Complete plastome sequences of two Neottia species and comparative analysis with other Neottieae species (Orchidaceae)
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.
Zhu, Zhi-Xin, Jian-Hua Wang, Shota Sakaguchi, et al. 2019. "Complete plastome sequences of two Neottia species and comparative analysis with other Neottieae species (Orchidaceae)." Folia Geobotanica 54(3-4): 257-266.