title: Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.
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.
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Germany Department of Evolutionary Biology (EBC), Uppsala University, Sweden alexander.suh@ebc.uu.se.
authors.forename: Alexander
authors.initials: A
authors.lastname: Suh
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Germany.
authors.forename: Gennady
authors.initials: G
authors.lastname: Churakov
authors.affiliation: 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.
authors.forename: Meganathan P
authors.initials: MP
authors.lastname: Ramakodi
authors.affiliation: 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.
authors.forename: Roy N
authors.initials: RN
authors.lastname: Platt
authors.affiliation: Genetic Information Research Institute, Mountain View, California.
authors.forename: Jerzy
authors.initials: J
authors.lastname: Jurka
authors.affiliation: Genetic Information Research Institute, Mountain View, California.
authors.forename: Kenji K
authors.initials: KK
authors.lastname: Kojima
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: Juan
authors.initials: J
authors.lastname: Caballero
authors.affiliation: Institute for Systems Biology, Seattle, Washington.
authors.forename: Arian F
authors.initials: AF
authors.lastname: Smit
authors.affiliation: Department of Biology, University of Florida.
authors.forename: Kent A
authors.initials: KA
authors.lastname: Vliet
authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University.
authors.forename: Federico G
authors.initials: FG
authors.lastname: Hoffmann
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Brosius
authors.affiliation: Department of Biomolecular Engineering, University of California.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
authors.affiliation: Department of Biology and Genetics Institute, University of Florida.
authors.forename: Edward L
authors.initials: EL
authors.lastname: Braun
authors.affiliation: 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.
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmitz
mesh_terms: D000489:Alligators and Crocodiles / Q000235:genetics; D000818:Animals; D019143:Evolution, Molecular; D016678:Genome; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D014426:Turtles / Q000235:genetics
chemical_list: D018626:Retroelements
keywords: amniotes; chicken repeat 1; comparative genomics; crocodilian genomes; phylogenomics; transposable elements