Alexander Suh, Gennady Churakov, Meganathan P. Ramakodi, Roy N. Platt II, Jerzy Jurka, Kenji K. Kojima, Juan Caballero, Arian Smit, Kent A. Vliet, Federico G. Hoffmann, Jürgen Brosius, Richard E. Green, Edward L. Braun, David A. Ray, and Jürgen Schmitz, 'Multiple Lineages of Ancient Cr1 Retroposons Shaped the Early Genome Evolution of Amniotes', Genome Biology and Evolution (2014).
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 twelve crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our largescale phylogenetic analysis of amniote CR1 subfamilies suggest 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 of these CR1 lineages across amniote genome evolution. Interestingly, amniotes such as birds and lepidosaurs retained the fewest ancient CR1 lineages 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 was littered with myriad CR1 elements from multiple ancient lineages, a situation that is still largely visible 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.