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

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dc.contributor.utaustinauthorHofmann, Hans A.en_US
dc.creatorSalzburger, Walteren_US
dc.creatorRenn, Susan C. P.en_US
dc.creatorSteinke, Dirken_US
dc.creatorBraasch, Ingoen_US
dc.creatorHofmann, Hans A.en_US
dc.creatorMeyer, Axelen_US
dc.date.accessioned2016-10-28T19:49:55Z
dc.date.available2016-10-28T19:49:55Z
dc.date.issued2008-02en_US
dc.description.abstractThe 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.en_US
dc.description.departmentIntegrative Biologyen_US
dc.description.sponsorshipMarie Curie Fellowship of the EUen_US
dc.description.sponsorshipLandesstiftung-Baden Württemberg gGmbHen_US
dc.description.sponsorshipCenter for Junior Research Fellowsen_US
dc.description.sponsorshipUniversity of Konstanzen_US
dc.description.sponsorshipNIH-NRSAen_US
dc.description.sponsorshipNIH-NIGMS GM068763en_US
dc.description.sponsorshipBauer Center for Genomics Research at Harvard Universityen_US
dc.description.sponsorshipInstitute for Cellular and Molecular Biology at the University of Texas, Austinen_US
dc.description.sponsorshipDeutsche Forschungsgemeinschaft (DFG)en_US
dc.description.sponsorshipThe University of Konstanzen_US
dc.identifierdoi:10.15781/T2SQ8QM1Q
dc.identifier.citationSalzburger, Walter, Susan CP Renn, Dirk Steinke, Ingo Braasch, Hans A. Hofmann, and Axel Meyer. "Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs." BMC genomics, Vol. 9, No. 1 (Feb., 2008): 1.en_US
dc.identifier.doi10.1186/1471-2164-9-96en_US
dc.identifier.issn1471-2164en_US
dc.identifier.urihttp://hdl.handle.net/2152/43170
dc.language.isoEnglishen_US
dc.relation.ispartofen_US
dc.relation.ispartofserialBMC Genomicsen_US
dc.rightsAdministrative deposit of works to Texas ScholarWorks: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access or the publisher allows a PDF version of the article to be freely posted online. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en_US
dc.rights.restrictionOpenen_US
dc.subjectgenetic-linkage mapen_US
dc.subjectlake victoriaen_US
dc.subjecthaplochromis-burtonien_US
dc.subjectbehavioralen_US
dc.subjectplasticityen_US
dc.subjectexplosive speciationen_US
dc.subjectsympatric speciationen_US
dc.subjectcdna microarrayen_US
dc.subjectspecies flocken_US
dc.subjectest databaseen_US
dc.subjectbac libraryen_US
dc.subjectbiotechnology & applied microbiologyen_US
dc.subjectgenetics & heredityen_US
dc.titleAnnotation of Expressed Sequence Tags for the East African Cichlid Fish Astatotilapia Burtoni and Evolutionary Analyses of Cichlid ORFsen_US
dc.typeArticleen_US

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