Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure

Mol Ecol. 2011 Sep;20(17):3599-616. doi: 10.1111/j.1365-294X.2011.05205.x. Epub 2011 Jul 29.


Elevated temperatures resulting from climate change pose a clear threat to reef-building corals; however, the traits that might influence corals' survival and dispersal during climate change remain poorly understood. Global gene expression profiling is a powerful hypothesis-forming tool that can help elucidate these traits. Here, we applied a novel RNA-Seq protocol to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef-building coral Acropora millepora. This analysis of a single full-sibling family revealed contrasting responses between short- (4-h) and long-term (5-day) exposures to elevated temperatures. Heat shock proteins were up-regulated only in the short-term treatment, while the long-term treatment induced the down-regulation of ribosomal proteins and up-regulation of genes associated with ion transport and metabolism (Ca(2+) and CO(3)(2-)). 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, accompanied by differential expression of genes with known developmental roles. Some genes were regulated only by the natural cue, which may correspond to the recruitment-associated behaviour and morphology changes that precede metamorphosis under CCA treatment, but are bypassed under GLW-amide treatment. Validation of these expression profiles using qPCR confirmed the quantitative accuracy of our RNA-Seq approach. Importantly, qPCR analysis of different larval families revealed extensive variation in these responses depending on genetic background, including qualitative differences (i.e. up-regulation in one family and down-regulation in another). Future studies of gene expression in corals will have to address this genetic variation, which could have important adaptive consequences for corals during global climate change.

MeSH terms

  • Animals
  • Anthozoa / genetics*
  • Anthozoa / metabolism
  • Climate Change*
  • Down-Regulation
  • Gene Expression Profiling / methods*
  • Genetic Variation
  • Heat-Shock Proteins / genetics
  • Heat-Shock Proteins / metabolism
  • Hot Temperature
  • Larva / genetics*
  • Larva / metabolism
  • Metamorphosis, Biological
  • Polymerase Chain Reaction
  • RNA / genetics
  • RNA / isolation & purification
  • Sequence Analysis, RNA / methods*
  • Temperature
  • Up-Regulation


  • Heat-Shock Proteins
  • RNA