Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Proc Natl Acad Sci U S A
2008 Jun 17;10524:8333-8. doi: 10.1073/pnas.0708705105.
Show Gene links
Show Anatomy links
Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis.
Sémon M, Wolfe KH.
???displayArticle.abstract???
As paleopolyploid genomes evolve, the expression profiles of retained gene pairs are expected to diverge. To examine this divergence process on a large scale in a vertebrate system, we compare Xenopus laevis, which has retained approximately 40% of loci in duplicate after a recent whole-genome duplication (WGD), with its unduplicated relative Silurana (Xenopus) tropicalis. This comparison of ingroup pairs to an outgroup allows the direction of change in expression profiles to be inferred for a set of 1,300 X. laevis pairs, relative to their single orthologs in S. tropicalis, across 11 tissues. We identify 68 pairs in which X. laevis is inferred to have undergone a significant reduction of expression in at least two tissues since WGD. Of these pairs, one-third show evidence of subfunctionalization, with decreases in the expression levels of different gene copies in two different tissues. Surprisingly, we find that genes with slow rates of evolution are particularly prone to subfunctionalization, even when the tendency for highly expressed genes to evolve slowly is controlled for. We interpret this result to be an effect of allopolyploidization. We then compare the outcomes of this WGD with an independent one that happened in the teleost fish lineage. We find that if a gene pair was retained in duplicate in X. laevis, the orthologous pair is more likely to have been retained in duplicate in zebrafish, suggesting that similar factors, among them subfunctionalization, determined which gene pairs survived in duplicate after the two WGDs.
Altschmied,
Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish.
2002, Pubmed
Altschmied,
Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish.
2002,
Pubmed Audic,
The significance of digital gene expression profiles.
1997,
Pubmed Aury,
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
2006,
Pubmed Birchler,
Dosage dependent gene regulation and the compensation of the X chromosome in Drosophila males.
2003,
Pubmed Blanc,
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution.
2004,
Pubmed Brunet,
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes.
2006,
Pubmed Byrne,
Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication.
2007,
Pubmed Casneuf,
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana.
2006,
Pubmed Chain,
Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization.
2008,
Pubmed
,
Xenbase Chain,
Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis.
2006,
Pubmed
,
Xenbase Chang,
Genomic sequence and spatiotemporal expression comparison of zebrafish mbx1 and its paralog, mbx2.
2006,
Pubmed Conant,
Asymmetric sequence divergence of duplicate genes.
2003,
Pubmed Cresko,
Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish.
2003,
Pubmed Cusack,
When gene marriages don't work out: divorce by subfunctionalization.
2007,
Pubmed Davis,
Do disparate mechanisms of duplication add similar genes to the genome?
2005,
Pubmed Davis,
Preferential duplication of conserved proteins in eukaryotic genomes.
2004,
Pubmed de Souza,
Subfunctionalization of expression and peptide domains following the ancient duplication of the proopiomelanocortin gene in teleost fishes.
2005,
Pubmed Drummond,
A single determinant dominates the rate of yeast protein evolution.
2006,
Pubmed Duarte,
Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
2006,
Pubmed Duret,
Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate.
2000,
Pubmed Evans,
Ancestry influences the fate of duplicated genes millions of years after polyploidization of clawed frogs (Xenopus).
2007,
Pubmed
,
Xenbase Evans,
Evolution of RAG-1 in polyploid clawed frogs.
2005,
Pubmed
,
Xenbase Force,
Preservation of duplicate genes by complementary, degenerative mutations.
1999,
Pubmed Gibson,
Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins.
1998,
Pubmed Hellsten,
Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis.
2007,
Pubmed
,
Xenbase Hoegg,
Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish.
2004,
Pubmed Hughes,
Evolution of duplicate genes in a tetraploid animal, Xenopus laevis.
1993,
Pubmed
,
Xenbase Jaillon,
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
2004,
Pubmed Lynch,
The probability of duplicate gene preservation by subfunctionalization.
2000,
Pubmed Lynch,
The probability of preservation of a newly arisen gene duplicate.
2001,
Pubmed Morin,
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.
2006,
Pubmed
,
Xenbase Nowak,
Evolution of genetic redundancy.
1997,
Pubmed Otto,
Polyploid incidence and evolution.
2000,
Pubmed Pollet,
Insights from Xenopus genomes.
2006,
Pubmed
,
Xenbase Scannell,
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts.
2006,
Pubmed Scannell,
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication.
2007,
Pubmed Seoighe,
Yeast genome evolution in the post-genome era.
1999,
Pubmed Spring,
Vertebrate evolution by interspecific hybridisation--are we polyploid?
1997,
Pubmed Steinke,
Many genes in fish have species-specific asymmetric rates of molecular evolution.
2006,
Pubmed Tirosh,
Comparative analysis indicates regulatory neofunctionalization of yeast duplicates.
2007,
Pubmed Vandepoele,
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates.
2004,
Pubmed Woolfe,
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization.
2007,
Pubmed Yu,
Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu.
2003,
Pubmed Zhang,
Mammalian housekeeping genes evolve more slowly than tissue-specific genes.
2004,
Pubmed
