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doi:10.1534/genetics.105.051714
A more recent version of this article appeared on May 1, 2006.
REGULAR RESEARCH PAPERS |
Genome-wide comparative analysis of the highly abundant transposable element DINE-1 suggests a recent transpositional burst in Drosophila yakuba
Hsiao-Pei H Yang 1*, Tzu-Ling Hung 1, Tzung-Lin You 1 and Tzung-Han Yang 1
1 National Yang-Ming University
* To whom correspondence should be addressed. E-mail: hpyang{at}ym.edu.tw.
Submitted on September 29, 2005
Revised on December 8, 2005
Accepted on 18 December 2005
DINE-1 (Drosophila interspersed element) is the most abundant repetitive sequence in the Drosophila genome derived from transposable elements. It comprises more than 1% of the Drosophila melanogaster genome (DMG) and is believed to be a relic from an ancient transpositional burst that occurred ~5-10 Myrs ago. We performed a genome-wide comparison of the abundance, sequence variation and chromosomal distribution of DINE-1 in D. melanogaster and D. yakuba. Unlike the highly diverged copies in DMG (pairwise distance ~15%), DINE-1s in Drosophila yakuba genome (DYG) have diverged by only 3.4%. Moreover, the chromosomal distribution of DINE-1 in the two species are very different, with a significant number of euchromatic insertions found only in D. yakuba. We propose that these different patterns are caused by a second transpositional burst of DINE-1s in the D. yakuba genome ~ 1.5 Myr ago. Based on the sequence of these recently transposed copies, we conclude that DINE-1 is likely to be a family of non-automomous DNA transposons. Analysis of the chromosomal distribution of two age groups of DINE-1s in D. yakuba indicates that (1) there is a negative correlation between recombination rates and the density of DINE-1s, and (2) younger copies are more evenly distributed in the chromosome arms, while older copies are mostly located near the centromere regions. Our results fit the predictions of a selection-transposition balance model. Our data on the whole-genome comparison of a highly abundant TE between Drosophila sibling species demonstrate the unexpectedly dynamic nature of TE activity in different host genomes.
Key Words: DINE-1, interspersed repetitive element, molecular evolution, recombination rat, transposable element
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