Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes

Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992, Churakov, Gennady, Ramakodi, Meganathan P., Platt, Roy N., Jurka, Jerzy, Kojima, Kenji K., Caballero, Juan, Smit, Arian F., Vliet, Kent A., Hoffmann, Federico G., Brosius, Jurgen, Green, Richard E., Braun, Edward L., Ray, David A. and Schmitz, Jurgen (2014) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution, 7 (1). pp. 205-217. ISSN 1759-6653

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Abstract

Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.

Item Type: Article
Additional Information: Publisher Copyright: © 2014 The Author(s).
Uncontrolled Keywords: amniotes,chicken repeat 1,comparative genomics,crocodilian genomes,phylogenomics,transposable elements,medicine(all) ,/dk/atira/pure/subjectarea/asjc/2700
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 16 Sep 2022 15:36
Last Modified: 01 Oct 2022 07:54
URI: https://ueaeprints.uea.ac.uk/id/eprint/88421
DOI: 10.1093/gbe/evu256

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