Bioinformatics Preprint 04-014
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Titel:
Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters:
Increased synonymous substitution rate and asymmetrical co-divergence
of coding and non-coding sequences.
Author(s):
Günter P. Wagner,
Kazuhiko Takahashi,
Vincent Lynch,
Sonja J. Prohaska,
Claudia Fried,
Peter F. Stadler,
Chris T. Amemiya
Submitted for publication in:
J. Mol. Evol.
Abstract:
In this study the molecular evolution of duplicated HoxA genes in zebrafish
and fugu has been investigated. All eighteen duplicated HoxA genes studied
have a higher nonsynonymous substitution rate than the corresponding genes
in either bichir or paddlefish, where these genes are not
duplicated. Surprisingly, though, the higher rate of evolution is not due
solely to a higher non-synonymous to synonymous rate ratio but to an
increase in both the non-synonymous as well as the synonymous substitution
rate. The synonymous rate increase can neither be explained by changes in
nucleotide composition nor codon bias. Thus, we suggest that the HoxA genes
may experience an increased mutation rate following cluster duplication. In
the non-Hox nuclear gene RAG1 only an increase in non-synonymous
substitutions could be detected, suggesting that the increased mutation
rate is specific to duplicated Hox clusters and might be related to the
structural instability of Hox clusters following duplication. The
divergence among paralog genes tends to be asymmetric with one paralog
diverging faster than the other. In fugu, all b-paralogs diverge faster
than a-paralogs, while in zebrafish Hoxa-13a diverges faster. This
asymmetry corresponds to the asymmetry in the divergence rate of conserved
non-coding sequences, i.e. putative cis-regulatory elements. In fugu, the
putative cis-regulatory elements of the b-paralog HoxA cluster diverge
faster, while in zebrafish those of the a-paralog cluster diverge
faster. Hence, we found evidence for a concerted asymmetric divergence of
coding sequences on the same cluster as well as between coding and
non-coding sequences. These results suggest that the 5 HoxA genes in the
same cluster belong to a co-evolutionary unit in which genes have a
tendency to diverge together.
Keywords:
Ray Finned Fishes, HoxA Cluster
Alternative Numbers:
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Last modified: 2004-03-28 19:56:33 studla