27 research outputs found
Ecological Transcriptomics of Lake-Type and Riverine Sockeye Salmon (Oncorhynchus nerka)
Get PDFBackground: There are a growing number of genomes sequenced with tentative functions assigned to a largeproportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment ofgene function, and the ecological context of gene function is lacking. This work addresses this shortcoming byinvestigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphologyand gene expression in natural juvenile sockeye populations related to river and lake habitats. Based on previouslydocumented divergent morphology, feeding strategy, and predation in association with these distinctenvironments, we expect that burst swimming is favored in riverine population and continuous swimming isfavored in lake-type population. In turn we predict that morphology and expressed genes promote burstswimming in riverine sockeye and continuous swimming in lake-type sockeye.Results: We found the riverine sockeye population had deep, robust bodies and lake-type had shallow,streamlined bodies. Gene expression patterns were measured using a 16K microarray, discovering 141 genes withsignificant differential expression. Overall, the identity and function of these genes was consistent with ourhypothesis. In addition, Gene Ontology (GO) enrichment analyses with a larger set of differentially expressed genesfound the “biosynthesis” category enriched for the riverine population and the “metabolism” category enriched forthe lake-type population.Conclusions: This study provides a framework for understanding sockeye life history from a transcriptomicperspective and a starting point for more extensive, targeted studies determining the ecological context of genes
Regulation and Expression of Sexual Differentiation Factors in Embryonic and Extragonadal Tissues of Atlantic salmon
Get PDFBackground: The products of cyp19, dax, foxl2, mis, sf1 and sox9 have each been associated with sex-determiningprocesses among vertebrates. We provide evidence for expression of these regulators very early in salmoniddevelopment and in tissues outside of the hypothalamic-pituitary-adrenal/gonadal (HPAG) axis. Although thefunction of these factors in sexual differentiation have been defined, their roles in early development before sexualfate decisions and in tissues beyond the brain or gonad are essentially unknown.Results: Bacterial artificial chromosomes containing salmon dax1 and dax2, foxl2b and mis were isolated and theregulatory regions that control their expression were characterized. Transposon integrations are implicated in theshaping of the dax and foxl2 loci. Splice variants for cyp19b1 and mis in both embryonic and adult tissues weredetected and characterized. We found that cyp19b1 transcripts are generated that contain 5’-untranslated regionsof different lengths due to cryptic splicing of the 3’-end of intron 1. We also demonstrate that salmon mistranscripts can encode prodomain products that present different C-termini and terminate before translation of theMIS hormone. Regulatory differences in the expression of two distinct aromatases cyp19a and cyp19b1 are exerted,despite transcription of their transactivators (ie; dax1, foxl2, sf1) occurring much earlier during embryonicdevelopment.Conclusions: We report the embryonic and extragonadal expression of dax, foxl2, mis and other differentiationfactors that indicate that they have functions that are more general and not restricted to steroidogenesis andgonadogenesis. Spliced cyp19b1 and mis transcripts are generated that may provide regulatory controls for tissueordevelopment-specific activities. Selection of cyp19b1 transcripts may be regulated by DAX-1, FOXL2 and SF-1complexes that bind motifs in intron 1, or by signals within exon 2 that recruit splicing factors, or both. Thepotential translation of proteins bearing only the N-terminal MIS prodomain may modulate the functions of otherTGF b family members in different tissues. The expression patterns of dax1 early in salmon embryogenesisimplicate its role as a lineage determination factor. Other roles for these factors during embryogenesis and outsidethe HPAG axis are discussed
Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2
Get PDF<p>Abstract</p> <p>Background</p> <p>Growth hormone (GH) is an important regulator of skeletal growth, as well as other adapted processes in salmonids. The GH gene (<it>gh</it>) in salmonids is represented by duplicated, non-allelic isoforms designated as <it>gh1 </it>and <it>gh2</it>. We have isolated and characterized <it>gh</it>-containing bacterial artificial chromosomes (BACs) of both Atlantic and Chinook salmon (<it>Salmo salar </it>and <it>Oncorhynchus tshawytscha</it>) in order to further elucidate our understanding of the conservation and regulation of these loci.</p> <p>Results</p> <p>BACs containing <it>gh1 </it>and <it>gh2 </it>from both Atlantic and Chinook salmon were assembled, annotated, and compared to each other in their coding, intronic, regulatory, and flanking regions. These BACs also contain the genes for skeletal muscle sodium channel oriented in the same direction. The sequences of the genes for interferon alpha-1, myosin alkali light chain and microtubule associated protein Tau were also identified, and found in opposite orientations relative to <it>gh1 </it>and <it>gh2</it>. Viability of each of these genes was examined by PCR. We show that transposon insertions have occurred differently in the promoters of <it>gh</it>, within and between each species. Other differences within the promoters and intronic and 3'-flanking regions of the four <it>gh </it>genes provide evidence that they have distinct regulatory modes and possibly act to function differently and/or during different times of salmonid development.</p> <p>Conclusion</p> <p>A core proximal promoter for transcription of both <it>gh1 </it>and <it>gh2 </it>is conserved between the two species of salmon. Nevertheless, transposon integration and regulatory element differences do exist between the promoters of <it>gh1 </it>and <it>gh2</it>. Additionally, organization of transposon families into the BACs containing <it>gh1 </it>and for the BACs containing <it>gh2</it>, are very similar within orthologous regions, but much less clear conservation is apparent in comparisons between the <it>gh1</it>- and <it>gh2</it>-containing paralogous BACs for the two fish species. This is consistent with the hypothesis that a burst of transposition activity occurred during the speciation events which led to Atlantic and Pacific salmon. The Chinook and other <it>Oncorhynchus </it>GH1s are strikingly different in comparison to the other GHs and this change is not apparent in the surrounding non-coding sequences.</p
A Salmonid EST Genomic Study: Genes, Duplications, Phylogeny and Microarrays
Get PDFBackground: Salmonids are of interest because of their relatively recent genome duplication, and their extensive usein wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different speciesprovide valuable genomic information for one of the most widely studied groups of fish.Results: 298,304 expressed sequence tags (ESTs) from Atlantic salmon (69% of the total), 11,664 chinook, 10,813sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in thisstudy and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmonclones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, genepredictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbowtrout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4,92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchusand Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae.Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of theavailable EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-specieshybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species.Conclusion: An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon,Atlantic salmon and charr are 94–96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is consistent withan ancestral salmonid genome duplication hypothesis. Genome resources, including a new 32 K microarray, providevaluable new tools to study salmonids
