The complete chloroplast genome of Chrysoglossum ornatum (Epidendroideae, Orchidaceae) and its phylogenetic analysis

Abstract

Chrysoglossum ornatum Blume, the type species of Chrysoglossum Blume, belongs to the tribe Collabieae of the subfamily Epidendroideae of Orchidaceae. In this study, we sequenced, assembled, and analyzed the complete chloroplast genome of C. ornatum. The result showed that the complete chloroplast genome of C. ornatum was 158,175 bp in size, consisting of a large single-copy (LSC) region of 87,235 bp, a small single-copy (SSC) region of 18,384 bp, and a pair of inverted repeats (IRs) of 26,278 bp. The chloroplast genome encoded 113 unique genes, comprising 80 protein-coding genes, 29 tRNA genes, and four rRNA genes. Phylogenetic analysis inferred from the complete chloroplast genome indicated that Chrysoglossum was closely related to Collabium Blume. This study provides genomic resources helpful for further phylogenetic and biodiversity research on Chrysoglossum.

Keywords: Chrysoglossum; Collabieae; phylogenetic relationship; plastid genome.

Figure 1.

Photos of Chrysoglossum ornatum. (A) Inflorescences; (B) plants; (C) flower. The photographs were taken by Wei Wu.

Figure 2.

The chloroplast genome map of Chrysoglossum ornatum. From the center outward, the map consists of six rings. The first circle represents the forward and reverse repeats connected with red and green arcs, respectively. The second circle shows the tandem repeats marked. The third circle displays the microsatellite sequences. The fourth circle indicates the sizes of feature regions, including a large single-copy (LSC), a small single-copy (SSC), and two inverted repeats (IRa and IRb). The fifth circle exhibits the GC content. The sixth circle presents the genes with different functions.

Figure 3.

Phylogenetic tree inferred from the complete chloroplast genomes comprising 33 species from Orchidaceae. The ML bootstrap (BS) and BI posterior probability (PP) that supported each node are shown under the branches. The following sequences were used: Acampe rigida (Liu et al. 2020), Bletilla formosana (Wu et al. 2019), Bletilla striata (Feng et al. 2019), Bulbophyllum hirtum (Yang et al. 2022), Bulbophyllum Orientale (Yang et al. 2022), Bulleyia yunnanensis (Ai et al. 2020), Calanthe sylvatica (Miao et al. 2019), Cremastra appendiculata (Mao et al. 2018), Cymbidium aloifolium (Chen et al. 2020), Cymbidium ensifolium (Jiang et al. 2019), Cymbidium mastersii (Zheng et al. 2019), Habenaria ciliolaris (Chen et al. 2019), Oreorchis patens (Kim et al. 2020), Ponerorchis gracilis (Kim et al. 2020), Robiquetia spathulata (Liu et al. 2020), Smitinandia micrantha (Liu et al. 2020), Tainia cordifolia (Zheng et al. 2019), and Tainia dunnii (Xie et al. 2019).