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

Author
item Liu, Ge - George
item JIANG, LU - UNIV OF MARYLAND
item TIAN, FEI - UNIV OF MARYLAND
item ZHU, BIN - UNIV OF MARYLAND
item SONG, JIUZHOU - UNIV OF MARYLAND

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/24/2009
Publication Date: 6/22/2009
Citation: Liu, G., Jiang, L., Tian, F., Zhu, B., Song, J. 2009. Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats. Genome Biology and Evolution. 2009:119-130.

Interpretive Summary: We previously did a large-scale comparative genome analysis on high-quality finished genomic sequence from cattle, dog, and human. Our results indicated that differential turn-over patterns of repeats account for the overall genome size differences. In a relevant study, we developed an evolutionary framework for further classification and refinement of the common repeat phylogeny. Using this framework, we studied Alu repeats as an example and demonstrated their contributions to the primate genome architecture. To test its usage in other vertebrates including mammals, we chose the chicken, which is an agriculturally and evolutionarily important species and is more challenging due to the lack of repeats. In this study, we successfully applied our framework to study the CR1 repeats, identified and validated 57 new chicken CR1 subfamilies and one novel turkey-specific CR1 subfamilies. These new CR1 subfamilies expand our understanding of their evolution and their contributions to the bird genome architecture. This work provided us an established software framework to further analyze the repeats and their contribution in the bovine and other genomes.

Technical 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. We also discovered one novel lineage-specific CR1 subfamilies in turkeys when compared with chickens. We build an evolutionary tree of these subfamilies and conclude that the history of CR1 evolution is more complex than previously recognized.