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.

Comparative Chloroplast Genome Analysis of Two Deciduous Phalaenopsis species, Phylogenetic Relationships, and Development of Indel markers

“…The ndings from the phylogenetic analysis did not align with numerous prior researches, which have established that P. wilsonii and P. lowii comprise a sister group [23,24,27]. Jiang et al (2021) concluded that P. zhejiangensis was most closely related to P. wilsonii [25]. However, another study has shown that P. wilsonii and P. stobartiana were most closely related, and the clade containing these two species was most closely related to the clade containing P. zhejiangensis and P. lowii [26].…”

“…Complete chloroplast genomes have been extensively applied to taxonomic studies and phylogeny reconstruction of plants [15,16,17]. Several chloroplast genomes of Phalaenopsis plants have been sequenced, including Phalaenopsis Aphrodite [18], Phalaenopsis 'Tiny Star' [19], Phalaenopsis lowii [20], Phalaenopsis lobbii [21], Phalaenopsis mannii [22], P. wilsonii MW194929 [23], P. wilsonii NC_057488 [24], Phalaenopsis zhejiangensis [25], Phalaenopsis stobartiana [26], and Phalaenopsis malipoensis [27]. No complete chloroplast genome sequences of P. wilsonii f. wilsonii and P. braceanum have been uploaded to the National Center for Biotechnology Information (NCBI) database.…”

Genetic diversity based on SSR markers of 30 Aeridinae sub-tribe orchid genetic resources of Indonesian Ornamental Crop Research Institute, Cianjur, Indonesia

“…The previous reports have indicated a relatively limited number of polymorphic SSR markers for the Aeridinae subtribe collection. The previously reported genetic analysis for the Aeridinae subtribe using molecular markers includes those reported by Yun et al ( 2020) for the genetic diversity of P. scolopendrifolia, Kim et al (2020) for the evolution and phylogenetics of the Aeridinae subtribe, Dwiati and Susanto (2021) for the intergeneric crosses between the genus Phalaenopsis and Vanda, and Jiang et al (2021) for the chloroplasts genomic of the Phalaenopsis zhejiangensis.…”