Journal Article

Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats

George E. Liu, Lu Jiang, Fei Tian, Bin Zhu and Jiuzhou Song

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 1, issue , pages 119-130
Published in print January 2009 |
Published online May 2009 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evp014

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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

Journal Article.  5224 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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