Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

• Published in: Nature communications Vol. 9; no. 1; pp. 2774 - 11
• Main Authors: Pasquesi, Giulia I. M., Adams, Richard H., Card, Daren C., Schield, Drew R., Corbin, Andrew B., Perry, Blair W., Reyes-Velasco, Jacobo, Ruggiero, Robert P., Vandewege, Michael W., Shortt, Jonathan A., Castoe, Todd A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.07.2018; Nature Publishing Group; Nature Portfolio
• Subjects: 45/22; 45/23; 49; 631/181/735; 631/208/212/2304; 631/208/212/2305; 631/208/212/748; Animals; Birds; Birds - classification; Birds - genetics; Demography; DNA Transposable Elements; Eukaryotes; Evolution; Evolution, Molecular; Genetic Variation; Genome Size; Genomes; Genomics; Humanities and Social Sciences; Landscape; Lizards; Lizards - classification; Lizards - genetics; Mammals - classification; Mammals - genetics; Microsatellite Repeats; Microsatellites; multidisciplinary; Phylogeny; Reptiles; Science; Science (multidisciplinary); Snakes; Snakes - classification; Snakes - genetics; Transposons; Variation
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-05279-1

Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25–73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny. Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.