This Article OPEN ACCESS ARTICLE Full Text Full Text (PDF) Supplemental Research Data All Versions of this Article: gr.6316407v1 17/9/1254    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Nakatani, Y. Articles by Morishita, S. Search for Related Content PubMed PubMed Citation Articles by Nakatani, Y. Articles by Morishita, S. Social Bookmarking                   What's this?

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates

¹ Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan; ² Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; ³ Center for Genetic Resource Information, National Institute of Genetics, Mishima 411-8540, Japan; ⁴ Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), Tokyo 102-8666, Japan

Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.

E-mail nakatani{at}cb.k.u-tokyo.ac.jp; fax 81-47-136-3977.

E-mail moris{at}cb.k.u-tokyo.ac.jp; fax 81-47-136-3977.

[Supplemental material is available online at www.genome.org.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6316407

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				C. L. Organ, R. G. Moreno, and S. V. Edwards Three tiers of genome evolution in reptiles Integr. Comp. Biol., June 21, 2008; (2008) icn046v1. [Abstract] [Full Text] [PDF]

				H. Tang, J. E. Bowers, X. Wang, R. Ming, M. Alam, and A. H. Paterson Synteny and Collinearity in Plant Genomes Science, April 25, 2008; 320(5875): 486 - 488. [Abstract] [Full Text] [PDF]

				A. Prachumwat and W.-H. Li Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes Genome Res., February 1, 2008; 18(2): 221 - 232. [Abstract] [Full Text] [PDF]