Thermal stress and predation risk have profound effects on rocky shore organisms, triggering changes in their feeding behaviour, morphology and metabolism. Studies of thermal stress have shown that underpinning such changes in several intertidal species are specific shifts in gene and protein expression (e.g. upregulation of heat-shock proteins). But relatively few studies have examined genetic responses to predation risk. Here, we use next-generation RNA sequencing (RNA-seq) to examine the transcriptomic (mRNA) response of the snail Nucella lapillus to thermal stress and predation risk. We found that like other intertidal species, N. lapillus displays a pronounced genetic response to thermal stress by upregulating many heat-shock proteins and other molecular chaperones. In contrast, the presence of a crab predator (Carcinus maenas) triggered few significant changes in gene expression in our experiment, and this response showed no significant overlap with the snail's response to thermal stress. These different gene expression profiles suggest that thermal stress and predation risk could pose distinct and potentially additive challenges for N. lapillus and that genetic responses to biotic stresses such as predation risk might be more complex and less uniform across species than genetic responses to abiotic stresses such as thermal stress.
Raw Read Count Expression Data for ND Chu et al 2014
Total raw read count expression data from Nucella lapillus from the accompanying publication. This file was created by eXpress (http://bio.math.berkeley.edu/eXpress/) for analysis in DEseq2. The sample names are as in the publication. Each row represents a transcript, as assembled in Trinity (see publication for transcriptome assembly accession; http://trinityrnaseq.sourceforge.net/). Experimental snails were collected from near Nahant, Massachusetts, USA.
NChuetal2014ReadCountTable.txt
Express Results File AC_006
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample AC_006, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_006results.xprs
Express Parameters File AC_006
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample AC_006, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_006params.xprs
Express Results File AC_008
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample AC_006, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_008results.xprs
Express Parameters File AC_008
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample AC_008, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_008params.xprs
Express Results File AC_43
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample AC_43, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_43results.xprs
Express Parameters File AC_43
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample AC_43, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_43params.xprs
Express Results File AC_42
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample AC_42, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_42results.xprs
Express Parameters File AC_42
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample AC_42, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
AC_42params.xprs
Express Results File ANC_003
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample ANC_003, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
ANC_003results.xprs
Express Parameters File ANC_003
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample ANC_003, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
ANC_003params.xprs
Express Results File ANC_34
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample ANC_34, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
ANC_34results.xprs
Express Parameters File ANC_34
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample ANC_34, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
ANC_34params.xprs
Express Results File ANC_41
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample ANC_41, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
ANC_41results.xprs
Express Parameters File ANC_41
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample ANC_41, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
ANC_41params.xprs
Express Results File HNC_31
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample HNC_31, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
HNC_31results.xprs
Express Parameters File HNC_31
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample HNC_31, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
HNC_31params.xprs
Express Results File HNC_37
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) results file for sample HNC_37, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
HNC_37results.xprs
Express Parameters File HNC_37
Raw eXpress (http://bio.math.berkeley.edu/eXpress/) parameters file for sample HNC_37, named as in Chu et al. 2014. Gene expression data is from Nucella lapillus collected near Nahant, Massachusetts, USA.
HNC_37params.xprs