320 research outputs found
Comparative Genomics Identifies Candidate Genes for Infectious Salmon Anemia (ISA) Resistance in Atlantic Salmon (Salmo salar)
Infectious salmon anemia (ISA) has been described as the hoof and mouth disease of salmon farming. ISA is caused by a lethal and highly communicable virus, which can have a major impact on salmon aquaculture, as demonstrated by an outbreak in Chile in 2007. A quantitative trait locus (QTL) for ISA resistance has been mapped to three microsatellite markers on linkage group (LG) 8 (Chr 15) on the Atlantic salmon genetic map. We identified bacterial artificial chromosome (BAC) clones and three fingerprint contigs from the Atlantic salmon physical map that contains these markers. We made use of the extensive BAC end sequence database to extend these contigs by chromosome walking and identified additional two markers in this region. The BAC end sequences were used to search for conserved synteny between this segment of LG8 and the fish genomes that have been sequenced. An examination of the genes in the syntenic segments of the tetraodon and medaka genomes identified candidates for association with ISA resistance in Atlantic salmon based on differential expression profiles from ISA challenges or on the putative biological functions of the proteins they encode. One gene in particular, HIV-EP2/MBP-2, caught our attention as it may influence the expression of several genes that have been implicated in the response to infection by infectious salmon anemia virus (ISAV). Therefore, we suggest that HIV-EP2/MBP-2 is a very strong candidate for the gene associated with the ISAV resistance QTL in Atlantic salmon and is worthy of further study
Bursts and Horizontal Evolution of DNA Transposons in the Speciation of Pseudotetraploid Salmonids
Background: Several genome duplications have occurred in the evolutionary history of teleostfish. In returning to a stable diploid state, the polyploid genome reorganized, and large portions arelost, while the fish lines evolved to numerous species. Large scale transposon movement has beenpostulated to play an important role in the genome reorganization process. We analyzed the DNAsequence of several large loci in Salmo salar and other species for the presence of DNA transposonfamilies.Results: We have identified bursts of activity of 14 families of DNA transposons (12 Tc1-like and2 piggyBac-like families, including 11 novel ones) in genome sequences of Salmo salar. Several ofthese families have similar sequences in a number of closely and distantly related fish, lamprey, andfrog species as well as in the parasite Schistosoma japonicum. Analysis of sequence similaritiesbetween copies within the families of these bursts demonstrates several waves of transpositionactivities coinciding with salmonid species divergence. Tc1-like families show a master gene-likecopying process, illustrated by extensive but short burst of copying activity, while the piggyBac-likefamilies show a more random copying pattern. Recent families may include copies with an openreading frame for an active transposase enzyme.Conclusion: We have identified defined bursts of transposon activity that make use of masterslaveand random mechanisms. The bursts occur well after hypothesized polyploidy events andcoincide with speciation events. Parasite-mediated lateral transfer of transposons are implicated
High gene expression of inflammatory markers and IL-17A correlates with severity of injection site reactions of Atlantic salmon vaccinated with oil-adjuvanted vaccines
<p>Abstract</p> <p>Background</p> <p>Two decades after the introduction of oil-based vaccines in the control of bacterial and viral diseases in farmed salmonids, the mechanisms of induced side effects manifested as intra-abdominal granulomas remain unresolved. Side effects have been associated with generation of auto-antibodies and autoimmunity but the underlying profile of inflammatory and immune response has not been characterized. This study was undertaken with the aim to elucidate the inflammatory and immune mechanisms of granuloma formation at gene expression level associated with high and low side effect (granuloma) indices.</p> <p>Groups of Atlantic salmon parr were injected intraperitoneally with oil-adjuvanted vaccines containing either high or low concentrations of <it>Aeromonas salmonicida </it>or <it>Moritella viscosa </it>antigens in order to induce polarized (severe and mild) granulomatous reactions. The established granulomatous reactions were confirmed by gross and histological methods at 3 months post vaccination when responses were known to have matured. The corresponding gene expression patterns in the head kidneys were profiled using salmonid cDNA microarrays followed by validation by real-time quantitative PCR (qPCR). qPCR was also used to examine the expression of additional genes known to be important in the adaptive immune response.</p> <p>Results</p> <p>Granulomatous lesions were observed in all vaccinated fish. The presence of severe granulomas was associated with a profile of up-regulation of innate immunity-related genes such as complement factors C1q and C6, mannose binding protein, lysozyme C, C-type lectin receptor, CD209, Cathepsin D, CD63, LECT-2, CC chemokine and metallothionein. In addition, TGF-β (p = 0.001), IL-17A (p = 0.007) and its receptor (IL-17AR) (p = 0.009) representing T<sub>H</sub>17 were significantly up-regulated in the group with severe granulomas as were arginase and IgM. None of the genes directly reflective of T<sub>H</sub>1 T cell lineage (IFN-γ, CD4) or T<sub>H</sub>2 (GATA-3) responses were differentially expressed.</p> <p>Conclusions</p> <p>Granulomatous reactions following vaccination with oil-based vaccines in Atlantic salmon have the profile of strong expression of genes related to innate immune responses. The expression of TGF-β, IL-17A and its receptor suggests an involvement of T<sub>H</sub>17 T cell lineage and is in conformity with strong infiltration of neutrophils and macrophages into inflamed areas. Arginase upregulation shows that macrophages in these reactions are alternatively activated, indicating also a T<sub>H</sub>2-profile. To what extent the expression of IL-17A and its receptor reflects an autoimmune vaccine-based reaction remains elusive but would be in conformity with previous observations of autoimmune reactions in salmon when vaccinated with oil-based vaccines.</p
A Linkage Map of the Atlantic Salmon (Salmo salar) Based on EST-Derived SNP mMarkers
Background: The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, thespecies displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with fullgenome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it isimportant to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundredsingle nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage mapscontaining SNP and microsatellite markers. We also investigated further the distribution of male and femalerecombination events across the genome, and estimated levels of LD between pairs of markers.Results: The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which weresuccessfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicatingthat there is little overlap between regions in which male and female crossovers occur. The female map is likely to haveclose to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regionswhere male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodalfashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence ofrecent admixture in the population, the population being a \u27synthetic\u27 breeding population with contributions fromseveral distinct rivers. Levels of r2 dropped to half its maximum value (above baseline) within 15 cM, and were higherthan 0.2 above baseline for unlinked markers (\u27useful LD\u27) at inter-marker distances less than 5 cM.Conclusion: The linkage map presented here is an important resource for genetic, comparative, and physical mappingof the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the malemap length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparentlysmall physical regions where male crossovers occur. \u27Useful LD\u27 was found at inter-marker distances less than 5 cM
A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers
<p>Abstract</p> <p>Background</p> <p>The Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers.</p> <p>Results</p> <p>The male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r<sup>2 </sup>increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r<sup>2 </sup>dropped to half its maximum value (above baseline) within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM.</p> <p>Conclusion</p> <p>The linkage map presented here is an important resource for genetic, comparative, and physical mapping of the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the male map length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparently small physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.</p
Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein
BACKGROUND: The mosaic sperm protein zonadhesin (ZAN) has been characterized in mammals and is implicated in species-specific egg-sperm binding interactions. The genomic structure and testes-specific expression of zonadhesin is known for many mammalian species. All zonadhesin genes characterized to date consist of meprin A5 antigen receptor tyrosine phosphatase mu (MAM) domains, mucin tandem repeats, and von Willebrand (VWD) adhesion domains. Here we investigate the genomic structure and expression of zonadhesin-like genes in three species of fish. RESULTS: The cDNA and corresponding genomic locus of a zonadhesin-like gene (zlg) in Atlantic salmon (Salmo salar) were sequenced. Zlg is similar in adhesion domain content to mammalian zonadhesin; however, the domain order is altered. Analysis of puffer fish (Takifugu rubripes) and zebrafish (Danio rerio) sequence data identified zonadhesin (zan) genes that share the same domain order, content, and a conserved syntenic relationship with mammalian zonadhesin. A zonadhesin-like gene in D. rerio was also identified. Unlike mammalian zonadhesin, D. rerio zan and S. salar zlg were expressed in the gut and not in the testes. CONCLUSION: We characterized likely orthologs of zonadhesin in both T. rubripes and D. rerio and uncovered zonadhesin-like genes in S. salar and D. rerio. Each of these genes contains MAM, mucin, and VWD domains. While these domains are associated with several proteins that show prominent gut expression, their combination is unique to zonadhesin and zonadhesin-like genes in vertebrates. The expression patterns of fish zonadhesin and zonadhesin-like genes suggest that the reproductive role of zonadhesin evolved later in the mammalian lineage
Regulatory Processes That Control Haploid Expression of Salmon Sperm mRNAs
Objective Various stages of mRNA processing are necessary for functionally important genes required during late-stage sperm differentiation. Protein–RNA complexes form that edit, stabilize, store, deliver, localize and regulate translation of sperm mRNAs. These regulatory processes are often directed by recognition sequence elements and the particular composition of the proteins associated with the mRNAs. Previous work has shown that the cAMP response element modulator (CREM), estrogen receptor-alpha (ERα) and forkhead box L2A (FOXL2A) proteins are present in late-stage salmon sperm. Here we investigate whether these and other regulatory proteins might control processing of mRNAs not expressed until the haploid stage of development. We also examine regulatory processes that prepare and present mRNAs that generate unique products essential for differentiating sperm (i.e. for flagellar assembly and function).
Results We provide evidence for potential sperm-specific recognition elements in 5′-untranslated regions (utrs) that may bind CREM, ERα, FOXL2A, Y-box and other proteins. We show that changes within the 5′-utrs and open reading frames of some sperm genes lead to distinct protein termini that may provide specific interfaces necessary for localization and function within the paternal gamete
Assignment of Atlantic salmon (Salmo salar) Linkage Groups to Specific Chromosomes: Conservation of Large Syntenic Blocks Corresponding to Whole Chromosome Arms in Rainbow Trout (Oncorhynchus mykiss)
Background: Most teleost species, especially freshwater groups such as the Esocidae which are theclosest relatives of salmonids, have a karyotype comprising 25 pairs of acrocentric chromosomes and 48–52 chromosome arms. After the common ancestor of salmonids underwent a whole genome duplication,its karyotype would have 100 chromosome arms, and this is reflected in the modal range of 96–104 seenin extant salmonids (e.g., rainbow trout). The Atlantic salmon is an exception among the salmonids as ithas 72–74 chromosome arms and its karyotype includes 12 pairs of large acrocentric chromosomes, whichappear to be the result of tandem fusions. The purpose of this study was to integrate the Atlantic salmon\u27slinkage map and karyotype and to compare the chromosome map with that of rainbow trout.Results: The Atlantic salmon genetic linkage groups were assigned to specific chromosomes in theEuropean subspecies using fluorescence in situ hybridization with BAC probes containing genetic markersmapped to each linkage group. The genetic linkage groups were larger for metacentric chromosomescompared to acrocentric chromosomes of similar size. Comparison of the Atlantic salmon chromosomemap with that of rainbow trout provides strong evidence for conservation of large syntenic blocks in thesespecies, corresponding to entire chromosome arms in the rainbow trout.Conclusion: It had been suggested that some of the large acrocentric chromosomes in Atlantic salmonare the result of tandem fusions, and that the small blocks of repetitive DNA in the middle of the armsrepresent the sites of chromosome fusions. The finding that the chromosomal regions on either side ofthe blocks of repetitive DNA within the larger acrocentric chromosomes correspond to different rainbowtrout chromosome arms provides support for this hypothesis
A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.)
<p>Abstract</p> <p>Background</p> <p>Atlantic salmon (<it>Salmo salar </it>L.) is an environmentally and economically important organism and its gene content is reasonably well characterized. From a transcriptional standpoint, it is important to characterize the changes in gene expression over the course of unperturbed early development, from fertilization through to the parr stage.</p> <p>Findings</p> <p><it>S. salar </it>samples were taken at 17 time points from 2 to 89 days post fertilization. Total RNA was extracted and cRNA was synthesized and hybridized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected to preliminary data analysis and submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE25938. <url>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938</url></p> <p>Conclusions</p> <p>Throughout the entire period of development, several thousand genes were found to be differentially regulated. This work represents the trancriptional characterization of a very large geneset that will be extremely valuable in further examination of the transcriptional changes in Atlantic salmon during the first few months of development. The expression profiles can help to annotate salmon genes in addition to being used as references against any number of experimental variables to which developing salmonids might be subjected.</p
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