Abstract
Bletilla formosana is a medicinal plant commonly used in the southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of B. formosana to investigate its phylogenetic relationship in the family Orchidaceae. The chloroplast genome of B. formosana was 160,036 bp in length with 37.2% overall GC content, including a large single-copy (LSC) region of 87,636 bp, a small single-copy (SSC) region of 18,792 bp and a pair of inverted repeats (IRs) of 26,804 bp. The cp genome contained 104 genes, including 71 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated B. formosana was closely related to Bletilla striata.
Bletilla is a genus of the Orchidaceae family, which includes six species in the world. Most of them are widely distributed in Myanmar, China and Japan in Asia. There are four species in China (Li and Ian Citation1994). Plants of this genus have been widely used in traditional Chinese medicine for thousands of years (Jiangsu New Medical College Citation1977). Among these species, Bletilla formosana is widely distributed in southwest China which have been used in ethnic medicine as Hemostasis, antibacterial, antitumor, antiulcer and other activities (Minru and Yi Citation2016; Zhi et al. Citation2018). However, up to now for such medicinal plant, many studies have mainly focused on describing its quality evaluation (Mei-Jun et al. Citation2017; Houbo et al. Citation2019), chemical compositions (Xian-Jie Ma et al. Citation2017), Pharmacological action (Diao et al. Citation2008), with little involvement in its molecular biology, so that no comprehensive genomic resource is conducted for it. Here, we report the chloroplast genome sequence of B. formosana and find its internal relationships within the family Orchidaceae.
Fresh and clean leave materials of B. formosana were collected from Lijiang city, Yunnan, China (N26°56′14.74″, E100°11′11.36″), and the plant materials and a voucher specimen (TC09) were Tourism and Culture College of Yunnan University (Lijiang). Total genomic DNA was extracted using the improved CTAB method (Doyle Citation1987; Yang et al. Citation2014), and sequenced with Illumina Hiseq 2500 (Novogene, Tianjin, China) platform with pair-end (2 × 300 bp) library. The raw data was filtered using Trimmomatic v.0.32 with default settings (Bolger et al. Citation2014). Then, paired-end reads of clean data were assembled into circular contigs using GetOrganelle.py (Jin et al. Citation2018) with Bletilla striata (NC_028422) as reference. Finally, the cpDNA was annotated by the Dual Organellar Genome Annotator (DOGMA; http://dogma.ccbb.utexas.edu/) (Wyman et al. Citation2004) and tRNAscan-SE (Lowe and Chan Citation2016) with manual adjustment using Geneious v. 7.1.3 (Kearse et al. Citation2012).
The circular genome map was generated with OGDRAW v.1.3.1 (Greiner et al. Citation2019). Then the annotated chloroplast genome was submitted to the GenBank under the accession number MT012412. The chloroplast genome of B. formosana was 160,036 bp in length with 37.2% overall GC content, including a large single-copy (LSC) region of 87,636 bp, a small single-copy (SSC) region of 18,792 bp and a pair of inverted repeats (IRs) of 26,804 bp. The cp genome contained 104 genes, including 71 protein-coding genes, 29 tRNA genes, and 4 rRNA genes.
To investigate its taxonomic status, a total of 14 cp genome sequences of Orchidaceae species were downloaded from the NCBI database used for phylogenetic analysis. After using MAFFT V.7.149 for aligning (Katoh and Standley Citation2013), a neighbor-joining (NJ) tree was constructed in MEGA v.7.0.26 (Kumar et al. Citation2016) with 1000 bootstrap replicates and five Liliaceae species (Fritillaria karelinii: KX354691, Fritillaria dajinensis: NC 044632, Fritillaria cirrhosa: MH244906, Fritillaria sinica: NC 044631, and Fritillaria przewalskii: NC 044636) were used as outgroups. The results showed that B. formosana was closely related to Bletilla striata (). Meanwhile, the phylogenetic relationship in Orchidaceae was consistent with previous studies and this will be useful data for developing markers for further studies.
Figure 1. Neighbor-joining (NJ) tree of 15 species within the family Orchidaceae based on the plastomes using five Liliaceae species as outgroups.
Disclosure statement
The authors are highly grateful to the published genome data in the public database. The authors declare no conflicts of interest and are responsible for the content.
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References
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