Ansell S W, Schneider H, Pedersen N, Grundmann M, Russell S J, Vogel J C
Department of Botany, The Natural History Museum, London, UK.
J Evol Biol. 2007 Nov;20(6):2400-11. doi: 10.1111/j.1420-9101.2007.01397.x.
Extensive intraspecific variation in the chloroplast trnL(UAA)-trnF(GAA) spacer of model plant Arabidopsis lyrata is caused by multiple copies of a tandemly repeated trnF pseudogene undergoing parallel independent changes in copy number. Linkage disequilibrium and secondary structure analyses indicate that the diversification of pseudogene copies is driven by complex processes of structurally mediated illegitimate recombination. Disperse repeats sharing similar secondary structures interact, facilitating reciprocal exchange of structural motifs between copies via intramolecular and intermolecular recombinations, forming chimeric sequences and iterative expansion and contraction in pseudogene copy numbers. Widely held assumptions that chloroplast sequence evolution is simple and structural changes are informative are violated. Our findings have important implications for the use of this highly variable region in Brassicaceae studies. The reticulate evolution and nonindependent nucleotide substitution render the pseudogene inappropriate for standard phylogenetic reconstruction, but over short evolutionary timescales they may be useful for assessing gene flow, hybridization and introgression.
模式植物琴叶拟南芥叶绿体trnL(UAA)-trnF(GAA)间隔区广泛的种内变异是由一个串联重复的trnF假基因的多个拷贝引起的，这些拷贝在拷贝数上经历了平行独立的变化。连锁不平衡和二级结构分析表明，假基因拷贝的多样化是由结构介导的非法重组的复杂过程驱动的。具有相似二级结构的分散重复序列相互作用，通过分子内和分子间重组促进拷贝之间结构基序的相互交换，形成嵌合序列，并导致假基因拷贝数的迭代扩增和收缩。叶绿体序列进化简单且结构变化具有信息性这一广泛持有的假设被打破。我们的发现对在十字花科研究中使用这个高度可变区域具有重要意义。网状进化和非独立的核苷酸取代使得该假基因不适用于标准的系统发育重建，但在较短的进化时间尺度上，它们可能有助于评估基因流动、杂交和基因渗入。
