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ABSTRACT: Endangered wild salmon infected by newly discovered viruses

PROVIDER: PRJNA547678 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR9216243_1.fastq.gz	Fastqsanger.gz
	SRR9216243_2.fastq.gz	Fastqsanger.gz
	SRR9216244_1.fastq.gz	Fastqsanger.gz
	SRR9216244_2.fastq.gz	Fastqsanger.gz

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Project description:Escaped domesticated individuals can introduce disadvantageous traits into wild populations due to both adaptive differences between population ancestors and human-induced changes during domestication. In contrast to their domesticated counterparts, some endangered wild Atlantic salmon populations encounter during their marine stage large amounts of suspended sediments, which may act as a selective agent. We used microarrays to elucidate quantitative transcriptional differences between a domesticated salmon strain, a wild population and their first-generation hybrids during their marine life stage, to describe transcriptional responses to natural suspended sediments, and to test for adaptive genetic variation in plasticity relating to a history of natural exposure or nonexposure to suspended sediments. We identified 67 genes differing in transcription level among salmon groups. Among these genes, processes related to energy metabolism and ion homoeostasis were over-represented, while genes contributing to immunity and actin-/myosin-related processes were also involved in strain differentiation. DomesticM-bM-^@M-^Swild hybrids exhibited intermediate transcription patterns relative to their parents for two-thirds of all genes that differed between their parents; however, genes deviating from additivity tended to have similar levels to those expressed by the wild parent. Sediments induced increases in transcription levels of eight genes, some of which are known to contribute to external or intracellular damage mitigation. Although genetic variation in plasticity did not differ significantly between groups after correcting for multiple comparisons, two genes (metallothionein and glutathione reductase) tended to be more plastic in response to suspended sediments in wild and hybrid salmon, and merit further examination as candidate genes under natural selection. Salmon of three genotypes (strains: 1. wild (Stewiacke River salmon), 2. domesticated (Saint John River salmon), and 3. first generation hybrids between the two strains, were exposed to two environments (treatment: 1. suspended sediments, 2. control: clear water), using eight biological replicates (individuals) of each of the six experimental groups, summing up to 48 individuals, each individual has two technical replicates , each technical replicate has been labelled with a different dye, each technical replicate appears on a different array, dye swaps are equilibrated for arrays that combine individuals from different genotypes and for arrays that combine individuals from the same genotype but different environments. Technical replicates of individuals always appear once on arrays that compare between environments and once on arrays that compare among genotypes. In total there are 48 arrays.

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