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Genome Biol Evol. 2014 Dec 11;7(1):205-17. doi: 10.1093/gbe/evu256.

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

Author information

1
Institute of Experimental Pathology (ZMBE), University of Münster, Germany Department of Evolutionary Biology (EBC), Uppsala University, Sweden alexander.suh@ebc.uu.se.
2
Institute of Experimental Pathology (ZMBE), University of Münster, Germany.
3
Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Present address: Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA Present address: Department of Biology, Temple University, Philadelphia, PA.
4
Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Biological Sciences, Texas Tech University.
5
Genetic Information Research Institute, Mountain View, California.
6
Institute for Systems Biology, Seattle, Washington.
7
Department of Biology, University of Florida.
8
Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University.
9
Department of Biomolecular Engineering, University of California.
10
Department of Biology and Genetics Institute, University of Florida.

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.

KEYWORDS:

amniotes; chicken repeat 1; comparative genomics; crocodilian genomes; phylogenomics; transposable elements

PMID:
25503085
PMCID:
PMC4316615
DOI:
10.1093/gbe/evu256
[Indexed for MEDLINE]
Free PMC Article

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