Shedlock, A. M.Botka, C. W.Zhao, S.Shetty, J.Zhang, T.Liu, JunDeschavanne, P. J.Edwards, Scott2016-05-132007Shedlock, A. M., C. W. Botka, S. Zhao, J. Shetty, T. Zhang, J. S. Liu, P. J. Deschavanne, and S. V. Edwards. 2007. “Phylogenomics of Nonavian Reptiles and the Structure of the Ancestral Amniote Genome.” Proceedings of the National Academy of Sciences 104 (8) (February 16): 2767–2772. doi:10.1073/pnas.0606204104.0027-8424http://nrs.harvard.edu/urn-3:HUL.InstRepos:27002630We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of ≈65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome.en-USBACReptiliaretroelementisochoreintronJournal Article2016-05-1310.1073/pnas.0606204104