Open Access Highly Accessed Research article

Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs

Walter Salzburger12, Susan CP Renn3, Dirk Steinke14, Ingo Braasch15, Hans A Hofmann6 and Axel Meyer1*

Author Affiliations

1 Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78467 Konstanz, Germany

2 Zoological Institute, University of Basel, 4051, Switzerland

3 Department of Biology, Reed College, Portland, Oregon 97202, USA

4 Guelph Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario N1G 2W1, Canada

5 Physiological Chemistry I, Biozentrum, University of Würzburg, 97074 Würzburg, Germany

6 Section of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA

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BMC Genomics 2008, 9:96  doi:10.1186/1471-2164-9-96

Published: 25 February 2008

Abstract

Background

The cichlid fishes in general, and the exceptionally diverse East African haplochromine cichlids in particular, are famous examples of adaptive radiation and explosive speciation. Here we report the collection and annotation of more than 12,000 expressed sequence tags (ESTs) generated from three different cDNA libraries obtained from the East African haplochromine cichlid species Astatotilapia burtoni and Metriaclima zebra.

Results

We first annotated more than 12,000 newly generated cichlid ESTs using the Gene Ontology classification system. For evolutionary analyses, we combined these ESTs with all available sequence data for haplochromine cichlids, which resulted in a total of more than 45,000 ESTs. The ESTs represent a broad range of molecular functions and biological processes. We compared the haplochromine ESTs to sequence data from those available for other fish model systems such as pufferfish (Takifugu rubripes and Tetraodon nigroviridis), trout, and zebrafish. We characterized genes that show a faster or slower rate of base substitutions in haplochromine cichlids compared to other fish species, as this is indicative of a relaxed or reinforced selection regime. Four of these genes showed the signature of positive selection as revealed by calculating Ka/Ks ratios.

Conclusion

About 22% of the surveyed ESTs were found to have cichlid specific rate differences suggesting that these genes might play a role in lineage specific characteristics of cichlids. We also conclude that the four genes with a Ka/Ks ratio greater than one appear as good candidate genes for further work on the genetic basis of evolutionary success of haplochromine cichlid fishes.