Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae

Abstract

Phalaenopsis zhejiangensis is a rare and endangered plant species with extremely small populations. The complete chloroplast (cp) genome of P. zhejiangensis was assembled, its structural organization was described and comparative genomic analyses was carried out. The cp genome of P. zhejiangensis is 143,547 bp in length, with a GC content of 37.2%, which includes a pair of inverted repeats (IRs) of 24,464 bp separated by a small single-copy region of 10,764 bp and a large single-copy region of 83,856 bp. The cp genome contains 126 genes, consisting of 80 protein-coding genes, 38 transfer RNAs, and eight ribosomal RNAs. Six protein-coding genes, including ψndhB (two copies), ψndhD, ψndhG, ψndhK, and ψndhI, are identified as pseudogenes. Another six ndh genes, ndhA, ndhC, ndhE, ndhF, ndhH, and ndhJ, are missing from the plastid genome. A total of 41 cp simple sequence repeats (SSRs) were identified, including 40 mono-nucleotides and one di-nucleotides. Phylogenic analysis revealed P. zhejiangensis was nested inside the Phalaenopsis species and sister to P. wilsonii. The assembly and analysis of P. zhejiangensis cp genome will provide essential data for further study of taxonomy and systematics of Orchidaceae.

Keywords:

• Phalaenopsis zhejiangensis
• rare and endangered species
• chloroplast genome
• phylogenetic analysis

Authors contributions

Conceived and designed the experiments: MJ and HJZ. Performed the experiments: MJ, WQ, and ZY. Analyzed the data: HZW and LQP. Contributed to reagents/materials/analysis tools: MJ and WQ. Wrote the paper: MJ and HJZ.

Disclosure statement

The authors declare that they have no competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Data availability statement

The data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MZ326749. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA734444, SRR14710950, and SAMN19491762, respectively.

Additional information

Funding

This work was supported by 211 Talent Training Fund of Taizhou under Grant number [2012].