Whole-Genome sequencing and comparative genomics of Mycobacterium spp. from farmed Atlantic and coho salmon in Chile

Antonie van Leeuwenhoek - Several members of the Mycobacterium genus cause invasive infections in humans and animals. According to a recent phylogenetic analysis, some strains of Mycobacterium...     

Serological and molecular heterogeneity among Yersinia ruckeri strains isolated from farmed Atlantic salmon Salmo salar in Chile

We investigated 11 strains of Yersinia ruckeri, the causative agent of enteric redmouth disease (ERM), that had been isolated from Atlantic salmon Salmo salar L. farmed in Chile and previously vaccinated against ERM. Phylogenetic analysis of the 16S rRNA gene sequences confirmed the identification of the salmon isolates as Y. ruckeri. A comparative analysis of the biochemical characteristics was made by means of traditional and commercial miniaturised methods. All studied isolates were motile and Tween 80 positive, and were identified as biotype 1. In addition, drug susceptibility tests determined high sensitivity to sulphamethoxazole/trimethroprim, oxytetracycline, ampicillin and enrofloxacin in all isolates. Serological assays showed the presence of O1a, O1b and O2b serotypes, with a predominance of the O1b serotype in 9 strains. Analysis of the lipopolysaccharide profiles and the correspondent immunoblot confirmed these results. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) of the outer membrane proteins revealed that all Chilean strains had profiles with a molecular weight range between 34 and 55 kDa, with 3 distinct groups based on differences in the major bands. Genotyping analyses by enterobacterial repetitive intergenic consensus (ERIC-) and repetitive extragenic palindromic (REP-)PCR techniques clearly indicated intraspecific genetic diversity among Chilean Y. ruckeri strains.     

Disaccharide analysis of chondroitin and heparin from farmed Atlantic salmon

The heparin disaccharides detected in farmed Atlantic salmon (Salmo salar) gills and intestines have, with one exception, been reported in porcine heparin. The relative amounts of disaccharides appear to be very different in the two species. Two chondroitin disaccharides with a proposed essential role in the zebrafish (Danio rerio) development and differentiation are detected in farmed Atlantic salmon. In addition, most of the chondroitin/dermatan sulfate and heparin disaccharides detected here have been reported in zebrafish, in support of the claims of the heparin presence in fish. The same chondroitin/dermatan disaccharides were detected in the bones of bony fishes. The rare disaccharide UA2S-GalNAc that was found in trace amounts in all 5 bony fishes was found in relative high amounts in gills and in significant amounts in intestines. The rare heparin disaccharide UA2S-GlcN was in relative highest amounts both in gills and intestines. In context with our previous reports, this communication suggests that glycosaminoglycans in farmed Atlantic salmon heparin need further studies in order to clarify structure and function.     

Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon

Farmed Atlantic salmon (Salmo salar) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome‐wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNPs in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage disequilibrium (LD) and imputation accuracy. Genetic diversity in Tasmanian Atlantic salmon was lower than observed within European populations when compared using four diversity metrics. The distribution of allele frequencies also showed a clear difference, with the Tasmanian animals carrying an excess of low minor allele frequency variants. The strength of observed LD was high at short distances (<25 kb) and remained above background for marker pairs separated by large chromosomal distances (hundreds of kb), in sharp contrast to the European Atlantic salmon tested. Genotypes were used to evaluate the accuracy of imputation from low density (0.5 to 5 K) up to increased density SNP sets (78 K). This revealed high imputation accuracies (0.89–0.97), suggesting that the use of low density SNP sets will be a successful approach for genomic prediction in this population. The long‐range LD, comparatively low genetic diversity and high imputation accuracy in Tasmanian salmon is consistent with known aspects of their population history, which involved a small founding population and an absence of subsequent introgression. The findings of this study represent an important first step towards the design of methods to apply genomics in this economically important population.     

Molecular cloning and sequencing of coho salmon growth hormone cDNA

A cDNA library was constructed using mRNA isolated from coho salmon pituitaries. By employing rainbow trout growth hormone cDNA as a probe, the coho salmon cDNA was isolated and the complete nucleotide (nt) sequence determined. The coding region contains 630 nt while the 5'- and 3'-untranslated regions are 64 and 489 nt in length, respectively. Comparison of the noncoding regions of coho and chum salmon cDNAs reveal identity at the 5' end but significant variation in the 3' end. Chum salmon and rainbow trout have identical amino acid (aa) sequences, but coho salmon growth hormone has a sequence that differs by 6 of the 188 predicted aa. Since salmonids are tetraploid, this difference may be the result of either divergence of the same growth hormone locus or of variation between different loci. Comparisons of the cDNA restriction maps of these three fish species suggest the former possibility.     

Sperm traits in farmed and wild Atlantic salmon Salmo salar

Differences in sperm metabolism and morphology between wild and non‐local farmed Atlantic salmon Salmo salar were assessed by measuring metabolic enzyme activities and length of sperm flagella. No differences were observed between wild and farmed S. salar sperm with regards to cell counts or any of the biochemical variables assessed. Flagella of sperm cells were significantly longer in wild than farmed S. salar; however, this did not result in higher energy levels or different fertilization rates.     

First detection, isolation and molecular characterization of infectious salmon anaemia virus associated with clinical disease in farmed Atlantic salmon (Salmo salar) in Chile

Background  

Several forms of progressive retinal atrophy (PRA) segregate in more than 100 breeds of dog with each PRA segregating in one or a few breeds. This breed specificity may be accounted for by founder effects and genetic drift, which have reduced the genetic heterogeneity of each breed, thereby facilitating the identification of causal mutations. We report here a new form of PRA segregating in the Border Collie breed. The clinical signs, including the loss of night vision and a progressive loss of day vision, resulting in complete blindness, occur at the age of three to four years and may be detected earlier through systematic ocular fundus examination and electroretinography (ERG).     

Plasma ammonia and urea levels in Atlantic salmon farmed in sea water

Plasma ammonia and urea levels were measured in feeding Atlantic salmon Salmo salar L. reared in two different commercial Norwegian sea farms. A very large individual variation of the plasma ammonia and urea levels in addition to the large influence of several factors suggest that it may be difficult to use these parameters in diagnostic work on fish.     

Movements and dispersal of farmed Atlantic salmon following a simulated-escape event

One of the major challenges for understanding the ecological impact of escaped farmed Atlantic salmon (Salmo salar L.) is predicting their dispersal patterns after an escape event. Here, we quantify the behaviour of escaped farmed salmon using a simulated-escape experiment within a Norwegian fjord system. Thirty-seven individuals were tagged with acoustic transmitters and their spatial distribution, horizontal movements and diving behaviour was monitored throughout the fjord and accompanying rivers using 29 acoustic receivers. A rapid movement away from the release site occurred. There was no movement into the rivers feeding the fjord and there was no preference for residence at the fish farms: nearly a third of the individuals had a final detection in the outer part of the fjord and no detections occurred from approximately 2 months after release. As it is unlikely that all fish died or remained undetected within the study area it is reasonable to assume that a substantial proportion of the fish moved out of the fjord system. If a recapture program is not implemented immediately after an escape event, we recommend spreading potential recapture efforts over a relatively large area.     

Yeast genome sequencing: the power of comparative genomics

For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide the background to use more yeast species in model studies, to combat pathogens and for efficient manipulation of industrial strains.     

Polyclonal hypergammaglobulinemia and autoantibody production induced by vaccination in farmed Atlantic salmon

The introduction of oil-adjuvanted vaccines in salmon aquaculture made large-scale production feasible by reducing the impact of infections. Vaccines given intraperitoneally (ip) contain oil adjuvant such as mineral oil. However, in rodents, a single ip injection of adjuvant hydrocarbon oil induces lupus-like systemic autoimmune syndrome. We have recently reported that autoimmune disease in farmed salmon, characterized by production of various autoantibodies, immune complex glomerulonephritis, liver thrombosis, and spinal deformity, are previously unrecognized side effects of vaccination. In the present study, we examined whether vaccination-induced autoantibody production in farmed Atlantic salmon is a mere result of polyclonal B-cell activation. Sera were collected from 205 vaccinated and unvaccinated Atlantic salmon (experimental, 7 farms) and wild salmon. Total IgM levels and autoantibodies to salmon blood cell (SBC) extract in sera were measured by ELISA and the relationship between hypergammaglobulinemia and autoantibody production was analyzed. Comparison of endpoint titers vs levels/units using a single dilution of sera in detection of autoantibodies to SBC showed near perfect correlation, justifying the use of the latter for screening. Both total IgM and anti-SBC antibodies are increased in vaccinated salmon compared with unvaccinated controls, however, they do not always correlate well when compared between groups or between individuals, suggesting the involvement of antigen-specific mechanisms in the production of anti-SBC autoantibodies. The primary considerations of successful vaccine for aquaculture are cost-effectiveness and safety. Vaccination-induced autoimmunity in farmed Atlantic salmon may have consequences on future vaccine development and salmon farming strategy. Evaluation for polyclonal hypergamamglobulinemia and autoimmunity should be included as an important trait when vaccine efficacy and safety are evaluated in future.     

Occupancy dynamics of escaped farmed Atlantic salmon in Canadian Pacific coastal salmon streams: implications for sustained invasions

Farmed non-native Atlantic salmon (Salmo salar) is the largest agriculture export product of British Columbia, Canada. Chronic low-volume escapes of salmon from farms into Pacific waters (“leakage”) are typically undetectable (Britton et al. 2011). Analysis of escape-reporting from farmers indicates that reports greatly underestimate the true number of Atlantic salmon inadvertently released from open-net pen rearing sites (Morton and Volpe 2002). To quantify the spatial extent of escaped Atlantic salmon in Canadian Pacific rivers, we systematically snorkel-surveyed 41 known Pacific salmon (Oncorhynchus spp.)-supporting rivers and creeks on Vancouver Island over a span of 3 years. We estimated and accounted for imperfect detections using multi-season occupancy models. We detected Atlantic salmon in 36.6 % of surveyed rivers. After accounting for imperfect detection, occupancy models estimated that over half of surveyed streams across the study area contained Atlantic salmon, and that 97 % of streams with high native salmon diversity were occupied by Atlantic salmon. Even in intensive snorkel surveys, Atlantic salmon are detected in occupied streams only 2/3 the time, suggesting abundance and distribution of non-native salmon is greater than indicated by the only existing data. Further, Atlantic salmon are more likely to occupy streams with high native Pacific salmon diversity—and more likely to maintain occupancy across years—potentially increasing competitive pressure on native salmonids. Understanding local biotic and abiotic predictors of Atlantic salmon occupancy, stream colonization, and local extinction requires more data; the same is true for the effects of escaped Atlantic salmon on local salmon diversity and sustainability. These data for the first time show that Atlantic salmon occupy Pacific coastal rivers for multiple years. The impact of Atlantic salmon occupancy in British Columbia rivers must be factored into policy decisions regarding the future of salmon farming in the provincial waters.     

An epidemiological study of cataracts in seawater farmed Atlantic salmon Salmo salar

Cataracts in farmed Atlantic salmon have been known for many years, but the aetiology and importance of the disease have not been clarified. A cross-sectional field study of 51 cages of Atlantic salmon at 49 randomly selected sea sites was performed during the summer of 1998. The target population was spring and autumn entry groups of the 1997 generation salmon. Approximately 15 fish from each cage, altogether 777 fish, were autopsied by the same person. Each eye of the fish was scored for cataracts on a scale from 0 to 4 using an otoscope lamp with magnification. The weight and length of each fish were measured. The prevalence of cataracts was 83 % and 79% in spring entry groups and autumn entry groups, respectively. The overall mean cataract index (mean score of both eyes) was 1.23, being significantly higher in the spring entry groups (1.36) than the autumn entry groups (0.85). The final results in the spring entry groups showed that the fish groups with higher weight at sea transfer also had a higher cataract index at inspection. The risk of development of cataracts varied significantly among the offspring from the 5 strains represented in the study. Fish from sites located in 2 counties in the southern part of Norway had a significantly higher cataract index than fish farmed in the northernmost county in the study. For the autumn entry groups none of the explanatory variables was significant. In the spring entry groups a significant negative relationship was observed between the cataract score and the weight of the fish at the time of inspection (Pearson's r = -0.17), while the corresponding correlation for the autumn released groups was r = -0.10. Among the spring entry groups the average weight of the fish with the highest cataract score was estimated to about a third of the weight of the fish with no visible cataracts.     

Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip

Genetic interactions between farmed and wild conspecifics are of special concern in fisheries where large numbers of domesticated individuals are released into the wild. In the Atlantic salmon (Salmo salar), selective breeding since the 1970's has resulted in rapid genetic changes in commercially important traits, such as a doubling of the growth rate. Each year, farmed salmon escape from net pens, enter rivers, and interbreed with wild salmon. Field experiments demonstrate that genetic introgression may weaken the viability of recipient populations. However, due to the lack of diagnostic genetic markers, little is known about actual rates of gene flow from farmed to wild populations. Here we present a panel of 60 single nucleotide polymorphisms (SNPs) that collectively are diagnostic in identifying individual salmon as being farmed or wild, regardless of their populations of origin. These were sourced from a pool of 7000 SNPs comparing historical wild and farmed salmon populations, and were distributed on all but two of the 29 chromosomes. We suggest that the generic differences between farmed and wild salmon at these SNPs have arisen due to domestication. The identified panel of SNPs will permit quantification of gene flow from farmed to wild salmon populations, elucidating one of the most controversial potential impacts of aquaculture. With increasing global interest in aquaculture and increasing pressure on wild populations, results from our study have implications for a wide range of species.