Shedlock Andrew M
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA.
Syst Biol. 2006 Dec;55(6):902-11. doi: 10.1080/10635150601091924.
It is unlikely that taxonomically diverse phylogenetic studies will be completed rapidly in the near future for nonmodel organisms on a whole-genome basis. However, one approach to advancing the field of "phylogenomics" is to estimate the structure of poorly known genomes by mining libraries of clones from suites of taxa, rather than from single species. The present analysis adopts this approach by taking advantage of megabase-scale end-sequence scanning of reptilian genomic clones to characterize diversity of CR1-like LINEs, the dominant family of transposable elements (TEs) in the sister group of mammals. As such, it helps close an important gap in the literature on the molecular systematics and evolution of retroelements in nonavian reptiles. Results from aligning more than 14 Mb of sequence from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta), Bahamian green anole (Anolis smaragdinus), Tuatara (Sphenodon punctatus), Emu (Dromaius novaehollandiae), and Zebra Finch (Taeniopygia guttata) against a comprehensive library approximately 3000 TE-encoding peptides reflect an increasing abundance of LINE and non-long-terminal-repeat (non-LTR) retrotransposon repeat types with the age of common ancestry among exemplar reptilian clades. The hypothesis that repeat diversity is correlated with basal metabolic rate was tested using comparative methods and a significant nonlinear relationship was indicated. This analysis suggests that the age of divergence between an exemplary clade and its sister group as well as metabolic correlates should be considered in addition to genome size in explaining patterns of retroelement diversity. The first phylogenetic analysis of the largely unexplored chicken repeat 1 (CR1) 3' reverse transcriptase (RT) conserved domains 8 and 9 in nonavian reptiles reveals a pattern of multiple lineages with variable branch lengths, suggesting presence of both old and young elements and the existence of several distinct well-supported clades not apparent from previous characterization of CR1 subfamily structure in birds and the turtle. This mode of CR1 evolution contrasts with historical patterns of LINE 1 diversification in mammals and hints toward the existence of a rich but still largely unexplored diversity of nonavian retroelements of importance to advancing both comparative vertebrate genomics and amniote systematics.
在不久的将来，不太可能在全基因组基础上迅速完成针对非模式生物的分类学多样化系统发育研究。然而，推进“系统发育基因组学”领域的一种方法是，通过挖掘来自一系列分类群的克隆文库，而非单个物种的克隆文库，来估计了解甚少的基因组结构。本分析采用了这种方法，利用对爬行动物基因组克隆进行的兆碱基规模末端序列扫描，来表征CR1样长散在核元件（LINE）的多样性，CR1样长散在核元件是哺乳动物姐妹类群中主要的转座元件（TE）家族。因此，它有助于填补关于非鸟类爬行动物反转录元件分子系统学和进化的文献中的一个重要空白。将美国短吻鳄（密西西比鳄）、锦龟、巴哈马绿安乐蜥、楔齿蜥、鸸鹋和斑胸草雀超过14 Mb的序列与一个约3000个编码TE的肽段的综合文库进行比对，结果显示，随着典型爬行动物类群共同祖先的年代增加，LINE和非长末端重复（non-LTR）反转录转座子重复类型的丰度不断增加。使用比较方法对重复多样性与基础代谢率相关的假设进行了检验，结果表明存在显著的非线性关系。该分析表明，除了基因组大小外，在解释反转录元件多样性模式时，还应考虑典型类群与其姐妹类群之间的分化年代以及代谢相关性。对非鸟类爬行动物中很大程度上未被探索的鸡重复元件1（CR1）3'逆转录酶（RT）保守结构域8和9进行的首次系统发育分析，揭示了一个具有可变分支长度的多谱系模式，表明存在古老和年轻的元件，以及几个明显不同且得到充分支持的分支，这在先前对鸟类和龟类CR1亚家族结构的表征中并不明显。CR1的这种进化模式与哺乳动物中LINE 1多样化的历史模式形成对比，并暗示存在丰富但仍在很大程度上未被探索的非鸟类反转录元件多样性，这对于推进比较脊椎动物基因组学和羊膜动物系统学都很重要。
