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Complete plastome sequences of two Neottia species and comparative analysis with other Neottieae species (Orchidaceae)
Folia Geobotanica ( IF 1.2 ) Pub Date : 2019-12-01 , DOI: 10.1007/s12224-019-09356-1
Zhi-Xin Zhu , Jian-Hua Wang , Shota Sakaguchi , Kun-Kun Zhao , Michael J. Moore , Hua-Feng Wang

The tribe Neottieae (Orchidaceae subfam. Epidendroideae) represents an excellent potential system for understanding plastome evolution in orchids. The tribe includes about 100 species with six recognized genera and includes both chlorophyllous and achlorophyllous taxa. Previously published Neottieae plastomes have revealed a complicated history of gene loss, particularly ndh gene loss, as well as plastome structural changes in achlorophyllous taxa. However, the plastome structure of most Neottieae taxa remains unknown. Here we investigate plastome structure in two newly sequenced Neottia species (N. suzukii and N. japonica) and characterize sequence divergence among Neottieae plastomes. We sequenced and analysed the complete plastomes of three individuals of two Neottia species (two individuals of N. japonica and one individual of N. suzukii) and compared them to seven additional published Neottia plastomes. The total genome lengths of the plastomes of N. japonica and N. suzukii ranged from 156,978 to 157,326 bp. The newly sequenced plastomes possessed the typical structure and gene content of angiosperm plastomes. Phylogenetic analyses based on complete plastomes and the nuclear internal transcribed spacer (ITS) showed that N. japonica and N. suzukii form a clade, but the two accessions of N. japonica were in phylogenetically incongruent positions in ITS vs plastome trees. Among all three newly sequenced Neottia plastomes, five regions (ndhH-ndhA spacer, ndhA intron, ycf3 intron, atpF intron, and trnL-ndhB spacer) showed high nucleotide divergence values (> 0.15), and are therefore considered useful molecular markers for future phylogenetic and phylogeographic studies of Neottia.

中文翻译:

两个 Neottia 物种的完整质体序列以及与其他 Neottieae 物种(兰科)的比较分析

Neottieae 部落(兰科亚群。表皮树科)代表了一个极好的潜在系统,可用于了解兰花的塑性体进化。该部落包括大约 100 个物种,其中有 6 个公认的属,包括叶绿素和无叶绿素类群。先前发表的新海藻塑性体揭示了基因丢失的复杂历史,尤其是 ndh 基因丢失,以及无叶绿素类群的塑性体结构变化。然而,大多数 Neottieae 类群的塑性体结构仍然未知。在这里,我们研究了两种新测序的新海豹属物种(铃木猪笼草和日本猪笼草)的塑性体结构,并表征了新海豹属塑性体之间的序列差异。我们对两个 Neottia 物种的三个个体(两个 N. japonica 个体和一个 N. japonica 个体)的完整塑性体进行了测序和分析。suzukii) 并将它们与另外七个已发表的 Neottia 塑性体进行比较。N. japonica 和 N. suzukii 的质体的总基因组长度介于 156,978 至 157,326 bp 之间。新测序的质体具有被子植物质体的典型结构和基因含量。基于完整塑性体和核内转录间隔区 (ITS) 的系统发育分析表明,日本猪笼草和铃木猪笼草形成了一个进化枝,但日本猪笼草的两个种质在 ITS 与塑性体树中处于系统发育不一致的位置。在所有三个新测序的 Neottia 质体中,五个区域(ndhH-ndhA 间隔区、ndhA 内含子、ycf3 内含子、atpF 内含子和 trnL-ndhB 间隔区)显示出高核苷酸差异值(> 0.15),
更新日期:2019-12-01
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