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Noble Crayfish Transcriptomics

Noble Crayfish Transcriptomics

Transcriptomics is the study of an organism´s or community’s transcribed genes through next-generation sequencing of steady-state RNA from the sample of interest. RNA-Seq is a quantitative examination of the transcriptional profile of an organism or community: what genes are active as well as relative levels of transcription. This allows an examination of the functional activity of a sample: identifying allele specific gene expression and finding novel transcripts. Comparison of RNA-Seq samples taken from different tissues or from the same source under different conditions allows examination of differential gene expression in response to a developmental program or to environmental changes. Frequently in transcriptome analysis, we want to identify groups of genes that show similar patterns of expression across multiple treatments or tissue types. These groups of genes, in sharing similar expression patterns, can then be hypothesized to function within common pathways in response to the treatment or tissue type in question.

In this project we use RNA-Seq data to infer the transcriptome of the noble crayfish (Astacus astacus) under varying crayfish plague infection states and with different strains of the crayfish plague agent (Aphanomyces astaci). We want to identify genes that are more or less expressed within the immune response cascade of noble crayfish under crayfish plague stress. With this noble approach we want to find the genetic reason why some noble crayfish seem to be resistant to some degree to the crayfish plague whereas other populations die on infection within a few days. Moreover, we want to investigate if the different strains of the crayfish plague agent, which show varying virulence and mortality rates, correspond to different expression patterns in the immune response of noble crayfish.




Cooperation partners:

Jenny Makkonen, Harri Kokko, University of Eastern Finland, Kuopio, Finland

Frank Lyko, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany