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Genome Biology and Evolution Advance Access originally published online on May 27, 2009
Genome Biology and Evolution (2009) Vol. 2009:119; doi:10.1093/gbe/evp014 published on June 22, 2009
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Published 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. Liu*, Lu Jiang{dagger}, Fei Tian{ddagger}, Bin Zhu{dagger} and Jiuzhou Song{ddagger}

* Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland
{dagger} Department of Bioengineering, University of Maryland
{ddagger} Department of Animal and Avian Sciences, University of Maryland

E-mail: george.liu{at}ars.usda.gov; songj88{at}umd.edu.


  Abstract

Chicken Repeat 1 (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

Accepted May 24, 2009

Yoshihito Niimura, Associate Editor


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