Researchers use RNA-Seq to understand bleaching of caribbean reef-building corals

Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene expression studies have revealed mechanisms by which the coral immune system responds to stress and disease.

The present investigation expands bioinformatic data available to study coral molecular physiology through the assembly and annotation of a reference transcriptome of the Caribbean reef-building coral, Orbicella faveolata. A team led by researchers from Washington University in St. Louis collected samples during a warm water thermal anomaly, coral bleaching event and Caribbean yellow band disease outbreak in 2010 in Puerto Rico.

Representative images of colonies sampled in the present study.


(A) Asymptomatic. (B) Caribbean yellow band-diseased. (C) Partially bleached colonies. (D) Completely bleached colonies. (E) Caribbean yellow band-diseased and bleached. Photos by E. Weil.

Multiplex sequencing of RNA on the Illumina GAIIx platform and de novo transcriptome assembly by Trinity produced 70,745,177 raw short-sequence reads and 32,463 O. faveolata transcripts, respectively. The reference transcriptome was annotated with gene ontologies, mapped to KEGG pathways, and a predicted proteome of 20,488 sequences was generated. Protein families and signaling pathways that are essential in the regulation of innate immunity across Phyla were investigated in-depth. The results were used to develop models of evolutionarily conserved Wnt, Notch, Rig-like receptor, Nod-like receptor, and Dicer signaling.

Phylogenetic analysis of Wnt-like protein sequences in O. faveolata transcriptome


Predicted protein sequences from N. vectensis (Nvec), O. faveolata (Ofav), A. pallida (Apall), A. digitifera (Adig), and A. millepora were used for maximum likelihood phylogeny estimation with 100 bootstraps.

O. faveolata is a coral species that has been studied widely under climate-driven stress and disease, and the present investigation provides new data on the genes that putatively regulate its immune system.

Anderson DA, Walz ME, Weil E, Tonellato P, Smith MC. (2016) RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity. PeerJ [epub ahead of print]. [article]

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