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

Salzburger W, Renn SC, Steinke D, Braasch I, Hofmann HA, Meyer A - BMC Genomics (2008)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78467 Konstanz, Germany. walter.salzburger@unibas.ch

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.

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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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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.

Mentions: A histogram of the abundance of amino acid sequence divergences of all five fish species with respect to homologous human genes is depicted in Fig. 3. The p-distances appear normally distributed. With 0.211, cichlids show the lowest average distance followed by Oncorhynchus mykiss (0.216), Danio rerio (0.239), Takifugu rubripes (0.242), and Tetraodon nigroviridis (0.258). The average distance of all five fish species to Homo sapiens is 0.233. We also used the 482 redundant sequences that were found in all three large haplochromine cichlid EST datasets (P. chilotes and P. sp. "redtail sheller" [30]; Astatotilapia burtoni, this study) to calculate mean pairwise p-distances. Within these three cichlid species, we found a mean p-distance of 0.14 between A. burtoni and P. chilotes, 0.17 between A. burtoni and P. sp. "redtail sheller", and 0.08 between the two Lake Victoria species P. chilotes and P. sp. "redtail sheller".


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

Salzburger W, Renn SC, Steinke D, Braasch I, Hofmann HA, Meyer A - BMC Genomics (2008)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2279125&req=5

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.
Mentions: A histogram of the abundance of amino acid sequence divergences of all five fish species with respect to homologous human genes is depicted in Fig. 3. The p-distances appear normally distributed. With 0.211, cichlids show the lowest average distance followed by Oncorhynchus mykiss (0.216), Danio rerio (0.239), Takifugu rubripes (0.242), and Tetraodon nigroviridis (0.258). The average distance of all five fish species to Homo sapiens is 0.233. We also used the 482 redundant sequences that were found in all three large haplochromine cichlid EST datasets (P. chilotes and P. sp. "redtail sheller" [30]; Astatotilapia burtoni, this study) to calculate mean pairwise p-distances. Within these three cichlid species, we found a mean p-distance of 0.14 between A. burtoni and P. chilotes, 0.17 between A. burtoni and P. sp. "redtail sheller", and 0.08 between the two Lake Victoria species P. chilotes and P. sp. "redtail sheller".

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78467 Konstanz, Germany. walter.salzburger@unibas.ch

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.

Show MeSH
Related in: MedlinePlus