Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation Export

@article{citeulike:1465825, abstract = {Author SummaryTransposable elements (TEs) are interspersed repetitive DNA families that are capable of copying themselves from place to place; they have literally infested our genome over evolutionary time, and now comprise as much as 45\% of our total DNA. Because of their great age and abundance, TEs are important in evolutionary genomics. However, estimates of their age based on DNA sequence composition have been unreliable, especially for older more diverged elements. Therefore, a novel method to estimate the age of TEs was developed based on the fact that as TEs spread throughout the genome, they inserted into and fragmented older TEs that were already present. Therefore, the age of TEs can be revealed by how often they have been fragmented over evolutionary time. We performed a genome-wide defragmention of TEs, and developed a novel objective function to derive the chronological order of TEs spanning >100 million years. This method has been used to infer the relative ages of TEs from seven sequenced mammalian genomes across all four major TE classes, including the oldest, most diverged elements. This age estimate is independent of TE sequence composition or divergence and does not rely on the assumption of a constant molecular clock. This study provides a novel analysis of the evolutionary history of some of the most abundant and ancient repetitive DNA elements in mammalian genomes, which is important for understanding the dynamic forces that shape our genomes during evolution.}, author = {Giordano, Joti and Ge, Yongchao and Gelfand, Yevgeniy and Abrus\'{a}n, Gy\"{o}rgy and Benson, Gary and Warburton, Peter E.}, booktitle = {PLoS Comput Biol}, citeulike-article-id = {1465825}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.0030137}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17630829}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17630829}, day = {13}, doi = {10.1371/journal.pcbi.0030137}, issn = {1553-7358}, journal = {PLoS Comput Biol}, keywords = {transposon}, month = {July}, number = {7}, pages = {e137+}, posted-at = {2007-07-18 23:36:51}, priority = {2}, publisher = {Public Library of Science}, title = {Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation}, url = {http://dx.doi.org/10.1371/journal.pcbi.0030137}, volume = {3}, year = {2007} }

TY - JOUR ID - citeulike:1465825 L3 - citeulike-article-id:1465825 N2 - Author SummaryTransposable elements (TEs) are interspersed repetitive DNA families that are capable of copying themselves from place to place; they have literally infested our genome over evolutionary time, and now comprise as much as 45% of our total DNA. Because of their great age and abundance, TEs are important in evolutionary genomics. However, estimates of their age based on DNA sequence composition have been unreliable, especially for older more diverged elements. Therefore, a novel method to estimate the age of TEs was developed based on the fact that as TEs spread throughout the genome, they inserted into and fragmented older TEs that were already present. Therefore, the age of TEs can be revealed by how often they have been fragmented over evolutionary time. We performed a genome-wide defragmention of TEs, and developed a novel objective function to derive the chronological order of TEs spanning >100 million years. This method has been used to infer the relative ages of TEs from seven sequenced mammalian genomes across all four major TE classes, including the oldest, most diverged elements. This age estimate is independent of TE sequence composition or divergence and does not rely on the assumption of a constant molecular clock. This study provides a novel analysis of the evolutionary history of some of the most abundant and ancient repetitive DNA elements in mammalian genomes, which is important for understanding the dynamic forces that shape our genomes during evolution. IS - 7 JF - PLoS Comput Biol SN - 1553-7358 TI - Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation PB - Public Library of Science VL - 3 T2 - PLoS Comput Biol SP - e137 KW - transposon AU - Giordano, Joti AU - Ge, Yongchao AU - Gelfand, Yevgeniy AU - Abrusán, György AU - Benson, Gary AU - Warburton, Peter PY - 2007/07/13/ UR - http://dx.doi.org/10.1371/journal.pcbi.0030137 ER -