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Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains.
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.
© 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.
Publication Date: 2010-11-26 PubMed ID: 21070282DOI: 10.1111/j.1365-2052.2010.02115.xGoogle Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
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This study investigates the diversity and distribution of repeated elements within the horse genome, finding that these can indicate conserved chromosomal areas and reveal information about the horse’s evolutionary history.
Research Goals
- The core aim of the research was to identify and understand the interspersed repeat elements in the horse (Equus caballus) genome.
- The study also sought to identify any unknown repeat elements in the equine genome and ascertain their characteristics.
- An investigation into how repeat classes relate spatially with each other, gene density, and G+C content was conducted.
- The research attempted to confirm whether ancestral or clade-specific genome territories defined by their repeat content existed.
Findings
- The horse genome contains typical eutherian mammal repeats and a significant number of hybrid repeats. It also possesses clade-specific Long Interspersed Nuclear Elements (LINE).
- The researchers identified five subfamilies of Equus caballus clade specific LINE 1 (L1) repeats. Three of these subfamilies had notably expanded.
- Out of 103 active copies of equine L1, 93 belonged to a single subfamily, indicating a recent rapid expansion.
- Analysis showed that some repeat classes are spatially correlated with each other, gene density, and G+C content.
- Ancient territories of the genome were consecutive, while newer territories were scattered throughout the genome, suggesting they had been extensively remodelled.
- Comparison with the human genome yielded similar results, indicating that these territories are evolutionarily conserved within mammals and can be identified through their repeat content.
Significance
- The research illustrates how the investigation of interspersed repeats in a genome can provide insights into the evolutionary history of a species.
- The existence of particular repeated elements within the horse genome can provide essential information on the evolutionary dynamics of genome remodeling, such as identifying ‘new’ and ‘old’ regions of the genome.
Cite This Article
APA
Adelson DL, Raison JM, Garber M, Edgar RC.
(2010).
Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains.
Anim Genet, 41 Suppl 2, 91-99.
https://doi.org/10.1111/j.1365-2052.2010.02115.x Publication
Researcher Affiliations
- School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia, Australia. david.adelson@adelaide.edu.au
MeSH Terms
- Animals
- Base Composition
- Chromosomes, Mammalian
- Genome
- Horses / genetics
- Microsatellite Repeats
- Retroelements
Citations
This article has been cited 11 times.- Ibrahim MA, Al-Shomrani BM, Simenc M, Alharbi SN, Alqahtani FH, Al-Fageeh MB, Manee MM. Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus. BMC Genomics 2021 Nov 20;22(1):842.
- Khalkhali-Evrigh R, Hedayat-Evrigh N, Hafezian SH, Farhadi A, Bakhtiarizadeh MR. Genome-Wide Identification of Microsatellites and Transposable Elements in the Dromedary Camel Genome Using Whole-Genome Sequencing Data. Front Genet 2019;10:692.
- Sookdeo A, Hepp CM, Boissinot S. Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction. Mob DNA 2018;9:12.
- Babii A, Kovalchuk S, Glazko T, Kosovsky G, Glazko V. Helitrons and Retrotransposons Are Co-localized in Bos taurus Genomes. Curr Genomics 2017 Jun;18(3):278-286.
- Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL. LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. Genome Biol Evol 2016 Dec 14;8(11):3301-3322.
- Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson DL, Chowdhary BP, Raudsepp T. Copy number variation in the horse genome. PLoS Genet 2014 Oct;10(10):e1004712.
- Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, Kwon YJ, Song S, Ko J, Yang YM, Lee HK, Park KD, Ahn K, Do KT, Ha HS, Han K, Yi JM, Cha HJ, Cho BW, Bhak J, Kim HS. Genome-wide analysis of DNA methylation patterns in horse. BMC Genomics 2014 Jul 15;15(1):598.
- Appels R, Adelson DL, Moolhuijzen P, Webster H, Barrero R, Bellgard M. Genome studies at the PAG 2011 conference. Funct Integr Genomics 2011 Mar;11(1):1-11.
- Kosovsky GY, Glazko GV, Skobel OI. Bos taurus and Bison bison conservative retrotransposon recombination products. Front Vet Sci 2025;12:1516731.
- Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023 Jul 21;55(1):50.
- Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, Rosen J, Storer JM, Hubley R, Smit AFA, Dávalos LM, Karlsson EK, Lindblad-Toh K, Ray DA. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science 2023 Apr 28;380(6643):eabn1430.
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