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Open Access Highly Accessed Research article

Evolutionary insights into scleractinian corals using comparative genomic hybridizations

Manuel Aranda1, Michael K DeSalvo2, Till Bayer1, Monica Medina3 and Christian R Voolstra1*

Author Affiliations

1 Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

2 Department of Anesthesia, UCSF School of Medicine, Mission Bay Campus, 600 16th St, Box 2200, San Francisco, CA 94158, USA

3 School of Natural Sciences, University of California Merced, 5200 North Lake Road, Merced, CA 95343, USA

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BMC Genomics 2012, 13:501  doi:10.1186/1471-2164-13-501

Published: 21 September 2012

Abstract

Background

Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization).

Results

Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate.

Conclusions

The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.

Keywords:
Coral reefs; Comparative genomic hybridization (CGH); Microarray; Mitochondria; Evolution