The Atlantic salmon whole blood transcriptome and how it relates to major locus maturation genotypes and other tissues
The Atlantic salmon (Salmo salar) is important to many ecosystems and local economies and has therefore become the focus of a broad range of research questions that have benefited from the availability of high-quality genomic resources. Albeit gene expression studies have been extensive for this spe...
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| Format: | Article in Journal/Newspaper |
| Language: | unknown |
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figshare
2020
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| Online Access: | https://dx.doi.org/10.6084/m9.figshare.c.5046893 https://figshare.com/collections/The_Atlantic_salmon_whole_blood_transcriptome_and_how_it_relates_to_major_locus_maturation_genotypes_and_other_tissues/5046893 |
| Summary: | The Atlantic salmon (Salmo salar) is important to many ecosystems and local economies and has therefore become the focus of a broad range of research questions that have benefited from the availability of high-quality genomic resources. Albeit gene expression studies have been extensive for this species, the transcriptome information for Atlantic salmon whole blood has been lacking. A transcriptome of Atlantic salmon blood would be a valuable resource for future studies, especially those wishing to take non-lethal samples. Here, we report a whole blood transcriptome for Atlantic salmon constructed from twelve 8-month old salmon parr using RNA-seq. We identify transcriptomic proxies for the genotype at the major maturation timing locus vestigial-like 3 (vgll3). Differentially expressed genes between the early and late maturing genotypes showed overrepresented Gene Ontology (GO) terms with the strongest result linked to 13 ribosomal subunit genes. To assess how the whole blood gene expression profile relates to other tissues, we compare the blood transcriptome to the reference transcriptome of fourteen other tissue types using both a common PCA method and a novel method. The novel method compares transcriptomes when gene expression is visualised as a layer using thin-plate spline smoothers. Both methods found similar patterns with the blood transcriptome being quite unique compared to the transcription profiles of other tissues. Appendix A. Supplementary data frames required to replicate analyses described in supplementary R code in Appendix B. Appendix B. Supplementary R code in R markdown format. The analyses conducted in R include the DEGs analyses, tissue comparisons and all figures and tables. Appendix C. Supplementary Figures (S1-S4) and tables (S1-S2), also includes a description of Appendix A contents |
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