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Comparative Study
. 2008 Feb 25;9:96.
doi: 10.1186/1471-2164-9-96.

Annotation of Expressed Sequence Tags for the East African Cichlid Fish Astatotilapia Burtoni and Evolutionary Analyses of Cichlid ORFs

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Free PMC article
Comparative Study

Annotation of Expressed Sequence Tags for the East African Cichlid Fish Astatotilapia Burtoni and Evolutionary Analyses of Cichlid ORFs

Walter Salzburger et al. BMC Genomics. .
Free PMC article

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.

Figures

Figure 1
Figure 1
The proportion of assembled haplochromine cichlid sequences with and without BLAST matches compared to three databases (Takifugu rubripes, Danio rerio, and Oncorhynchus mykiss). The pie charts indicate the relative number of BLAST hits (blue) versus the percentage fraction, for which no BLAST hit was retrieved (red) for three different e-values (< 10-50, < 10-15, and <10-5, respectively).
Figure 2
Figure 2
Ternary representation of relative distances of ORFs of three fish species compared to their human orthologs. (a) Haplochromine cichlid, Danio rerio, and Takifugu rubripes, (b) Danio rerio, Oncorhynchus mykiss, and Takifugu rubripes. Each dot represents a single ORF, the position of the dot within the ternary diagram indicates the relative distance of this ORF in each of the three fish species compared to the orthologous ORF in human. We were interested in identifying those ORFs that show a faster or slower rate of molecular evolution in the haplochromine cichlids.
Figure 3
Figure 3
Histogram of the abundance of amino acid sequence divergences of all five fish species (haplochromine cichlid, Danio rerio, Takifugu rubripes, Tetraodon nigroviridis, and Oncorhynchus mykiss) with respect to human genes. P-distances have been calculated for a set of 759 ORFs found in all five fish species and plotted in categories of 0.1.

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