Limits...
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.

Show MeSH

Related in: MedlinePlus

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

License
getmorefigures.php?uid=PMC2279125&req=5

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.

Mentions: In order to identify sequences that evolve significantly more rapidly or more slowly in the haplochromine cichlid, we applied the triangle method implemented in EverEST [37] to calculate the p-distance for each of these 759 ORFs in all fish species relative to the human ortholog. There were 22 cases in which more than one haplochromine sequence was found. In these cases, we used the longest sequence for further analyses. The relative p-distances for three fish species were then mapped in ternary diagrams. An example of such a ternary diagram is shown in Fig. 2a, in this case showing the relative p-distances of cichlid, Takifugu rubripes, and Danio rerio amino acid sequences with respect to the homologous Homo sapiens genes. Figure 2b depicts a diagram with Oncorhynchus mykiss amino acid sequence divergence instead of haplochromine cichlid. The ternary diagrams show that in all combinations most genes are clustered around the center of the respective triangle, which indicates that, in general, the p-distances relative to the human outgroup are similar in all fish species.


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)

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

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

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.
Mentions: In order to identify sequences that evolve significantly more rapidly or more slowly in the haplochromine cichlid, we applied the triangle method implemented in EverEST [37] to calculate the p-distance for each of these 759 ORFs in all fish species relative to the human ortholog. There were 22 cases in which more than one haplochromine sequence was found. In these cases, we used the longest sequence for further analyses. The relative p-distances for three fish species were then mapped in ternary diagrams. An example of such a ternary diagram is shown in Fig. 2a, in this case showing the relative p-distances of cichlid, Takifugu rubripes, and Danio rerio amino acid sequences with respect to the homologous Homo sapiens genes. Figure 2b depicts a diagram with Oncorhynchus mykiss amino acid sequence divergence instead of haplochromine cichlid. The ternary diagrams show that in all combinations most genes are clustered around the center of the respective triangle, which indicates that, in general, the p-distances relative to the human outgroup are similar in all fish species.

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