two modifies residues. A high degree of conservation (53.18-100.00 %) was observed in the Fxrα protein among most aquatic species and higher vertebrates. The transcription of fxrα was mainly observed in intestine, liver and kidney. Then fish (35.0 ± 0.15 g) were fed two diets containing 33 % and 45 % carbohydrate levels for 12weeks. High-carbohydrate diet significantly elevated the total cholesterol concentrations in plasma, liver and hindgut as well as the triglyceride concentrations in both liver and hindgut, but decreased the total bile acid concentrations in plasma, liver and hindgut. High dietary carbohydrate levels also significantly enhanced hepatic transcriptions of 3-hydroxy-3-methylglutaryl-CoA reductase (the rate-limiting enzyme in cholesterol synthesis), and those of fxrα (a bile acid receptor) and multidrug resistance associated protein 2 (a bile acid transporter) in hindgut. Furthermore, high dietary carbohydrate levels significantly decreased the transcriptions of cholesterol 7α-hydroxylase (the rate-limiting enzyme in bile acid synthesis) and organic anion-transporting polypeptides (a bile acid transporter) in liver as well as that of takeda G-protein-coupled bile acid receptor in hindgut. The results demonstrated that the fxrα gene of blunt snout bream is highly conserved compared with other vertebrates. Besides, high dietary carbohydrate levels increased total cholesterol concentrations, and up-regulated the transcription of fxrα, thus decreasing the biosynthesis and reabsorption of bile acids by mediating various target genes.

Molecular characterization, expression, and functional analysis of cystatin B in the big-belly seahorse (Hippocampus abdominalis)

Cystatins are a diverse group of cysteine protease inhibitors widely present among various organisms. Beyond their protease inhibitor function, cystatins play a crucial role in diverse pathophysiological conditions in animals, including neurodegenerative disorders, tumor progression, inflammatory diseases, and immune response. However, the role of cystatins in immunity against viral and bacterial infections in fish remains to be elucidated. In this study, the cystatin B from big-belly seahorse, Hippocampus abdominalis, designated as HaCSTB, was identified and characterized. HaCSTB shared the highest homology with type 1 cystatin family members of teleosts and had three cystatin catalytic domains with no signal peptides or disulfide bonds. HaCSTB transcripts were mainly expressed in peripheral blood cells (PBCs), followed by the testis and pouch of healthy big-belly seahorses. Immune challenge with lipopolysaccharides (LPS), polyinosinic:polycytidylic acid (Poly I:C), and Streptococcus iniae induced upregulation of relative HaCSTB mRNA expression in PBCs. Subcellular localization analysis revealed the distribution of HaCSTB in the cytosol, mitochondria, and nuclei of fathead minnow cells (FHM). Recombinant HaCSTB (rHaCSTB) exhibited potent in vitro inhibitory activity against papain, a cysteine protease, in a concentration-, pH-, and temperature-dependent manner. Overexpression of HaCSTB in viral hemorrhagic septicemia virus (VHSV)-susceptible FHM cells increased cell viability and reduced VHSV-induced apoptosis. Collectively, these results suggest that HaCSTB might engage in the teleostean immune protection against bacteria and viruses.

The intestinal histopathology, innate immune response and antioxidant capacity of blunt snout bream (Megalobrama amblycephala) in response to Aeromonas hydrophila

The present study was performed to determine the effects of Aeromonas hydrophila infection on intestinal -histopathology, innate immune response and changes in antioxidant capacity of blunt snout bream (Megalobrama amblycephala). A series of histopathological changes, innate immune enzyme activities, antioxidant enzyme activities, and the corresponding mRNA relative genes expressions in intestines were measured at 0, 1, 2, and 3 weeks post-treatment of Aeromonas hydrophila (1✕10⁷ CFU mL^-1) infection. The results showed that Aeromonas hydrophila induced changes in intestinal morphology, including the decreased muscularis thickness, the proliferated goblet cells, and the atrophied intestine villi height. Moreover, the innate immune enzymes activities in serum such as acid phosphatase, alkaline phosphatase, lysozyme activities and immunoglobulin M were significantly reduced after infection at 1week, 2week and 3week. The contents of complement 3 and complement 4 were significantly decreased after infection as well. In addition, the antioxidant enzymes activities, including superoxide dismutase, catalase and glutathione peroxidase in the experimental groups were significantly decreased compared with the control group, whereas the content of malondialdehyde was significantly increased after infection at 1week, 2week and 3week. Furthermore, the mRNA relative expressions of the inflammatory cytokines such as tumor necrosis factor-α, interleukins-1β, interferon-γ, and interleukins-6 were significantly increased after infection with Aeromonas hydrophila. The TJ-related gene expressions in the intestine of zonula occluden-1, occludin, occludin-1, occludin-2 were significantly reduced throughout the infection period. The mRNA relative expressions of signal transducers and activators of transcription 4 and janus kinase-3 in the intestine were significantly ascended compared with the non-infected group. Overall, the results elucidated that the intestine tissue injury and innate immune response reduction, as well as antioxidant capacity attenuation were occurred against Aeromonas hydrophila infection of the blunt snout bream.

Heat Shock Procedure Affects Cell Division-Associated Genes in Gynogenetic Manipulation

Heat shock procedure is crucial for gynogenetic manipulation leading to diploidization of the maternal genomes; however, the underlying molecular mechanism especially the transcriptomic changes during this procedure has still not been unveiled yet. Here, the artificial gynogenesis of zebrafish (Danio rerio) using inactivated sperm from rare minnow (Gobiocypris rarus) was conducted. We found that artificial gynogenetic manipulation, including pseudo-fertilization and heat shock, decreased hatching rates, whereas heat shock treatment alone had medium hatching rates. The first cleavage changed the expression of genes associated with RNA transcription and protein synthesis. A co-expression network regulated by hub genes GIT1, Sepsecs, and FLNB was significantly correlated with heat shock procedure. The cyclin family and cyclin-dependent kinase-related genes were lowly expressed in embryos from gynogenetic zebrafish, and genes involved in controlling the cell cycle and genomic stability were significantly altered by the gynogenetic treatment. Our results show the effects of artificial gynogenesis on embryos and describe changes in gene expression that suggest drastic changes take place in cell division by heat shock procedure. These findings will contribute to an understanding of the molecular basis for germplasm improving, including the purifying effect and allogynogenetic biological effect by gynogenesis.