The Structure and Early Evolution of Recently Arisen Gene Duplicates in the Caenorhabditis elegans Genome

Corresponding author: Vaishali Katju, Jordan Hall 142, Indiana University, 1001 E. Third St., Bloomington, IN 47405., vkatju{at}bio.indiana.edu (E-mail)

Communicating editor: S. P. OTTO

The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with 10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms.

This article has been cited by other articles:

				A. D. Cutter Divergence Times in Caenorhabditis and Drosophila Inferred from Direct Estimates of the Neutral Mutation Rate Mol. Biol. Evol., April 1, 2008; 25(4): 778 - 786. [Abstract] [Full Text] [PDF]

				W. Qian and J. Zhang Evolutionary dynamics of nematode operons: Easy come, slow go Genome Res., March 1, 2008; 18(3): 412 - 421. [Abstract] [Full Text] [PDF]

				M. Irimia, J. L. Rukov, D. Penny, J. Garcia-Fernandez, J. Vinther, and S. W. Roy Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis Mol. Biol. Evol., February 1, 2008; 25(2): 375 - 382. [Abstract] [Full Text] [PDF]

				G. Stanvitch and L. L. Moore cin-4, a Gene With Homology to Topoisomerase II, Is Required for Centromere Resolution by Cohesin Removal From Sister Kinetochores During Mitosis Genetics, January 1, 2008; 178(1): 83 - 97. [Abstract] [Full Text] [PDF]

				E. W. Ganko, B. C. Meyers, and T. J. Vision Divergence in Expression between Duplicated Genes in Arabidopsis Mol. Biol. Evol., October 1, 2007; 24(10): 2298 - 2309. [Abstract] [Full Text] [PDF]

				S. W. Roy and D. Penny On the Incidence of Intron Loss and Gain in Paralogous Gene Families Mol. Biol. Evol., August 1, 2007; 24(8): 1579 - 1581. [Abstract] [Full Text] [PDF]

				M. Lynch Colloquium Papers: The frailty of adaptive hypotheses for the origins of organismal complexity PNAS, May 15, 2007; 104(suppl_1): 8597 - 8604. [Abstract] [Full Text] [PDF]

				J. L. Rukov, M. Irimia, S. Mork, V. K. Lund, J. Vinther, and P. Arctander High Qualitative and Quantitative Conservation of Alternative Splicing in Caenorhabditis elegans and Caenorhabditis briggsae Mol. Biol. Evol., April 1, 2007; 24(4): 909 - 917. [Abstract] [Full Text] [PDF]

				B. P. Cusack and K. H. Wolfe Not Born Equal: Increased Rate Asymmetry in Relocated and Retrotransposed Rodent Gene Duplicates Mol. Biol. Evol., March 1, 2007; 24(3): 679 - 686. [Abstract] [Full Text] [PDF]

				E. D. Akhunov, A. R. Akhunova, and J. Dvorak Mechanisms and Rates of Birth and Death of Dispersed Duplicated Genes during the Evolution of a Multigene Family in Diploid and Tetraploid Wheats Mol. Biol. Evol., February 1, 2007; 24(2): 539 - 550. [Abstract] [Full Text] [PDF]

				J. H. Thomas Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants Genome Res., August 1, 2006; 16(8): 1017 - 1030. [Abstract] [Full Text] [PDF]

				V. Katju and M. Lynch On the Formation of Novel Genes by Duplication in the Caenorhabditis elegans Genome Mol. Biol. Evol., May 1, 2006; 23(5): 1056 - 1067. [Abstract] [Full Text] [PDF]

				J. H. Thomas Concerted Evolution of Two Novel Protein Families in Caenorhabditis Species Genetics, April 1, 2006; 172(4): 2269 - 2281. [Abstract] [Full Text] [PDF]

				M. Lynch The Origins of Eukaryotic Gene Structure Mol. Biol. Evol., February 1, 2006; 23(2): 450 - 468. [Abstract] [Full Text] [PDF]

				J. H. Thomas Analysis of Homologous Gene Clusters in Caenorhabditis elegans Reveals Striking Regional Cluster Domains Genetics, January 1, 2006; 172(1): 127 - 143. [Abstract] [Full Text] [PDF]

				S. Bhushan, A. Stahl, S. Nilsson, B. Lefebvre, M. Seki, C. Roth, D. McWilliam, S. J. Wright, D. A. Liberles, K. Shinozaki, et al. Catalysis, Subcellular Localization, Expression and Evolution of the Targeting Peptides Degrading Protease, AtPreP2 Plant Cell Physiol., June 1, 2005; 46(6): 985 - 996. [Abstract] [Full Text] [PDF]

				C. D. Jones, A. W. Custer, and D. J. Begun Origin and Evolution of a Chimeric Fusion Gene in Drosophila subobscura, D. madeirensis and D. guanche Genetics, May 1, 2005; 170(1): 207 - 219. [Abstract] [Full Text] [PDF]

				A. Force, W. A. Cresko, F. B. Pickett, S. R. Proulx, C. Amemiya, and M. Lynch The Origin of Subfunctions and Modular Gene Regulation Genetics, May 1, 2005; 170(1): 433 - 446. [Abstract] [Full Text] [PDF]

				J. B. Pereira-Leal and S. A. Teichmann Novel specificities emerge by stepwise duplication of functional modules Genome Res., April 1, 2005; 15(4): 552 - 559. [Abstract] [Full Text] [PDF]

				P. H. Shah, R. C. MacFarlane, D. Bhattacharya, J. C. Matese, J. Demeter, S. E. Stroup, and U. Singh Comparative Genomic Hybridizations of Entamoeba Strains Reveal Unique Genetic Fingerprints That Correlate with Virulence Eukaryot. Cell, March 1, 2005; 4(3): 504 - 515. [Abstract] [Full Text] [PDF]

				L. Huminiecki and K. H. Wolfe Divergence of Spatial Gene Expression Profiles Following Species-Specific Gene Duplications in Human and Mouse Genome Res., October 1, 2004; 14(10a): 1870 - 1879. [Abstract] [Full Text] [PDF]

				A.-M. Mallon, L. Wilming, J. Weekes, J. G.R. Gilbert, J. Ashurst, S. Peyrefitte, L. Matthews, M. Cadman, R. McKeone, C. A. Sellick, et al. Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse Genome Res., October 1, 2004; 14(10a): 1888 - 1901. [Abstract] [Full Text] [PDF]