Transcriptomics

Dataset Information

2

Sockeye salmon (Oncorhynchus nerka) from Aniakchak National Monument and Preserve muscle transcriptome


ABSTRACT: This dataset was gene expression from natural sockeye salmon populations used to test the preservation of coexpression networks that were found in lake whitefish. Here is the abstract of the manuscript:Background : A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high throughput transcriptomic technologies. Functional analysis of co-expressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited. Results : Here we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of co-expressed genes in muscle and brain tissue of a lake whitefish backcross progeny. Modules were connected to gradients of known adaptive traits involved in the ecological speciation process between benthic and limnetic ecotypes. Key drivers, i.e. hub genes of functional modules related to reproduction, growth, and behavior were identified, and module preservation was assessed in natural populations. Using this approach, we identified modules of co-expressed genes involved in phenotypic divergence and their key drivers, and further characterized the underlying regulatory structure governing these complex traits. Conclusions : Functional analysis of transcriptomic data can significantly contribute to the understanding of the mechanisms underlying ecological speciation. Our findings point to BMP and Calcium signaling as common pathways involved in coordinated evolution of trophic behavior, trophic morphology (gill rakers), and reproduction. Results also point to housekeeping pathways implicating hemoglobins and constitutive stress response (HSP70) governing growth in lake whitefish. Here are 49 female sockeye salmon transcriptomes as measured by the 16k cGRASP microarray.

ORGANISM(S): Oncorhynchus nerka  

SUBMITTER: Scott A Pavey   Jérôme St-Cyr  Marie Filteau  Louis Bernatchez 

PROVIDER: E-GEOD-42985 | ArrayExpress | 2013-02-01

SECONDARY ACCESSION(S): GSE42985PRJNA184018

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka).

Pavey Scott A SA   Sutherland Ben J G BJ   Leong Jong J   Robb Adrienne A   von Schalburg Kris K   Hamon Troy R TR   Koop Ben F BF   Nielsen Jennifer L JL  

BMC ecology 20111202


BACKGROUND:There are a growing number of genomes sequenced with tentative functions assigned to a large proportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment of gene function, and the ecological context of gene function is lacking. This work addresses this shortcoming by investigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphology and gene expression in natural juvenile sockeye populations relate  ...[more]

Similar Datasets

2011-09-09 | E-GEOD-31214 | ArrayExpress
2008-09-01 | GSE12068 | GEO
2008-09-01 | E-GEOD-12068 | ArrayExpress
2008-09-01 | E-GEOD-11378 | ArrayExpress
2013-12-15 | E-GEOD-50054 | ArrayExpress
2010-05-16 | E-GEOD-19630 | ArrayExpress
2013-11-01 | E-GEOD-42555 | ArrayExpress
2013-11-01 | E-GEOD-42556 | ArrayExpress
2014-06-17 | E-GEOD-58537 | ArrayExpress
| PRJNA276907 | ENA