Shedlock Andrew M, Botka Christopher W, Zhao Shaying, Shetty Jyoti, Zhang Tingting, Liu Jun S, Deschavanne Patrick J, Edwards Scott V
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2767-72. doi: 10.1073/pnas.0606204104. Epub 2007 Feb 16.
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 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 approximately 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. The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174).
我们报告了对哺乳动物的姐妹类群——爬行纲进行的兆碱基规模系统发育基因组分析的结果。对一只乌龟、一只短吻鳄和一只蜥蜴的基因组克隆进行大规模末端序列扫描，发现了在鸡中未发现的多样的、类似哺乳动物的逆转录元件景观和简单序列重复序列（SSRs）。包括CR1样长散在元件（LINEs）独特的系统发育谱系和富含A - T的SSRs缺乏等几个全局基因组特征，是乌龟和主龙类基因组的特征，而串联重复序列的较高频率和较低的全局GC含量揭示了绿安乐蜥具有类似哺乳动物的特征。非鸟类爬行动物基因组还拥有在鸡或哺乳动物中未发现的高频率多样且新颖的50碱基单位串联重复序列。大约65,000个8聚体寡核苷酸的频率分布表明，爬行动物中DNA词频变化率比哺乳动物慢一个数量级。这些结果表明羊膜动物的共同祖先中存在各种各样的散在元件和SSRs，以及爬行动物中逆转录元件的基因组保守性和逐渐丧失，最终形成了极简的鸡基因组。本文报道的序列已存入GenBank数据库（登录号：CZ 250707 - CZ 257443和DX 390731 - DX 389174）。
