Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec (QC), Canada.
Sci Rep. 2017 Apr 20;7(1):994. doi: 10.1038/s41598-017-01144-1.
The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.
许多藻类和几乎所有陆地植物的叶绿体基因组都携带两个相同的大片段反向重复（IR）序列，这些序列可以配对进行翻转重组，并发生扩展/收缩。尽管在绿藻的进化过程中，IR 已经多次丢失，但其中的潜在机制仍在很大程度上未知。最近对来自绿藻门的 Ulvophyceae（Ulotrichales）的无 IR 和有 IR 的叶绿体基因组的比较表明，IR 拷贝中基因的差异消除可能导致 IR 丢失。为了更深入地了解 Ulvophyceae 叶绿体基因组的进化历史，我们分析了 Ignatius tetrasporus 和 Pseudocharacium americanum（Ignatiales，一个以前未取样的目）、Dangemannia microcystis（Oltmannsiellopsidales）、Pseudoneochloris marina（Ulvales）以及 Chamaetrichon capsulatum 和 Trichosarcina mucosa（Ulotrichales）的基因组。我们将这六个叶绿体基因组与以前报道的九个 Ulvophyceae 的基因组进行比较，发现了意想不到的变异性。所有新检查的基因组都具有 IR，但值得注意的是，Ignatiales、Pseudoneochloris 和 Chamaetrichon 中的 IR 拷贝在序列上存在差异，rRNA 操纵子中的 tRNA 基因在一个 IR 拷贝中缺失。讨论了这一前所未有的发现对 IR 丢失和翻转重组机制的影响。
