Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome
Edited by James E. Womack, Texas A&M University, College Station, TX, and approved June 19, 2009
Abstract
Interspersed repeat composition and distribution in mammals have been best characterized in the human and mouse genomes. The bovine genome contains typical eutherian mammal repeats, but also has a significant number of long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata. Our analysis of the BovB repeats has indicated that only a few of them are currently likely to retrotranspose in cattle. However, bovine L1 repeats (L1 BT) have many likely active copies. Comparison of substitution rates for BovB and L1 BT indicates that L1 BT is a younger repeat family than BovB. In contrast to mouse and human, L1 occurrence is not negatively correlated with G+C content. However, BovB, Bov A2, ART2A, and Bov-tA are negatively correlated with G+C, although Bov-tAs correlation is weaker. Also, by performing genome wide correlation analysis of interspersed and simple sequence repeats, we have identified genome territories by repeat content that appear to define ancestral vs. ruminant-specific genomic regions. These ancestral regions, enriched with L2 and MIR repeats, are largely conserved between bovine and human.
Acknowledgments.
We thank the Bovine Genome Sequencing Project for providing segmental duplication data (E. Eichler, Seattle, WA), GLEAN gene models (C. Elsik, Washington, DC), and their coordinates; and the anonymous reviewers who helped improve this report.
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Cover image: Pictured is a microbial mat growing near White Creek in Yellowstone National Park. These microbial communities produce lipids with unusually large variations in their deuterium content. Zhang et al. show that such variations likely relate to the different metabolic pathways employed by the microbes and suggest that deuterium variations in ancient lipids could be used to identify pathways of energy metabolism active in the past. See the Feature Article by Xinning Zhang et al. on pages 12580–12586. Image by Alex Sessions.
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© 2009.
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Received: February 5, 2009
Published online: August 4, 2009
Published in issue: August 4, 2009
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Acknowledgments
We thank the Bovine Genome Sequencing Project for providing segmental duplication data (E. Eichler, Seattle, WA), GLEAN gene models (C. Elsik, Washington, DC), and their coordinates; and the anonymous reviewers who helped improve this report.
Notes
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/cgi/content/full/0901282106/DCSupplemental.
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The authors declare no conflict of interest.
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