RNA-Seq expression profiling coral larvae
Expression profiling responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure.
Although the elevated temperatures resulting from climate change present a clear threat to reef-building corals, the traits that might influence corals' fitness and survival during climate change remain poorly understood. Global gene expression profiling is a powerful hypothesis-forming tool that can help elucidate these traits.  We used a novel RNA-Seq approach to study stress responses and settlement in aposymbiotic larvae of the reef-building coral Acropora millepora.  This analysis revealed contrasting responses between short- (4 hr) and long-term (5 d) exposures to elevated temperatures.  Heat shock proteins were up-regulated only in the short-term treatment, and a group of genes associated with ion transport and metabolism (Ca2+, CO3-) were up-regulated only in the long-term treatment.  We also profiled responses to settlement cues using a natural cue (crustose coralline algae, CCA) and a synthetic neuropeptide (GLW-amide).  Both cues resulted in metamorphosis, and the differential expression of transcription factors with known developmental roles in pattern formation.  Larvae exposed to CCA displayed typical searching behavior and attachment prior to metamorphosis, while the neuropeptide induced immediate metamorphosis.  We identified a set of genes regulated by the natural cue but not the neuropeptide that might play a role in these subtle pre-metamorphic changes.  Validation of these expression profiles using qPCR revealed strong agreement between methods, confirming the quantitative accuracy of our RNA-Seq approach.  There was extensive variation in these responses across different larval families, suggesting genetic variation in these traits that might provide material for natural selection during the ongoing climate change.