Dabbagh Nadja, Bennett Matthew S, Triemer Richard E, Preisfeld Angelika
Faculty of Mathematics and Natural Sciences, Zoology and Didactics of Biology, Bergische Universität Wuppertal, Wuppertal, Germany.
Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America.
PeerJ. 2017 Aug 25;5:e3725. doi: 10.7717/peerj.3725. eCollection 2017.
Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome of , and the spread and peculiarities of introns.
The cpGenome was sequenced, annotated and afterwards examined in structure, size, gene order and intron content. These features were compared with other euglenoid cpGenomes as well as those of prasinophyte green algae, including .
With about 130,561 bp the chloroplast genome of , a basal taxon in the phototrophic euglenoids, was considerably larger than the two other Eutreptiales cpGenomes sequenced so far. Although the detected quadripartite structure resembled most green algae and plant chloroplast genomes, the gene content of the single copy regions in was completely different from those observed in green algae and plants. The gene composition of was extensively changed and turned out to be almost identical to other Eutreptiales and Euglenales, and not to . Furthermore, the cpGenome of was unexpectedly permeated by a high number of introns, which led to a substantially larger genome. The 51 identified introns of showed two major unique features: (i) more than half of the introns displayed a high level of pairwise identities; (ii) no group III introns could be identified in the protein coding genes. These findings support the hypothesis that group III introns are degenerated group II introns and evolved later.
在过去几年中，多项研究表明，眼虫藻目叶绿体基因组（cp基因组）的大小以及基因簇的排列存在很大差异。然而，虽然这些基因组为眼虫藻目及其属内cp基因组的进化提供了重要见解，但仅对眼虫藻目和真眼点藻目之间以及内部的基因组变异性进行了两个基因组的分析。为了更好地理解早期进化的真眼点藻目叶绿体基因组进化的动态过程，本研究聚焦于[具体物种]的cp基因组以及内含子的分布和特性。
对[具体物种]的cp基因组进行测序、注释，随后检查其结构、大小、基因顺序和内含子含量。将这些特征与其他眼虫藻cp基因组以及绿藻门绿藻（包括[具体物种]）的cp基因组进行比较。
作为光合眼虫藻中的一个基部类群，[具体物种]的叶绿体基因组约为130,561 bp，比迄今为止测序的另外两个真眼点藻目cp基因组大得多。尽管检测到的四分体结构与大多数绿藻和植物叶绿体基因组相似，但[具体物种]单拷贝区域的基因含量与绿藻和植物中观察到的完全不同。[具体物种]的基因组成发生了广泛变化，结果显示与其他真眼点藻目和眼虫藻目几乎相同，而与[另一物种]不同。此外，[具体物种]的cp基因组意外地被大量内含子渗透，这导致基因组大幅增大。[具体物种]中鉴定出的51个内含子表现出两个主要独特特征：（i）超过一半的内含子显示出高水平的成对同一性；（ii）在蛋白质编码基因中未鉴定到III类内含子。这些发现支持了III类内含子是退化的II类内含子且进化较晚的假说。
