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Activin pathway gene expression atlas in rainbow trout

ABSTRACT: The genome of many plant and animal species are heavily influenced by ancestral whole genome duplication (WGD) events. These events transform the regulation and function of gene networks, yet the evolutionary forces at work on duplicated genomes are not fully understood. Genes involved in cell surface signaling pathways are commonly retained following WGD. To understand the mechanisms driving functional evolution of duplicated cell signaling pathways, we performed the activin receptor signaling pathway in rainbow trout (RBT). Rainbow trout are a model salmonid species that exhibit a duplicated genome as a result of an ancestral WGD that occurred in all teleost fish, and a second more recent WGD found in salmonid fishes. This makes RBT a powerful system for studying ohnolog evolution in a single species. We observed that regulation of the duplicated activin receptor signaling pathway is commonly driven by tissue-specific expression of inhibitors and ligands along with the subfunctionalization of ligand ohnologs. Evidence suggests that for inhibitors and R-Smad signaling molecules, there is ongoing pressure to establish a single copy state which may be driven, in part, by regulatory suppression of select ohnologs. The core transmembrane receptors and Co-Smad signaling cascade members are high duplicated yet exhibit contrasting expression dynamics where receptors tend to share expression across tissues while dominance of a single ohnolog is common for the Smad4, Co-Smad gene family. Our findings provide support for a generalized model where gene function and gene dosage have a complementary role in ohnolog evolution following WGD.

ORGANISM(S): Oncorhynchus mykiss

PROVIDER: GSE224617 | GEO | 2023/02/07

REPOSITORIES: GEO

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Project description:Whirling disease, caused by the pathogen Myxobolus cerebralis, afflicts several salmonid species. Rainbow trout are particularly susceptible and suffer high mortality rates. The disease is persistent and spreading in hatcheries and natural waters of several countries, including the U.S., and the economic losses associated with whirling disease have been extremely large. In this study, gene expression profiling was conducted for resistant and susceptible rainbow trout strains following pathogen exposure with the primary objective of identifying specific genes associated with whirling disease resistance. Several genes were significantly up-regulated in skin following pathogen exposure for both the resistant Hofer and susceptible Trout Lodge rainbow trout strains. For both strains, response to infection appears to be associated with the interferon system. Metallothionein is differentially expressed between the resistant and susceptible strains and is a good candidate for future studies due to its diverse functional roles in inflammation and immune response. The present study has provided the first examination into the genetic basis underlying rainbow trout’s immune response and resistance to the whirling disease pathogen. The identified genes have allowed us to gain initial insight into the molecular mechanisms associated with a salmonid host’s immune response and resistance to whirling disease infection. Keywords: Disease state comparison. 1st comparison: exposed vs control. 2nd comparison: resistant vs susceptible strains Resistant (Hofer) and susceptible (Trout Lodge) rainbow trout strains were exposed to 2,000 triactinomyxons (whirling disease pathogen) per fish. Unexposed controls for each strain were treated identically to exposed other than their lack of pathogen exposure. After twenty-four hours, caudal fin tissue was collected for RNA extraction. Amplified RNA was competitively hybridized (exposed versus control) for each strain. Four biological replicates were used for each experimental condition and a balanced block design was incorporated.

Project description:We have constructed a rainbow trout high-density oligonucleotide microarray by using all the available tentative consensus (TC) sequences from the Rainbow Trout Gene Index database (The Computational Biology and Functional Genomics Lab., Dana Farber Cancer Institute and Harvard School of Public Health). The Rainbow Trout Gene Index integrates research data from all available international rainbow trout genomic research projects. The newly designed microarray incorporates 37,394 unique transcript-specific oligonucleotide probes, 60-mer long each. The microarray was printed according to our design by Agilent Technologies using the 4 X 44-design format and contains 1417 Agilent control spots. The performance of the new microarray platform was evaluated by analyzing gene expression associated with the rainbow trout vitellogenesis-induced muscle atrophy. These chips can be ordered from Agilent using design number 016320. This microarray is anticipated to open new avenues of research that will aid in the development of novel strategies to enhance growth efficiency and quality in salmonid species. Keywords: Development of an oligo-array for rainbow trout The performance of the new microarray platform was evaluated by analyzing transcriptome response associated with the rainbow trout vitellogenesis-induced muscle atrophy. Severe muscle deterioration accompanies the physiological responses of the energetic demands of the rainbow trout spawning/vitellogenesis. Atrophying muscle of fertile fish had 11% less extractable muscle (g/bw) and 11% less protein content compared to non-atrophying muscle of sterile fish (p<0.01). The rainbow trout was used to profile changes in gene expression of atrophying muscles. Gene expression levels were determined by comparing the amount of mRNA transcript present in the experimental sample (fertile fish) to the control (sterile fish). RNAs isolated from each experimental fish were run on separate microarrays in independent experiments, with no pooling. A total of 8 fish were used in the microarray experiments (4 replicates x 2 groups). Fluorophors (Cy3 and Cy5) were randomly assigned to RNA from each of the atrophying and nonatrophying muscles to limit the dye effect.

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Activin pathway gene expression atlas in rainbow trout

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