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United States Department of Agriculture

Agricultural Research Service


item Grahn, Robert
item Rinehart, Timothy
item Cantrell, Michael
item Wichman, Holly

Submitted to: Cytogenetics and Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/8/2004
Publication Date: 6/30/2005
Citation: Grahn, R.A., Rinehart, T.A., Cantrell, M.A., Wichman, H.A. 2005. Extinction of line-14 activity coincident with a major mammalian radiation in rodents. Cytogenetics and Genome Research Vol 110, No. 1-4, pp 407-415.

Interpretive Summary: In general, transposons have been labeled 'junk' DNA because they do not appear to contain directions for organismal or cellular development. However, groups of transposons make up the bulk of DNA found in human and rodent genomes. It is perplexing that such a large part of the genome is made up of useless information and there is ongoing research to explore why and how this came to be. One of the proposed reasons there are so many copies of transposons in our genome is that they selfishly make copies of themselves generation after generation. This paper explores recent evolutionary history of LINE transposons in rodents. Our results suggest that LINE transposons lost their selfish behavior in marsh rats about 8.8 million years ago and this loss appears to affect several related rodent species. This is the first comprehensive report of a group of rodents lacking recent LINE copies and introduces these species as good models for exploring whether transposons are selfish or useful.

Technical Abstract: LINE-1 transposable elements (L1s) are ubiquitous in mammals and are thought to have remained active since before the mammalian radiation. Only one L1 extinction event, in South American rodents in the genus Oryzomys, has been convincingly demonstrated. Here we examine the phylogenetic limits and evolutionary tempo of that extinction event by characterizing L1s in related rodents. Fourteen genera from five tribes within the Sigmodontinae family were examined. Only the Sigmodontini, the most basal tribe in this group, demonstrate recent L1 activity. The Oryzomyini, Akodontini, Phyllotini, and Thomasomyini contain only L1s that appear to have inserted long ago: their L1s lack open reading frames, have mutations at conserved amino acid residues, and show numerous private mutations. They also lack restriction site-defined L1 subfamilies specific to any species, genus or tribe examined, and fail to form monophyletic species, genus or tribal L1 clusters. We determine here that this L1 extinction event occurred roughly 8.8 million years ago, near the divergence of Sigmodon from the remaining Sigmodontinae species. These species appear to be ideal model organisms for studying the impact of L1 inactivity on mammalian genomes.

Last Modified: 06/25/2017
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