ArticleJournal of molecular evolution2005
Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.
Article in Journal of molecular evolution, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 37 citations in OpenAlex.
- From pairs of most similar sequences to phylogenetic best matches.Algorithms for molecular biology : AMB · 2020Article
- Article
- Expansion by whole genome duplication and evolution of the sox gene family in teleost fish.PloS one · 2017Article
- An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference.Genome biology and evolution · 2012Article
- Zebrafish IGF genes: gene duplication, conservation and divergence, and novel roles in midline and notochord development.PloS one · 2009Article
- Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha).Theory in biosciences = Theorie in den Biowissenschaften · 2009Article
- Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes.PLoS genetics · 2009Article
- Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes.Genome biology · 2009Article
- A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13.Journal of molecular evolution · 2008Article
- Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes.Molecular phylogenetics and evolution · 2008Article
- SynBlast: assisting the analysis of conserved synteny information.BMC bioinformatics · 2008Article
- Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni.BMC genomics · 2007Article
- Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications.BMC genomics · 2007Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All 18 duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. 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 be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or 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 the 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. 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.
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