Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon.

Whole-genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Ma. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue-specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained regulatory divergence. Patterns of genetic diversity across natural populations inferred from resequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.

The Center of Origin and Colonization Routes of Noble Salmons of the Genus Salmo (Salmonidae, Actinopterigii).

Genetic diversity and colonization routes of noble salmons were studied using a partial nucleotide sequence of the mitochondrial COI gene. The brown trout S. trutta, which is the most ancient species of the genus, was concluded to originate from the modern southeastern Pontic-Caspian area, which is currently inhabited by members of the subspecies S. trutta oxianus. Migrating westward while the Paratethys was in existence (5-34 million years ago), species of the genus colonized ancient water bodies in the modern Mediterranean basin and formed many isolated populations that survived desiccation of the Mediterranean Sea (5-6 million years ago). The Strait of Gibraltar mediated brown trout migrations to Northern Europe; the subspecies S. trutta trutta belongs to a relatively young phylogenetic lineage of the species. A separate brown trout lineage, currently classified as the subspecies S. trutta labrax, formed most likely in the area of the modern Danube basin, which was a relatively separate part of the Paratethys and was sometimes isolated as the Pannonian Lake. A highly divergent phylogenetic lineage of Atlantic salmon (S. salar) haplotypes originates from a haplotype of the brown trout that inhabited the area of the modern Strait of Gibraltar.

Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon.

Genomic selection enables cumulative genetic gains in key production traits such as disease resistance, playing an important role in the economic and environmental sustainability of aquaculture production. However, it requires genome-wide genetic marker data on large populations, which can be prohibitively expensive. Genotype imputation is a cost-effective method for obtaining high-density genotypes, but its value in aquaculture breeding programs which are characterized by large full-sibling families has yet to be fully assessed. The aim of this study was to optimize the use of low-density genotypes and evaluate genotype imputation strategies for cost-effective genomic prediction. Phenotypes and genotypes (78,362 SNPs) were obtained for 610 individuals from a Scottish Atlantic salmon breeding program population (Landcatch, UK) challenged with sea lice, Lepeophtheirus salmonis The genomic prediction accuracy of genomic selection was calculated using GBLUP approaches and compared across SNP panels of varying densities and composition, with and without imputation. Imputation was tested when parents were genotyped for the optimal SNP panel, and offspring were genotyped for a range of lower density imputation panels. Reducing SNP density had little impact on prediction accuracy until 5,000 SNPs, below which the accuracy dropped. Imputation accuracy increased with increasing imputation panel density. Genomic prediction accuracy when offspring were genotyped for just 200 SNPs, and parents for 5,000 SNPs, was 0.53. This accuracy was similar to the full high density and optimal density dataset, and markedly higher than using 200 SNPs without imputation. These results suggest that imputation from very low to medium density can be a cost-effective tool for genomic selection in Atlantic salmon breeding programs.

Close relatives in population samples: Evaluation of the consequences for genetic stock identification.

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self-assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI.

Rapid Identification of Rainbow Trout Adulteration in Atlantic Salmon by Raman Spectroscopy Combined with Machine Learning.

This study intends to evaluate the utilization potential of the combined Raman spectroscopy and machine learning approach to quickly identify the rainbow trout adulteration in Atlantic salmon. The adulterated samples contained various concentrations (0-100% w/w at 10% intervals) of rainbow trout mixed into Atlantic salmon. Spectral preprocessing methods, such as first derivative, second derivative, multiple scattering correction (MSC), and standard normal variate, were employed. Unsupervised algorithms, such as recursive feature elimination, genetic algorithm (GA), and simulated annealing, and supervised K-means clustering (KM) algorithm were used for selecting important spectral bands to reduce the spectral complexity and improve the model stability. Finally, the performances of various machine learning models, including linear regression, nonlinear regression, regression tree, and rule-based models, were verified and compared. The results denoted that the developed GA-KM-Cubist machine learning model achieved satisfactory results based on MSC preprocessing. The determination coefficient (R2) and root mean square error of prediction sets (RMSEP) in the test sets were 0.87 and 10.93, respectively. These results indicate that Raman spectroscopy can be used as an effective Atlantic salmon adulteration identification method; further, the developed model can be used for quantitatively analyzing the rainbow trout adulteration in Atlantic salmon.

The application of CRISPR-Cas for single species identification from environmental DNA.

We report the first application of CRISPR-Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows noninvasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR-based techniques to detect a given species from eDNA samples, posing a logistical challenge for on-site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR-Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof-of-concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (<2.5 hr). This approach simplifies the challenge of building a biosensor device for rapid target species detection in the field and can be easily adapted to detect any species from eDNA samples from a variety of sources enhancing the capabilities of eDNA as a tool for monitoring biodiversity.

Functional divergence of thyrotropin beta-subunit paralogs gives new insights into salmon smoltification metamorphosis.

Smoltification is a metamorphic event in salmon life history, which initiates downstream migration and pre-adapts juvenile salmon for seawater entry. While a number of reports concern thyroid hormones and smoltification, few and inconclusive studies have addressed the potential role of thyrotropin (TSH). TSH is composed of a α-subunit common to gonadotropins, and a ß-subunit conferring hormone specificity. We report the presence and functional divergence of duplicated TSH ß-subunit paralogs (tshßa and tshßb) in Atlantic salmon. Phylogeny and synteny analyses allowed us to infer that they originated from teleost-specific whole genome duplication. Expression profiles of both paralogs in the pituitary were measured by qPCR throughout smoltification in Atlantic salmon from the endangered Loire-Allier population raised in a conservation hatchery. This revealed a striking peak of tshßb expression in April, concomitant with downstream migration initiation, while tshßa expression remained relatively constant. In situ hybridization showed two distinct pituitary cell populations, tshßa cells in the anterior adenohypophysis, and tshßb cells near to the pituitary stalk, a location comparable to the pars tuberalis TSH cells involved in seasonal physiology and behaviour in birds and mammals. Functional divergence of tshß paralogs in Atlantic salmon supports a specific role of tshßb in smoltification.

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly.

Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.

Influence of strain origin on osmoregulatory and endocrine parameters of two non-native strains of Atlantic salmon (Salmo salar L.).

Non-native strains of Atlantic salmon are used in reinstatement trials where populations are extinct. Environmental cues like photoperiod and temperature are known to influence the smolting process and there is evidence of strain-, stock- or population-specific differences associated with seaward migration or smoltification. The objective of this study was to compare morphological, osmoregulatory and endorcrine features between two strains, one originating from a cold and short river in Ireland (Cong) and another from a long and warm river in France (Loire-Allier), reared under Belgian conditions in order to highlight major differences in restocking adaptability. Comprehensive endocrine profiles, consistent with their interactive role of mediating changes associated with smolting, have been observed. Na+/K+ATPase activity (1.3-10.5 µmol ADP∗mg prot.-1∗h-1) and hormone plasma levels (e.g. 55-122 ng∗mL-1 of cortisol and 4.5-6.4 ng∗mL-1 of GH) were consistent with reported values. We observed strain-related differences of the influence of temperature and daylength on cortisol, GH and sodium plasma levels. These may be related to the respective environmental conditions prevailing in the river of origin, which have impacted the genetic background for smoltification. Using Na+/K+ATPase activity as an indicator, both strains smoltified successfully and simultaneously testifying a prevailing influence of environmental cues over genetic factors for smoltification.

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations.

The gut microbial community in vertebrates plays a role in nutrient digestion and absorption, development of intestine and immune systems, resistance to infection, regulation of bone mass and even host behavior and can thus impact host fitness. Atlantic salmon (Salmo salar) reintroduction efforts into Lake Ontario, Canada, have been unsuccessful, likely due to competition with non-native salmonids. In this study, we explored interspecific competition effects on the gut microbiota of two Atlantic salmon populations (LaHave and Sebago) resulting from four non-native salmonids. After 10 months of rearing in semi-natural stream tanks under six interspecific competition treatments, we characterized the gut microbiota of 178 Atlantic salmon by parallel sequencing the 16S rRNA gene. We found 3978 bacterial OTUs across all samples. Microbiota alpha diversity and abundance of 27 OTUs significantly differed between the two populations. Interspecific competition reduced relative abundance of potential beneficial bacteria (six genera of lactic acid bacteria) as well as 13 OTUs, but only in the LaHave population, indicating population-specific competition effects. The pattern of gut microbiota response to interspecific competition may reflect local adaptation of the host-microbiota interactions and can be used to select candidate populations for improved species reintroduction success.

Water management applied to the processing of Atlantic Salmon (Salmo salar) and Dolphinfish (Coryphaena hippurus) in a fish cold storage warehouse in Rio de Janeiro, Brazil / Gerenciamento hídrico aplicado ao beneficiamento de Salmão-do-Atlântico (Salmo salar) e Dourado-do-mar (Coryphaena hippurus) em entreposto de pescado no Rio de Janeiro, Brasil

The high consumption of water and uncontrolled wastewater generation commonly seen in fish processing plants are a matter of concern. Sustainable actions must be taken to addres this issue. The present study aimed to quantify the water used in the processing of Atlantic Salmon (Salmo salar) and Dolphinfish (Coryphaena hippurus) in a fish warehouse in Rio de Janeiro, Brazil, through water balance and mass balance at each development stage. According to the data obtained, the warehouse showed higher total water use, both in general (7,173.28±265.77m3/month), with most water use intended for processing support activities, approximately 45.00% (3,186.82±407.57m3/month); specifically, in the processing of the selected raw materials, with greater consumption of water for obtaining one kg of Dolphinfish fillets and slices, around 4.80 x 103m3/kg in both. This suggests the use of sustainable methodologies that result in decreased water consumption and in reuse of solid waste, since the three processing stages studied generated a high amount of solid waste, with emphasis to filleting in both species, with 55.00% of residual production each. The present study will also serve as the basis to other studies on the same issue in the fishing area.(AU)

Comumente relacionado à indústria de pescado, o alto consumo de água e geração de efluentes de forma não controlada é preocupante. Ações sustentáveis são necessárias diante do problema. Objetivou-se, com o presente estudo, quantificar a água utilizada no processamento de salmão-do-atlântico (Salmo salar) e dourado-do-mar (Coryphaena hippurus), em um entreposto de pescado localizado no Rio de Janeiro, Brasil, por meio dos balanços hídrico e de massa de cada etapa de processamento. Com base nos dados obtidos, observou-se que o entreposto apresentou um elevado uso de água total, tanto de forma geral, 7.173,28±265,77m3/mês, com o maior gasto destinado às atividades de apoio ao processamento, aproximadamente 45,00%, quanto de forma específica, no processamento das matéria-prima selecionada, com o maior consumo de água para obtenção de um kg de filé e um kg de posta de dourado, cerca de 4,80 x 103m3/kg em ambos os processos. Sugere-se a aplicação de metodologias sustentáveis de redução no uso hídrico, além do reaproveitamento de resíduos sólidos, uma vez que os três beneficiamentos estudados geram elevada quantidade de resíduos sólidos, com destaque para a filetagem em ambas as espécies, com produção residual de 55,00% cada. O presente estudo também serve como base para outros de mesma temática na área de pescado.(AU)

Consistent melanophore spot patterns allow long-term individual recognition of Atlantic salmon Salmo salar.

The present study shows that permanent melanophore spot patterns in Atlantic salmon Salmo salar make it possible to use images of the operculum to keep track of individual fish over extended periods of their life history. Post-smolt S. salar (n = 246) were initially photographed at an average mass of 98 g and again 10 months later after rearing in a sea cage, at an average mass of 3088 g. Spots that were present initially remained and were the most overt (largest) 10 months later, while new and less overt spots had developed. Visual recognition of spot size and position showed that fish with at least four initial spots were relatively easy to identify, while identifying fish with less than four spots could be challenging. An automatic image analysis method was developed and shows potential for fast match processing of large numbers of fish. The current findings promote visual recognition of opercular spots as a welfare-friendly alternative to tagging in experiments involving salmonid fishes.

Temporal and spatial instability in neutral and adaptive (MHC) genetic variation in marginal salmon populations.

The role of marginal populations for the long-term maintenance of species' genetic diversity and evolutionary potential is particularly timely in view of the range shifts caused by climate change. The Centre-Periphery hypothesis predicts that marginal populations should bear reduced genetic diversity and have low evolutionary potential. We analysed temporal stability at neutral microsatellite and adaptive MHC genetic variation over five decades in four marginal Atlantic salmon populations located at the southern limit of the species' distribution with a complicated demographic history, which includes stocking with foreign and native salmon for at least 2 decades. We found a temporal increase in neutral genetic variation, as well as temporal instability in population structuring, highlighting the importance of temporal analyses in studies that examine the genetic diversity of peripheral populations at the margins of the species' range, particularly in face of climate change.

Identification and expressional analysis of NLRC5 inflammasome gene in smolting Atlantic salmon (Salmo salar).

The NOD-like receptors (NLRs) were recently identified as an intracellular pathogen recognition receptor family in vertebrates. While the immune system participation of NLRs has been characterized and analyzed in various mammalian models, few studies have considered NLRs in teleost species. Therefore, this study analyzed the Atlantic salmon (Salmo salar) NLRC5. Structurally, Atlantic salmon NLRC5 presented leucine-rich repeat subfamily genes. Phylogenetically, NLRC5 was moderately conserved between S. salar and other species. Real-time quantitative PCR revealed NLRC5 expression in almost all analyzed organs, with greatest expressions in the head kidney, spleen, and hindgut. Furthermore, NLRC5 gene expression decreased during smolt stage. These data suggest that NLRC5 participates in the Atlantic salmon immune response and is regulated, at least partly, by the smoltification process, suggesting that there is a depression of immune system from parr at smolt stage. This is the first report on the NLRC5 gene in salmonid smolts.

Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection.

BACKGROUND: Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. RESULTS: In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13-15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. CONCLUSION: Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation.

The Atlantic salmon genome provides insights into rediploidization.

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

The genetic relationship between extirpated and contemporary Atlantic salmon Salmo salar L. lines from the southern Baltic Sea.

BACKGROUND: The genetic relationship between original Atlantic salmon populations that are now extinct in the southern Baltic Sea and the present-day populations has long been controversial. To investigate and clarify this issue, we successfully genotyped individuals of the historical populations from the Oder and Vistula Rivers using DNA extracted from dried scales with the Atlantic salmon single nucleotide polymorphism array. RESULTS: Our results showed a global F ST of 0.2515 for all pairs of loci, which indicates a high level of genetic differentiation among the groups analyzed in this study. Pairwise F ST values were significant for all comparisons and the highest values were found between present-day reintroduced Slupia River salmon and extinct Vistula River Atlantic salmon. Bayesian analysis of genetic structure revealed the existence of substructures in the extirpated Polish populations and three main clades among studied stocks. CONCLUSIONS: The historical salmon population from the Oder River was genetically closer to present-day salmon from the Neman River than to the historical salmon from the Vistula River. Vistula salmon clearly separated from all other analyzed salmon stocks. It is likely that the origins of the Atlantic salmon population from the Morrum River and the Polish historical native populations are different.

Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations.

A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.

Molecular characterization of a transmembrane C-type lectin receptor gene from ayu (Plecoglossus altivelis) and its effect on the recognition of different bacteria by monocytes/macrophages.

C-type lectin receptors (CTLRs) play vital roles in immune responses as pattern-recognition receptors (PRRs). In this study, we identified a novel C-type lectin receptor (PaCTLRC) gene from ayu, Plecoglossus altivelis. Predicted PaCTLRC is a single transmembrane receptor with a typical carbohydrate recognition domain (CRD) at its C-terminus. Sequence comparison and phylogenetic tree analysis showed that PaCTLRC was most closely related to Atlantic salmon (Salmo salar) CLRC, but was significantly different from two other ayu CTLRs, aCLR and PaCD209L. PaCTLRC transcript was detected in all tested tissues and cells, with high levels in the liver; and its expression was significantly altered upon Vibrio anguillarum infection. Refolded recombinant PaCTLRC (rPaCTLRC) agglutinated three types of Gram-positive bacteria (Listeria monocytogenes, Staphylococcus aureus and Streptococcus iniae) and four types of Gram-negative bacteria (Aeromonas hydrophila, Escherichia coli, V. anguillarum and Vibrio parahaemolyticus) in a Ca(2+)-dependent manner in vitro, and Gram-positive bacteria were shown to be biologically relevant ligands for PaCTLRC. rPaCTLRC bound to d-mannose, d-galactose, l-fucose, N-acetyl-d-glucosamine (GlcNAc), lipopolysaccharide (LPS) and peptidoglycan (PGN), exhibiting a relative binding strength to d-mannose and PGN. d-Mannose, l-fucose, GlcNAc, LPS and PGN could inhibit the agglutinating activity of rPaCTLRC, while d-galactose did not functioned. PaCTLRC neutralization using anti-PaCTLRC IgG resulted in the inhibition of phagocytosis by ayu monocytes/macrophages (MO/MΦ) of S. aureus but not of E. coli, and produced a consistently higher survival rate of S. aureus than that of E. coli. d-Mannose, LPS and PGN treatment had no significant influence on the phagocytosis of ayu MO/MΦ. These results suggest that PaCTLRC may serve as a Gram-positive bacteria-preferred PRR which is involved in pathogen recognition and signal transduction in ayu MO/MΦ.

Sequence analysis and identification of new isoform of EP4 receptors in different atlantic salmon tissues (Salmo salar L.) and its role in PGE2 induced immunomodulation in vitro.

PGE2 plays an important role in a broad spectrum of physiological and pathological processes mediated through a membrane-bound G protein-coupled receptor (GPCR) called EP receptor. In mammals, four subtypes of EP receptor (EP 1-4) are identified and each of them functions through different signal transduction pathways. Orthologous EP receptors have also been identified in other non-mammalian species, such as chicken and zebrafish. EP4 is the only identified PGE2 receptor to date in Atlantic salmon but its tissue distribution and function have not been studied in any detail. In this study, we first sequenced EP4 receptor in different tissues and found that the presence of the 3nt deletion in the 5' untranslated region was accompanied by silent mutation at nt 668. While attempting to amplify the same sequence in TO cells (an Atlantic salmon macrophage-like cell line), we failed to obtain the full-length product. Further investigation revealed different isoform of EP4 receptor in TO cells and we subsequently documented its presence in different Atlantic salmon tissues. These two isoforms of EP4 receptor share high homology in their first half of sequence but differ in the second half part with several deletion segments though the final length of coding sequence is the same for two isoforms. We further studied the immunomodulation effect of PGE2 in TO cells and found that PGE2 inhibited the induction of CXCL-10, CCL-4, IL-8 and IL-1ß genes expression in a time dependent manner and without cAMP upregulation.