Duplicated RNA genes in teleost fish genomes.
Teleost fishes share a duplication of their entire genomes. We report here on a computational survey of structured non-coding RNAs (ncRNAs) in teleost genomes, focusing on the fate of fish-specific duplicates. As in other metazoan groups, we find evidence of a large number (11,543) of structured RNAs, most of which (~86%) are clade-specific or evolve so fast that their tetrapod homologs cannot be detected. In surprising contrast to protein-coding genes, the fish-specific genome duplication did not lead to a large number of paralogous ncRNAs: only 188 candidates, mostly microRNAs, appear in a larger copy number in teleosts than in tetrapods, suggesting that large-scale gene duplications do not play a major role in the expansion of the vertebrate ncRNA inventory.
Rose
Dominic
D
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany. dominic@bioinf.uni-leipzig.de
Jöris
Julian
J
Hackermüller
Jörg
J
Reiche
Kristin
K
Li
Qiang
Q
Stadler
Peter F
PF
D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics*; D018628:Gene Dosage; D020440:Gene Duplication; D016678:Genome; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000235:genetics*
D035683:MicroRNAs; D022661:RNA, Untranslated