{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T13:53:10Z","timestamp":1791294790130,"version":"4.1.0"},"reference-count":43,"publisher":"National Academy of Sciences","issue":"8","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2007,2,20]]},"abstract":"<jats:p>\n                    We 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\n                    <jats:italic>Anolis<\/jats:italic>\n                    . 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 \u224865,000 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.\n                  <\/jats:p>","DOI":"10.1073\/pnas.0606204104","type":"journal-article","created":{"date-parts":[[2007,2,16]],"date-time":"2007-02-16T20:57:20Z","timestamp":1171659440000},"page":"2767-2772","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":118,"title":["Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome"],"prefix":"10.1073","volume":"104","author":[{"given":"Andrew M.","family":"Shedlock","sequence":"first","affiliation":[{"name":"Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher W.","family":"Botka","sequence":"additional","affiliation":[{"name":"Research Division, Joslin Diabetes Center, Harvard Medical School, One Joslin Place, Boston, MA 02215;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaying","family":"Zhao","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyoti","family":"Shetty","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun S.","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick J.","family":"Deschavanne","sequence":"additional","affiliation":[{"name":"Equipe de Bioinformatique Genomique et Moleculaire, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale (INSERM), 2 Place Jussieu, 75005 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott V.","family":"Edwards","sequence":"additional","affiliation":[{"name":"Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2007,2,20]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026278"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature01858"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature03025"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.ecolsys.34.011802.132351"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature03154"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1086\/342079"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/46555"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2005.01.015"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-006-1035-8"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/35057062"},{"key":"e_1_3_4_11_2","volume-title":"Animal Cytogenetics: Chordata: Reptilia","author":"Olmo E","year":"1986","unstructured":"E Olmo Animal Cytogenetics: Chordata: Reptilia (Gebr\u00fcder Borntraeger, Berlin) Vol 4 (1986)."},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.88.13.5814"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a025730"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003768"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msh069"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(02)00732-1"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0320(19980201)31:2<100::AID-CYTO5>3.0.CO;2-Q"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature01262"},{"key":"e_1_3_4_19_2","first-page":"886","volume":"11","author":"Vandergon TL","year":"1994","unstructured":"TL Vandergon, M Reitman Mol Biol Evol 11, 886\u2013898 (1994).","journal-title":"Mol Biol Evol"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.6.2869"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1006\/mpev.1996.0390"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.1991.tb04385.x"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.7.5.471"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026048"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.91.26.12832"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.283.5404.998"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/384453a0"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-005-0986-5"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.24.14226"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(00)00425-X"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi075"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1055-7903(03)00108-8"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1038\/31927"},{"key":"e_1_3_4_35_2","volume-title":"COMPARE","author":"Martins EP","year":"2004","unstructured":"EP Martins COMPARE (Department of Biology, Indiana Univ, Bloomington, IN, Version 4.6b. 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