Niu Zhitao, Pan Jiajia, Zhu Shuying, Li Ludan, Xue Qingyun, Liu Wei, Ding Xiaoyu
College of Life Sciences, Nanjing Normal University, Nanjing, China.
Front Plant Sci. 2017 Oct 4;8:1713. doi: 10.3389/fpls.2017.01713. eCollection 2017.
Apostasioideae, consists of only two genera, and , which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of and were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., and ), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase () genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci- intron, , , , , , , , , and -that had the highest degrees of sequence variability were identified as mutational hotspots for the plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.
拟兰亚科仅由两个属组成，即 Apostasia 和 Neuwiedia，主要分布在东南亚和澳大利亚北部。拟兰亚科的花结构、分类学、生物地理学和基因组变异已得到深入研究。然而，尚未对其质体基因组的组成和结构进行详细分析，也未与其他兰花亚科进行比较。在此，对 Apostasia 和 Neuwiedia 的完整质体基因组序列进行了测序，并与之前发表的 43 个光合兰花质体基因组进行比较，以表征兰花质体基因组的结构和进化。与许多兰花质体基因组（如 Cymbidium 和 Phalaenopsis）不同，拟兰亚科的质体基因组包含全套 11 个功能性 NADH 脱氢酶（ND）基因。重复序列和简单序列重复元件的分布进一步证明非编码区的突变率高于编码区。10 个位点——trnK - intron、rpoC1、rpoB、rbcL、atpB、ndhF、ndhH、ndhG、ndhD 和 ndhA——具有最高程度的序列变异性，被确定为 Apostasioideae 质体基因组的突变热点。此外，我们的结果表明，质体基因在不同兰花属内和属间表现出可变的进化速率。考虑到编码区和非编码区的多样化进化，我们认为兰花物种的全质体基因组进化是不均衡的。此外，根据是否存在 ycf1 基因，光合兰花质体基因组的反向重复/小单拷贝（IR/SSC）连接处两侧的序列被分为三种类型。还提出了三种光合兰花质体基因组 IR/SSC 类型各自不同的进化动态。
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