The complete chloroplast genome of Cymbidium floribundum var. pumilum (Orchidaceae).

Cymbidium floribundum var. pumilum is an epiphytic orchid distributed in the southern China. It has a high ornamental value and always be used as a hybrid parent. In this study, we obtained a complete chloroplast genome of C. floribundum var. pumilum from BGISEQ-500 sequencing data. The total chloroplast genome was 155,291 bp in length, consisting of a large single copy region (LSC 84,415 bp), a small single copy region (SSC 17,484 bp), and two inverted repeat regions (IRA and IRB 26,696 bp). The complete chloroplast genome contains 139 genes, including 80 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. In addition, the phylogenetic analysis indicates that C. floribundum var. pumilum was sister to section Geocymbidium, section Pachyrhizanthe and section Jensoa. The chloroplast genome will contribute to establish an effective conservation strategy for C. floribundum var. pumilum.

The genus Cymbidium (Orchidaceae) are terrestrial, epiphytic or rarely lithophytic, consisting of three subgenera, divided into ten sections and comprising approximately 55 species are found in the Asia with over 49 species distributed in China (Liu et al. 2006, 2009). The species of C. floribundum was first reported by Lindl in1833, and it is an epiphytic orchid usually grows on trees or rocks at altitudes of 100–3300 m in the subtropics and tropical areas of Asia (Liu et al. 2006; Chen 2011). However, the species of C. pumilum was originally published as an independent similar species not a variant of C. floribundum by Rolfe in 1907. Until 1980, it was merged into a variant of C. floribundum by Wu et al. Then, the C. floribundum var. pumilum was directly classified into the C. floribundum by Du Puy et al. in 1988 (Liu et al. 2006). Nonetheless, we compared the morphology and firmly believe that the C. floribundum var. pumilum is a variant of the C. floribundum. Therefore, we reported the complete chloroplast genome of C. floribundum var. pumilum, in order to better understand the relationship between C. floribundum var. pumilum and related genera.

In this study, the samples of C. floribundum var. pumilum were collected from Gushan Mountain Scenic Area in Fuzhou, Fujian Province, China (26°03'N, 119°24'E) and the specimens were kept in the Herbarium of Fujian Agriculture and Forestry University (specimen code DHL-GS). The total genomic DNA of C. floribundum var. pumilum was extracted from fresh leaves using a modified CTAB method (Doyle and Doyle 1987), and then sequenced by the BGISEQ-500 platform.

The complete chloroplast genome of C. floribundum var. pumilum was assembled by the GetOrganelle pipe-line (Jin et al. 2018). Then, we performed the annotation work by using the Geneious R11.15 (Kearse et al. 2012) with the chloroplast genome of C. macrorhizon (NC_029713) and C. lancifolium (NC_029712) as reference sequences. Finally, we obtained a complete chloroplast genome of C. floribundum var. pumilum and submitted to GenBank with accession number MN_173778.

The total chloroplast genome of C. floribundum var. pumilum is 155,291 bp in length and has a GC content of 36.8%. It contains a large single copy (LSC) region of 84,415 bp, a small single copy (SSC) region of 17,484 bp, and two inverted repeat regions (IRA and IRB) of 26,696 bp. Besides, the complete chloroplast genome of C. floribundum var. pumilum contains 139 genes, including 80 protein-coding genes, 38 tRNA genes, and 8 rRNA genes.

In order to investigate the phylogenetic position of C. floribundum var. pumilum, a phylogenetic tree was constructed by RAxML (Stamatakis 2014) with 1000 ultrafast bootstrap (UFBoot) replicates (Minh et al. 2013; Chernomor et al. 2016) based on 12 complete chloroplast genome sequences of Cymbidium (C. tortisepalum, C. kanran, C. lancifolium, C. floribundum var. pumilum, C. sinense, C. goeringii, C. ensifolium, C. faberi, C. macrorhizon, C. mannii, C. aloifolium, C. tracyanum) and 2 other genera (Oncidium sphacelatum, Eulophia zollingeri) as outgroups. The results showed that C. floribundum var. pumilum (from section Floribunde) was sister to the C. goeringii, C. ensifolium, C. tortisepalum, C. faberi, C. kanran, C. sinense (from section Jensoa), C. lancifolium (from section Geocymbidium) and C. macrorhizon (from section Pachyrhizanthe) with 100% bootstrap support (Figure 1).

Figure 1.

A phylogenetic tree constructed based on 12 complete chloroplast genome sequences of cymbidium (C. tortisepalum, C. ensifolium, C. kanran, C. aloifolium, C. faberi, C. tracyanum, C. lancifolium, C. floribundum var. pumilum, C. sinense, C. mannii, C. macrorhizon) and two other genera (Oncidium sphacelatum, Eulophia zollingeri) as outgroups, all of them downloaded from NCBI GenBank.