Abstract
BackgroundThe genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera. Platanthera ussuriensis, formerly named as Tulotis ussuriensis, is a small terrestrial orchid species and has been listed as wild plant under State protection (category II) in China. An improved understanding of the genomic information will enable future applications of conservation strategy as well as phylogenetic studies for this rare orchid species. The objective of this research was to characterize and compare the chloroplast genome of P. ussuriensis with other closely related species of Orchidaceae.ResultsThe chloroplast genome sequence of P. ussuriensis is 155,016 bp in length, which included a pair of inverted repeats (IRs) of 26,548 bp that separated a large single copy (LSC) region of 83,984 bp and a small single copy (SSC) region of 17,936 bp. The annotation contained a total of 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The simple sequence repeat (SSR) analysis showed that there were 104 SSRs in the chloroplast genome of P. ussuriensis. RNA editing sites recognition indicated 72 RNA editing events occurred, and all codon changes were C to T conversions. Comparative genomics showed that the chloroplast sequence of Platanthera related species were relatively conserved, while there were still some high variation regions that could be used as molecular markers. Moreover, Platanthera related species showed similar IR/SSC and IR/LSC borders. The phylogenetic analysis suggested that P. ussuriensis had a closer evolutionary relationship with P. japonica followed by the remaining Platanthera species.ConclusionOrchidaceae is a key group of biodiversity protection and also a hot spot group in the plant taxonomy and evolution studies due to their characteristics of high specialization and rapid evolution. This research determined the complete chloroplast genome of P. ussuriensis for the first time, and compared the sequence with other closely related orchid species. These results provide a foundation for future genomic and molecular evolution of the Orchidaceae species, and provide insights into the development of conservation strategy for Platanthera species.
Highlights
IntroductionHan et al BMC Genomics (2022) 23:84 all kinds of terrestrial ecosystems in the world, and is a hot spot group in the plant taxonomy and evolution studies due to the characteristics of high specialization and rapid evolution [3]
The genus Tulotis has been classified into the genus Platanthera in the present taxonomic studies since the morphological characteristics of this genus is very similar to that of Platanthera
General feature of the chloroplast genome The chloroplast genome of P. ussuriensis is a circular molecule of 155,016 bp (Fig. 1), consisting of a large single copy (LSC) region of 83,984 bp, a small single copy (SSC) region of 17,936 bp, and a pair of inverted repeats (IRa and IRb) of 26,548 bp
Summary
Han et al BMC Genomics (2022) 23:84 all kinds of terrestrial ecosystems in the world, and is a hot spot group in the plant taxonomy and evolution studies due to the characteristics of high specialization and rapid evolution [3]. It is widely recognized that the identification of orchid species is difficult, especially in the non-flowering period when many orchid species plants have very similar morphological characteristics. Many orchid species could crossbreed successfully in a wide range, resulting in many intermediate types and large natural variations. All of these make it very difficult for traditional taxonomy based on the morphological characteristics of orchids [5,6,7,8,9]. It is difficult to understand the phylogenetic relationship between various groups because of the relatively complex evolutionary process and multi lineage origin of many orchid genera [10, 11]
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