Molecular characterization, spatio-temporal expression patterns of crtc2 gene and its immune roles in yellow catfish (Pelteobagrus fulvidraco).

cAMP response element binding (CREB) protein 2 (CRTC2) is a transcriptional coactivator of CREB and plays an important role in the immune system. Thus far, the physiological roles of Crtc2 in teleost are still poorly understood. In this study, the crtc2 gene was identified and characterized from yellow catfish (Pelteobagrus fulvidraco; therefore, the gene is termed as pfcrtc2), and its evolutionary and molecular characteristics as well as potential immunity-related roles were investigated. Our results showed that the open reading frame of pfcrtc2 was 2346 bp in length, encoding a protein with 781 amino acids. Gene structure analysis revealed its existence of 14 exons and 13 introns. A phylogenetic analysis proved that the tree of crtc2 was clustered into five groups, exhibiting a similar evolutionary topology with species evolution. Multiple protein sequences alignment demonstrated high conservation of the crtc2 in various vertebrates with similar structure. Syntenic and gene structural comparisons further established that crtc2 was highly conserved, implying its similar roles in diverse vertebrates. Tissue distribution pattern detected by quantitative real-time PCR showed that the pfcrtc2 gene was almost expressed in all detected tissues except for eyes, with the highest expression levels in the gonad, indicating that Crtc2 may play important roles in various tissues. In addition, pfcrtc2 was transcribed at all developmental stages in yellow catfish, showing the highest expression levels at 12 h after fertilization. Finally, the transcriptional profiles of crtc2 were significantly increased in yellow catfishes injected with Aeromonas hydrophila or Poly I:C, which shared a consistent change pattern with four immune-related genes including IL-17A, IL-10, MAPKp38, and NF-κBp65, suggesting pfCrtc2 may play critical roles in preventing both exogenous bacteria and virus invasion. In summary, our findings lay a solid foundation for further studies on the functions of pfcrtc2, and provide novel genetic loci for developing new strategies to control disease outbreak in teleost.

Molecular characterization of a teleost-specific toll-like receptor 22 (tlr22) gene from yellow catfish (Pelteobagrus fulvidraco) and its transcriptional change in response to poly I:C and Aeromonas hydrophila stimuli.

Toll-like receptors (TLRs) are a class of pattern recognition receptors (PRRs) that can recognize pathogen-associated molecular patterns (PMPs) and play important roles in the innate immune system in vertebrates. In this study, we identified a teleost-specific tlr22 gene from yellow catfish (Pelteobagrus fulvidraco) and its immune roles in response to different pathogens were also determined. The open reading frame (ORF) of the tlr22 was 2892 bp in length, encoding a protein of 963 amino acids. Multiple protein sequences alignment, secondary and three-dimensional structure analyses revealed that TLR22 is highly conserved among different fish species. Phylogenetic analysis showed that the phylogenetic topology was divided into six families of TLR1, TLR3, TLR4, TLR5, TLR7 and TLR11, and TLR22 subfamily was clustered into TLR11 family. Meanwhile, synteny and gene structure comparisons revealed functional and evolutionary conservation of the tlr22 gene in teleosts. Furthermore, tlr22 gene was shown to be widely expressed in detected tissues except barbel and eye, with highest expression level in liver. The transcription of tlr22 was significantly increased in spleen, kidney, liver and gill tissues at different timepoints after Poly I:C infection, suggesting TLR22 plays critical roles in defensing virus invasion. Similarly, the transcription of tlr22 was also dramatically up-regulated in spleen, kidney and gill tissues with different patterns after Aeromonas hydrophila infection, indicating that TLR22 is also involved in resisting bacteria invasion. Our findings will provide a solid basis for the investigation the immune functions of tlr22 gene in teleosts, as well as provide useful information for disease control and treatment for yellow catfish.

Characterization of two kcnk3 genes in Nile tilapia (Oreochromis niloticus): Molecular cloning, tissue distribution, and transcriptional changes in various salinity of seawater.

As one important member of the two-pore-domain potassium channel (K2P) family, potassium channel subfamily K member 3 (KCNK3) has been reported for thermogenesis regulation, energy homeostasis, membrane potential conduction, and pulmonary hypertension in mammals. However, its roles in fishes are far less examined and published. In the present study, we identified two kcnk3 genes (kcnk3a and kcnk3b) in an euryhaline fish, Nile tilapia (Oreochromis niloticus), by molecular cloning, genomic survey and laboratory experiments to investigate their potential roles for osmoregulation. We obtained full-length coding sequences of the kcnk3a and kcnk3b genes (1209 and 1173 bp), which encode 402 and 390 amino acids, respectively. Subsequent multiple sequence alignments, putative 3D-structure model prediction, genomic survey and phylogenetic analysis confirmed that two kcnk3 paralogs are widely presented in fish genomes. Interestingly, a DNA fragment inversion of a kcnk3a cluster was found in Cypriniforme in comparison with other fishes. Quantitative real-time PCRs demonstrated that both the tilapia kcnk3 genes were detected in all the examined tissues with a similar distribution pattern, and the highest transcriptions were observed in the heart. Meanwhile, both kcnk3 genes in the gill were proved to have a similar transcriptional change pattern in response to various salinity of seawater, implying that they might be involved in osmoregulation. Furthermore, three predicted transcription factors (arid3a, arid3b, and arid5a) of both kcnk3 genes also showed a similar pattern as their target genes in response to the various salinity, suggesting their potential positive regulatory roles. In summary, we for the first time characterized the two kcnk3 genes in Nile tilapia, and demonstrated their potential involvement in osmoregulation for this economically important fish.

Characterization of two kcnk3 genes in rabbitfish (Siganus canaliculatus): Molecular cloning, distribution patterns and their potential roles in fatty acids metabolism and osmoregulation.

KCNK3 is a two-pore-domain (K2P) potassium channel involved in maintaining ion homeostasis, mediating thermogenesis, controlling breath and modulating electrical membrane potential. Although the functions of this channel have been widely described in mammals, its roles in fishes are still rarely known. Here, we identified two kcnk3 genes from the euryhaline rabbitfish (Siganus canaliculatus), and their roles related to fatty acids metabolism and osmoregulation were investigated. The open reading frames of kcnk3a and kcnk3b were 1203 and 1176 bp in length, encoding 400 and 391 amino acids respectively. Multiple sequences alignment and phylogenetic analysis revealed that the two isotypes of kcnk3 were extensively presented in fishes. Quantitative real-time PCRs indicated that both genes were widely distributed in examined tissues but showed different patterns. kcnk3a primary distributed in adipose, eye, heart, and spleen tissues, while kcnk3b was mainly detectable in heart, kidney, muscle and spleen tissues. In vivo experiments showed that fish fed diets with fish oil as dietary lipid (rich in long chain polyunsaturated fatty acids, LC-PUFA) induced higher mRNA expression levels of kcnk3 genes in comparison with fish fed with plant oil diet at two different salinity environments (32 and 15‰). Meanwhile, the expression levels of kcnk3 genes were higher in seawater (32‰) than that in brackish water (15‰) when fishes were fed with both types of feeds. In vitro experiments with rabbitfish hepatocytes showed that LC-PUFA significantly improved hepatic kcnk3a expression level compared with treatment of linolenic acid. These results suggest that two kcnk3 genes are widely existed and they might be functionally related to fatty acids metabolism and osmoregulation in the rabbitfish.

Molecular cloning of two kcnk3 genes from the Northern snakehead (Channa argus) for quantification of their transcriptions in response to fasting and refeeding.

Potassium channel subfamily K member 3 (KCNK3) has been reported to play important roles in membrane potential conduction, pulmonary hypertension and thermogenesis regulation in mammals. However, its roles remain largely unknown and scarce reports were seen in fish. In the present study, we for the first time identified two kcnk3 genes (kcnk3a and kcnk3b) from the carnivorous Northern snakehead (Channa argus) by molecular cloning and a genomic survey. Subsequently, their transcription changes in response to different feeding status were investigated. Full-length coding sequences of the kcnk3a and kcnk3b genes are 1203 and 1176 bp, encoding 400 and 391 amino acids, respectively. Multiple alignments, 3D-structure prediction and phylogenetic analysis further suggested that these kcnk3 genes may be highly conserved in vertebrates. Tissue distribution analysis by real-time PCR demonstrated that both the snakehead kcnk3s were widely transcribed in majority of the examined tissues but with different distribution patterns. In a short-term (24-h) fasting experiment, we observed that brain kcnk3a and kcnk3b genes showed totally opposite transcription patterns. In a long-term (2-week) fasting and refeeding experiment, we also observed differential change patterns for the brain kcnk3 genes. In summary, our findings suggest that the two kcnk3 genes are close while present different transcription responses to fasting and refeeding. They therefore can be potentially selected as novel target genes for improvement of production and quality of this economically important fish.

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes.

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.

Molecular characterization and expression of toll-like receptor 5 genes from Pelteobagrus vachellii.

Toll-like receptor 5 (TLR5) is an important pathogen recognition receptor (PRR) that recognizes the flagellin protein of pathogenic bacteria and plays a fundamental role in activating the innate immune response. In this study, full-length pvTLR5m (membrane) and pvTLR5s (soluble) genes were cloned from darkbarbel catfish Pelteobagrus vachellii, and their expression and that of downstream genes were analyzed following exposure to the Aeromonas hydrophila pathogen. The 3009 bp pvTLR5m cDNA includes a 2652 bp open reading frame (ORF) encoding 884 amino acids. The 2422 bp pvTLR5s cDNA includes a 1944 bp ORF encoding a predicted protein of 648 amino acids. The genes are most closely related to TLR5m (75%) and TLR5s (69%) from Ictalurus punctatus, respectively, and both have a typical TLR structure. Both genes were constitutively expressed in all examined tissues, and most abundantly in the head kidney and spleen. Following pathogen challenge, pvTLR5m and pvTLR5s expression was increased significantly (P <0.05) and peaked at 24 and 12 h post-exposure in the liver, 24 and 12 h in the head kidney, and 48 and 24 h in the spleen, respectively. The downstream genes interleukin-1ß (IL-1ß), IL-12 and tumor necrosis factor-alpha (TNF-α) were significantly up-regulated following pathogen exposure in spleen, and the NF-kB inhibitor (IκB) was down-regulated. These findings indicated that pvTLR5 may play an important role in the immune responses to A. hydrophila. These results provide new insight to elucidate the immune signalling pathways of fish TLR.

Molecular cloning, tissue distribution, and effect of fasting and refeeding on the expression of neuropeptide Y in Channa argus.

Neuropeptide Y (NPY) is a 36 amino-acid amidated peptide of the pancreatic polypeptide (PP) family, which plays an important role in appetite regulation and energy expenditure in mammals. Although several teleost NPY have been identified, its roles remain unclear in fish. We herein reported on the molecular cloning, tissue distribution and the effect of fasting on the expression of NPY in Channa argus, and designated as CaNPY. It consisted of a 300 bp open reading frame predicted to encode a prepro-NPY of 99 amino acids. Sequence analysis revealed that CaNPY was highly conserved (>60%) with other vertebrate NPY. Phylogenetic analysis highly supported CaNPY was closely related to piscine NPY. In addition, except for muscle and spleen tissues, CaNPY was found to extensively expressed in all other detected tissues, with the highest level in brain. Futhermore, the CaNPY transcript was found to significantly increase after short-term and long-term food deprivation, and dramatically decrease following refeeding. These findings suggested that CaNPY might be involved in food intake regulation and it could be as a potential target locus to improve commercial production of this kind of fish.

Uncoupling protein 1 in snakehead (Channa argus): Cloning, tissue distribution, and its expression in response to fasting and refeeding.

In mammals, uncoupling protein 1 (UCP1) is well known for its thermogenic role in brown adipose tissue (BAT). However, the UCP1 physiological roles are still unclear in fish, although several teleost ucp1 genes have been identified. The aim of this study is to investigate the potential roles of fish UCP1 involved in food intake regulation and energy homeostasis. We herein report on the molecular cloning, tissue distribution and the effect of fasting and refeeding on the expression of ucp1 in Channa argus. UCP1 consisted of a 921 bp open reading frame predicted to encode 306 amino acids. Sequence analysis revealed that snakehead UCP1 was highly conserved (>80%) with teleost UCP1, but shared a lower identity (60-72%) with mammals. Phylogenetic analysis supported that snakehead UCP1 was closely related to piscine UCP1. In addition, ucp1 was found to extensively expressed in all detected tissues, with the highest level in liver. Futhermore, the hepatic ucp1 was found to significantly increased after short-term and long-term food deprivation, and dramatically increased following refeeding. These findings suggested that snakehead UCP1 might play important roles in food intake regulation and fatty acid metabolism in snakehead fish, and it could be as a potential target locus to improve commercial production of this kind of fish.

Transcriptome analysis of the spleen of the darkbarbel catfish Pelteobagrus vachellii in response to Aeromonas hydrophila infection.

Intensive aquaculture has increased the susceptibility of fish to Aeromonas hydrophila, and this has led to severe economic damage. There has been little study of the host defense mechanism against A. hydrophila infection in scaleless fish. Therefore, in the present study, the transcriptome profiles of the spleen of Pelteobagrus vachellii were examined after infection with A. hydrophila. In total, 37,730 unigenes from 322 KEGG pathways were identified. Following A. hydrophila infection, 27,803 differentially expressed genes were identified, including 13,934 upregulated and 13,869 downregulated genes. Significant enrichment analysis of these differentially expressed unigenes showed that the major immune pathways were involved, including toll-like receptor pathways, B-cell receptor signaling pathways, Fcγ receptor-mediated phagocytosis, complement and coagulation cascades, and natural killer cell-mediated cytotoxicity pathways. From these pathways, 59 key immune-related differentially expressed genes were selected: 53 genes that were upregulated, including those coding for complement components, interferons, and interleukins, and six DEGs that were downregulated, including inhibitor of nuclear factor kappa-B kinase. Finally, nine DEGs, which were randomly selected, were confirmed by qRT-PCR to be differentially expressed. The results indicated that complement components, interferons and Fcγ receptor-mediated phagocytosis played key role in the response to A. hydrophila infection in the spleen of P. vachellii, which may prove useful in the future for the development of therapeutic regimens.

Effect of ammonia-N and pathogen challenge on complement component 8α and 8ß expression in the darkbarbel catfish Pelteobagrus vachellii.

The complement components C8α and C8ß mediate the formation of the membrane attack complex (MAC) to resist pathogenic bacteria and play important roles in innate immunity. Full-length complement C8α (Pv-C8α) and C8ß (Pv-C8ß) cDNA were identified in the darkbarbel catfish Pelteobagrus vachellii, and their mRNA expression levels were analyzed after ammonia-N and pathogen treatment. The Pv-C8α gene contained 1983 bp, including a 1794-bp open reading frame (ORF) encoding 598 amino acids. The Pv-C8ß gene contained 1952 bp, including a 1761-bp ORF encoding 587 amino acids. Pv-C8α and Pv-C8ß had the highest amino acid identity with rainbow trout Oncorhynchus mykiss C8α (62%) and Japanese flounder Paralichthys olivaceus C8ß (83%), respectively. Sequence analysis indicated that both Pv-C8α and Pv-C8ß contained a thrombospondin type-1 (TSP1) domain, a low-density lipoprotein receptor class A (LDLR-A) domain, a membrane attack complex/perforin (MACPF) domain and an epidermal growth factor-like (EGF-like) domain. In addition, Pv-C8α and Pv-C8ß were mainly distributed in the liver, head kidney, spleen, and eggs. Under ammonia-N stress, the Pv-C8α and Pv-C8ß mRNA levels significantly decreased (P < 0.05), with minimum levels, respectively, attained at 24 and 48 h in the liver, 48 and 24 h in the head kidney, and 24 and 24 h in the spleen. After Aeromonas hydrophila challenge, the Pv-C8α and Pv-C8ß mRNA levels significantly increased (P < 0.05), with maximum levels, respectively, attained at 48 and 24 h in the liver, 24 and 48 h in the head kidney, and 48 and 48 h in the spleen. The present study indicated that Pv-C8α and Pv-C8ß exhibited important immune responses to infection and that ammonia-N in water decreased the immune responses of Pv-C8α and Pv-C8ß.

Transcriptome analysis of food habit transition from carnivory to herbivory in a typical vertebrate herbivore, grass carp Ctenopharyngodon idella.

BACKGROUND: Although feeding behavior and food habit are ecologically and economically important properties, little is known about formation and evolution of herbivory. Grass carp (Ctenopharyngodon idella) is an ecologically appealing model of vertebrate herbivore, widely cultivated in the world as edible fish or as biological control agents for aquatic weeds. Grass carp exhibits food habit transition from carnivory to herbivory during development. However, currently little is known about the genes regulating the unique food habit transition and the formation of herbivory, and how they could achieve higher growth rates on plant materials, which have a relatively poor nutritional quality. RESULTS: We showed that grass carp fed with duckweed (modeling fish after food habit transition) had significantly higher relative length of gut than fish before food habit transition or those fed with chironomid larvae (fish without transition). Using transcriptome sequencing, we identified 10,184 differentially expressed genes between grass carp before and after transition in brain, liver and gut. By eliminating genes potentially involved in development (via comparing fish with or without food habit transition), we identified changes in expression of genes involved in cell proliferation and differentiation, appetite control, circadian rhythm, and digestion and metabolism between fish before and after food habit transition. Up-regulation of GHRb, Egfr, Fgf, Fgfbp1, Insra, Irs2, Jak, STAT, PKC, PI3K expression in fish fed with duckweed, consistent with faster gut growth, could promote the food habit transition. Grass carp after food habit transition had increased appetite signal in brain. Altered expressions of Per, Cry, Clock, Bmal2, Pdp, Dec and Fbxl3 might reset circadian phase of fish after food habit transition. Expression of genes involved in digestion and metabolism were significantly different between fish before and after the transition. CONCLUSIONS: We suggest that the food habit transition from carnivory to herbivory in grass carp might be due to enhanced gut growth, increased appetite, resetting of circadian phase and enhanced digestion and metabolism. We also found extensive alternative splicing and novel transcript accompanying food habit transition. These differences together might account for the food habit transition and the formation of herbivory in grass carp.

Two homologs of rho-class and polymorphism in alpha-class glutathione S-transferase genes in the liver of three tilapias.

To clarify detoxification metabolism of tilapia, a natural and biological control for removing the leftover toxicants in fresh water, sequence structure, expression profile and polymorphisms of members of glutathione S-transferase (GST) genes were analyzed in Nile tilapia, blue tilapia and their hybrid. Full-length mRNA sequences of alpha-class GST (GSTA) and two homologs of rho-class GST (GSTR) were identified. Sequence analysis confirmed the similarity in conserved domain regions and their phylogenetic relationships with GST genes in other fishes. In addition, three single nucleotide polymorphisms of GSTA genes were identified in the three populations, two (C266T and G525A) of which showed significant association. The relative mRNA expression of GSTA gene was significantly (P<0.05) increased in the liver of Nile tilapia at 24h post-injection of MC-LR, significantly (P<0.05) decreased in blue tilapia whereas slightly decreased (P>0.05) in hybrid tilapia.

Molecular Identification and Functional Characterization of LC-PUFA Biosynthesis Elongase (elovl2) Gene in Chinese Sturgeon (Acipenser sinensis).

Elongases of very-long-chain fatty acids (Elovls) are critical rate-limiting enzymes that are involved in LC-PUFA biosynthesis through catalyzing the two-carbon elongation of a pre-existing fatty acyl chain. Thus far, several Elovls have been extensively studied in teleost. However, the functional and physiological roles of Elovls in chondrichthyans have rarely been reported. In this study, we identified and characterized elovl2 from the endangered Chinese sturgeon (Acipenser sinensis) by whole genome scanning. The results show that the coding sequence of elovl2 was 894 bp in length, for a putative protein of 297 amnio acids. Comparative genomic analyses indicated that Chinese sturgeon elovl2 was evolutionarily conserved. Functional characterization in yeast demonstrated that the Chinese sturgeon Elovl2 could efficiently elongate C20 (ARA and EPA) and C22 (22:4n-6 and 22:5n-3) substrates, confirming its critical roles in LC-PUFA biosynthesis. Spatial and temporal expression analyses showed high elovl2 mRNA levels were detected in the liver and brain and showed an increase trend both in embryonic and post-hatching stages. Interestingly, diets with vegetable oils as lipid sources could significantly induce the high expression of elovl2 in Chinese sturgeon, implying that the endogenous LC-PUFA biosynthesis pathway was stimulated by lack of LC-PUFA in their diets. Our findings will enhance our understanding about the evolutionary and functional roles of elovl2 and provide novel insights into the LC-PUFA biosynthesis mechanism in vertebrates.

5 mC modification of steroid hormone biosynthesis-related genes orchestrates feminization of channel catfish induced by high-temperature.

To elucidate the mechanism behind channel catfish feminization induced by high temperature, gonad samples were collected from XY pseudo-females and wild-type females and subjected to high-throughput sequencing for Whole-Genome-Bisulfite-Seq (WGBS) and transcriptome sequencing (RNA-Seq). The analysis revealed 50 differentially methylated genes between wild-type females and XY pseudo-females, identified through the analysis of KEGG pathways and GO enrichment in the promoter of the genome and differentially methylated regions (DMRs). Among these genes, multiple differential methylation sites observed within the srd5a2 gene. Repeatability tests confirmed 7 differential methylation sites in the srd5a2 gene in XY pseudo-females compared to normal males, with 1 specific differential methylation site (16608174) distinguishing XY pseudo-females from normal females. Interestingly, the expression of these genes in the transcriptome showed no difference between wild-type females and XY pseudo-females. Our study concluded that methylation of the srd5a2 gene sequence leads to decreased expression, which inhibits testosterone synthesis while promoting the synthesis of 17ß-estradiol from testosterone. This underscores the significance of the srd5a2 gene in the sexual differentiation of channel catfish, as indicated by the ipu00140 KEGG pathway analysis.

Chromosome-level genome assemblies of vulnerable male and female elongate loach (Leptobotia elongata).

Endemic to the upper and middle reaches of the Yangtze River in China, elongate loach (Leptobotia elongata) has become a vulnerable species mainly due to overfishing and habitat destruction. Thus far, no genome data of this species are reported. As a result, lacking of such genomic information has restricted practical conservation and utilization of this economic fish. Here, we constructed chromosome-level genome assemblies for both male and female elongate loach by integration of MGI, PacBio HiFi and Hi-C sequencing technologies. Two primary genome assemblies (586-Mb and 589-Mb) were obtained for female and male fishes, respectively. Indeed, 98.22% and 98.61% of the contig sequences were anchored onto 25 chromosomes, with identification of 26.22% and 25.92% repeat contents in both assembled genomes. Meanwhile, a total of 25,215 and 25,253 protein-coding genes were annotated, of which 97.41% and 98.8% could be predicted with functions. Taken together, our genome data presented here provide a valuable genomic resource for in-depth evolutionary and functional research, as well as molecular breeding and conservation of this economic fish species.

Characterization of three lamp genes from largemouth bass (Micropterus salmoides): molecular cloning, expression patterns, and their transcriptional levels in response to fast and refeeding strategy.

Lysosomes-associated membrane proteins (LAMPs), a family of glycosylated proteins and major constituents of the lysosomal membranes, play a dominant role in various cellular processes, including phagocytosis, autophagy and immunity in mammals. However, their roles in aquatic species remain poorly known. In the present study, three lamp genes were cloned and characterized from Micropterus salmoides. Subsequently, their transcriptional levels in response to different nutritional status were investigated. The full-length coding sequences of lamp1, lamp2 and lamp3 were 1251bp, 1224bp and 771bp, encoding 416, 407 and 256 amino acids, respectively. Multiple sequence alignment showed that LAMP1-3 were highly conserved among the different fish species, respectively. 3-D structure prediction, genomic survey, and phylogenetic analysis were further confirmed that these genes are widely existed in vertebrates. The mRNA expression of the three genes was ubiquitously expressed in all selected tissues, including liver, brain, gill, heart, muscle, spleen, kidney, stomach, adipose and intestine, lamp1 shows highly transcript levels in brain and muscle, lamp2 displays highly expression level in heart, muscle and spleen, but lamp3 shows highly transcript level in spleen, liver and kidney. To analyze the function of the three genes under starvation stress in largemouth bass, three experimental treatment groups (fasted group and refeeding group, control group) were established in the current study. The results indicated that the expression of lamp1 was significant induced after starvation, and then returned to normal levels after refeeding in the liver. The expression of lamp2 and lamp3 exhibited the same trend in the liver. In addition, in the spleen and the kidney, the transcript level of lamp1 and lamp2 was remarkably increased in the fasted treatment group and slightly decreased in the refed treatment group, respectively. Collectively, our findings suggest that three lamp genes may have differential function in the immune and energetic organism in largemouth bass, which is helpful in understanding roles of lamps in aquatic species.

Effects of polymorphisms in pepsinogen (PEP), amylase (AMY) and trypsin (TRY) genes on food habit domestication traits in mandarin fish.

Mandarin fish (Siniperca chuatsi) have a peculiar feeding habit of only accepting live fish prey and refusing dead prey and artificial diets. However, previous research has shown that some individuals accept dead prey after gradual domestication. Digestive enzymes are correlated with feeding habits in fish. In the current study, SNPs in the mandarin fish genes for pepsinogen (PEP), amylase (AMY), and trypsin (TRY) were evaluated for associations with feeding habits in domesticated mandarin fish by scanning their complete genomic sequence. In total, two SNPs were found in PEP, one was found in TRY, and none were found in AMY. The D1(CTCC) and D5(TTTT) diplotypes in the PEP gene tended to show strong effects on the feeding habits of domesticated fish (p < 0.01). The results indicate that PEP may be associated with the genetic mechanism for feeding habits in mandarin fish, and the D1(CTCC) and D5(TTTT) diplotypes in the PEP gene may be useful markers for selecting mandarin fish with appropriate feeding habits for domestication.

Toll-like Receptor 3 in the Hybrid Yellow Catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂): Protein Structure, Evolution and Immune Response to Exogenous Aeromonas hydrophila and Poly (I:C) Stimuli.

As a major mediator of cellular response to viral infection in mammals, Toll-like receptor 3 (TLR3) was proved to respond to double-stranded RNA (dsRNA). However, the molecular mechanism by which TLR3 functions in the viral infection response in teleosts remains to be investigated. In this study, the Toll-like receptor 3 gene of the hybrid yellow catfish was identified and characterized by comparative genomics. Furthermore, multiple sequence alignment, genomic synteny and phylogenetic analysis suggested that the homologous TLR3 genes were unique to teleosts. Gene structure analysis showed that five exons and four introns were common components of TLR3s in the 12 examined species, and interestingly the third exon in teleosts was the same length of 194 bp. Genomic synteny analysis indicated that TLR3s were highly conserved in various teleosts, with similar organizations of gene arrangement. De novo predictions showed that TLR3s were horseshoe-shaped in multiple taxa except for avian (with a round-shaped structure). Phylogenetic topology showed that the evolution of TLR3 was consistent with the evolution of the studied species. Selection analysis showed that the evolution rates of TLR3 proteins were usually higher than those of TLR3-TIR domains, indicating that the latter were more conserved. Tissue distribution analysis showed that TLR3s were widely distributed in the 12 tested tissues, with the highest transcriptions in liver and intestine. In addition, the transcription levels of TLR3 were significantly increased in immune-related tissues after infection of exogenous Aeromonas hydrophila and poly (I:C). Molecular docking showed that TLR3 in teleosts forms a complex with poly (I:C). In summary, our present results suggest that TLR3 is a pattern recognition receptor (PRR) gene in the immune response to pathogen infections in hybrid yellow catfish.

Characterization of TLR1 and expression profiling of TLR signaling pathway related genes in response to Aeromonas hydrophila challenge in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂).

Toll-like receptor 1 (TLR1) mediates the innate immune response to a variety of microbes through recognizing cell wall components (such as bacterial lipoproteins) in mammals. However, the detailed molecular mechanism of TLR1 involved in pathogen immunity in the representative hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂) has not been well studied. In the present study, we identified the TLR1 gene from the hybrid yellow catfish, and further comparative synteny data from multiple species confirmed that the TLR1 gene is highly conserved in teleosts. Phylogenetic analysis revealed distinguishable TLR1s in diverse taxa, suggesting consistence in evolution of the TLR1 proteins with various species. Structural prediction indicated that the three-dimensional structures of TLR1 proteins are relatively conserved among different taxa. Positive selection analysis showed that purifying selection dominated the evolutionary process of TLR1s and TLR1-TIR domain in both vertebrates and invertebrates. Expression pattern analysis based on the tissue distribution showed that TLR1 mainly transcribed in the gonad, gallbladder and kidney, and the mRNA levels of TLR1 in kidney were remarkably up-regulated after Aeromonas hydrophila stimulation, indicating that TLR1 participates in the inflammatory responses to exogenous pathogen infection in hybrid yellow catfish. Homologous sequence alignment and chromosomal location indicated that the TLR signaling pathway is very conserved in the hybrid yellow catfish. The expression patterns of TLR signaling pathway related genes (TLR1- TLR2 - MyD88 - FADD - Caspase 8) were consistent after pathogen stimulation, revealing that the TLR signaling pathway is triggered and activated after A. hydrophila infection. Our findings will lay a solid foundation for better understanding the immune roles of TLR1 in teleosts, as well as provide basic data for developing strategies to control disease outbreak in hybrid yellow catfish.