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International Journal of Evolutionary Biology
Volume 2012 (2012), Article ID 917678, 11 pages
http://dx.doi.org/10.1155/2012/917678
Research Article

Genomic Structure and Evolution of Multigene Families: “Flowers” on the Human Genome

1Center for the Promotion of Integrated Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan
2Department of Biochemistry and Molecular Biology, Pennsylvania State University, 312 Wartik Laboratory, University Park, PA 16802, USA
3Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima 739-8526, Japan
4Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
5Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan
6The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan

Received 29 December 2011; Revised 6 April 2012; Accepted 9 April 2012

Academic Editor: Hirohisa Kishino

Copyright © 2012 Hie Lim Kim et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We report the results of an extensive investigation of genomic structures in the human genome, with a particular focus on relatively large repeats (>50 kb) in adjacent chromosomal regions. We named such structures “Flowers” because the pattern observed on dot plots resembles a flower. We detected a total of 291 Flowers in the human genome. They were predominantly located in euchromatic regions. Flowers are gene-rich compared to the average gene density of the genome. Genes involved in systems receiving environmental information, such as immunity and detoxification, were overrepresented in Flowers. Within a Flower, the mean number of duplication units was approximately four. The maximum and minimum identities between homologs in a Flower showed different distributions; the maximum identity was often concentrated to 100% identity, while the minimum identity was evenly distributed in the range of 78% to 100%. Using a gene conversion detection test, we found frequent and/or recent gene conversion events within the tested Flowers. Interestingly, many of those converted regions contained protein-coding genes. Computer simulation studies suggest that one role of such frequent gene conversions is the elongation of the life span of gene families in a Flower by the resurrection of pseudogenes.