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Type: Journal article
Title: Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains
Author: Adelson, D.
Raison, J.
Garber, M.
Edgar, R.
Citation: Animal Genetics, 2010; 41(Suppl 2):91-99
Publisher: Blackwell Publishing Ltd
Issue Date: 2010
ISSN: 0268-9146
Statement of
D. L. Adelson, J. M. Raison, M. Garber and R. C. Edgar
Abstract: The interspersed repeat content of mammalian genomes has been best characterized in human, mouse and cow. In this study, we carried out de novo identification of repeated elements in the equine genome and identified previously unknown elements present at low copy number. The equine genome contains typical eutherian mammal repeats, but also has a significant number of hybrid repeats in addition to clade-specific Long Interspersed Nuclear Elements (LINE). Equus caballus clade specific LINE 1 (L1) repeats can be classified into approximately five subfamilies, three of which have undergone significant expansion. There are 1115 full-length copies of these equine L1, but of the 103 presumptive active copies, 93 fall within a single subfamily, indicating a rapid recent expansion of this subfamily. We also analysed both interspersed and simple sequence repeats (SSR) genome-wide, finding that some repeat classes are spatially correlated with each other as well as with G+C content and gene density. Based on these spatial correlations, we have confirmed that recently-described ancestral vs. clade-specific genome territories can be defined by their repeat content. The clade-specific Short Interspersed Nuclear Element correlations were scattered over the genome and appear to have been extensively remodelled. In contrast, territories enriched for ancestral repeats tended to be contiguous domains. To determine if the latter territories were evolutionarily conserved, we compared these results with a similar analysis of the human genome, and observed similar ancestral repeat enriched domains. These results indicate that ancestral, evolutionarily conserved mammalian genome territories can be identified on the basis of repeat content alone. Interspersed repeats of different ages appear to be analogous to geologic strata, allowing identification of ancient vs. newly remodelled regions of mammalian genomes.
Keywords: equine; horse; mobile element; repeat; retroposon; transposon
Rights: Copyright 2010 The Authors, Journal compilation Copyright 2010 Stichting International Foundation for Animal Genetics
RMID: 0020101563
DOI: 10.1111/j.1365-2052.2010.02115.x
Appears in Collections:Molecular and Biomedical Science publications
Environment Institute publications

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