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Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats
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 ri...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817409/ https://www.ncbi.nlm.nih.gov/pubmed/20333183 http://dx.doi.org/10.1093/gbe/evp014 |
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author | Liu, George E. Jiang, Lu Tian, Fei Zhu, Bin Song, Jiuzhou |
author_facet | Liu, George E. Jiang, Lu Tian, Fei Zhu, Bin Song, Jiuzhou |
author_sort | Liu, George E. |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2817409 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-28174092010-03-22 Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats Liu, George E. Jiang, Lu Tian, Fei Zhu, Bin Song, Jiuzhou Genome Biol Evol Research Articles 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. Oxford University Press 2009 2009-05-27 /pmc/articles/PMC2817409/ /pubmed/20333183 http://dx.doi.org/10.1093/gbe/evp014 Text en Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 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/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Liu, George E. Jiang, Lu Tian, Fei Zhu, Bin Song, Jiuzhou Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats |
title | Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats |
title_full | Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats |
title_fullStr | Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats |
title_full_unstemmed | Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats |
title_short | Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats |
title_sort | calibration of mutation rates reveals diverse subfamily structure of galliform cr1 repeats |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817409/ https://www.ncbi.nlm.nih.gov/pubmed/20333183 http://dx.doi.org/10.1093/gbe/evp014 |
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