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Genome Biology and Evolution Advance Access published online on May 27, 2009
Genome Biology and Evolution, doi:10.1093/gbe/evp014
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Published by Oxford University Press 2009.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats

George E. Liu1,*, Lu Jiang2, Fei Tian3, Bin Zhu2 and Jiuzhou Song3,*

1 USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA
2 Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
3 Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland, 20742, USA

* Corresponding Authors: Dr. George E. Liu, USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA, Tel: 301-504-9843, Fax 301-504-8414, E-mail: george.liu{at}ars.usda.gov; Dr. Jiuzhou Song, Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland, 20742, USA, Tel: 301-405-5943, Fax: 301-405-7980, E-mail: songj88{at}umd.edu.


  Abstract

CR1 repeats are the most abundant family of repeats in the chicken genome, with more than 200,000 copies accounting for ~80% of the chicken interspersed repeats. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to the 22 CR1 subfamilies as previously reported in Repbase. We performed a global assessment of the divergence distributions, phylogenies and consensus sequences of CR1 repeats in the chicken genome. We identified and validated 57 chicken CR1 subfamilies and further analyzed the correlation between these subfamilies and their regional GC contents. We also discovered one novel lineage-specific CR1 subfamilies in turkeys when compared with chickens. We built an evolutionary tree of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

Keywords: CR1 repeats, comparative genomics, chicken genome

Received February 13, 2009; Revised April 14, 2009; Revised May 19, 2009; Revised May 21, 2009; Accepted May 24, 2009


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