Research article

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

Walter Salzburger^{* 1,2} , Susan CP Renn^{* 3} , Dirk Steinke^{* 1,4} , Ingo Braasch^1,5 , Hans A Hofmann⁶ and Axel Meyer¹

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

²Zoological Institute, University of Basel, 4051, Switzerland

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

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

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

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

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:96doi: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 K_a/K_s 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 K_a/K_s ratio greater than one appear as good candidate genes for further work on the genetic basis of evolutionary success of haplochromine cichlid fishes.