The complete chloroplast genome of Korean endemic species, Cirsium rhinoceros (H.Lév. & vaniot) Nakai (Asteraceae).

Cirsium rhinoceros (H.Lév. & Vaniot) Nakai has been used a traditional medicine. Complete chloroplast genome of C. rhinoceros is 152,576 bp long and has four subregions: 87,262 bp of large single copy (LSC) and 21,486 bp of small single copy (SSC) regions that are separated by 18,742 bp of inverted repeat (IR) regions including 133 genes (88 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.7% and in the LSC, SSC, and IR regions are 36.0%, 31.4%, and 43.8%, respectively. Phylogenetic trees show that Cirsium species are clustered along with their distribution.

Cirsium rhinoceros (H.Lév. & Vaniot) Nakai, which is Korean endemic species distributed in Jeju island, Republic of Korea, has been utilized as traditional medicine. It contains useful compounds, such as polyacetylene, three flavonoids, and norisoprenoids (Lee et al. 1994; Chung et al. 2002; Soon-Ho et al. 2003). Five Cirsium chloroplast genomes have been sequenced including two Korean species, which have also been used as traditional medicine. The rest three are from North America and one from Europe (Dann et al. 2017), which is a good resource for understanding the phylogenetic relationship based on geographical distribution. Complete chloroplast genomes have been used for understanding the phylogenetic position of endemic species, such as genus Pseudostellaria longipedicellata and Pseudostellaria palibiniana (Kim et al. 2018; Kim and Park 2019), Salix koriyanagi (Kim et al. 2019), a new variety candidate of Potentilla (Heo et al. 2019), and etc.

To understand the phylogenetic position of C. rhinoceros, its total DNA isolated from Jeju island, Republic of Korea (38.0960 N 127.4762 E) was extracted from fresh leaves by using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The voucher was deposited in InfoBoss Cyber Herbarium (IN; IBS-00010). The genome was sequenced using HiSeqX at Macrogen Inc., Korea, and de novo assembly and confirmation were performed by Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for annotation based on Cirsium vulgare chloroplast genome (NC_036967; Dann et al. 2017).

The chloroplast genome of C. rhinoceros (Genbank accession is MK922360) is 152,576 bp long (GC ratio is 37.7%) and has four subregions: 87,262 bp of large single copy (LSC; 36.0%) and 21,486 bp of small single copy (SSC; 31.4%) regions are separated by 18,742 bp of inverted repeat (IR; 43.8%). It contains 133 genes (88 protein-coding genes, 8 rRNAs, and 37 tRNAs); 16 genes (six protein-coding genes, four rRNAs, and six tRNAs) are duplicated in IR regions.

Six Cirsium including C. rhinoceros, two Cynara, one Centaurea, and one Saussurea chloroplast genomes were used for constructing neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenic trees using MEGA X (Kumar et al. 2018) after aligning whole chloroplast genomes using MAFFT 7.388 (Katoh and Standley 2013). Phylogenetic trees show that C. rhinoceros is clustered with two varieties of Cirsium japonicum distributed in the Korean peninsula and two Cirsium species in North America, and Cirsium eriophorum in Europe are separately clustered with three Korean Cirsium (Figure 1). It presents that Cirsium species have been evolved separately along with different geographical distribution. Many Korean Cirsium species will give chances to understand Cirsium phylogenetic relationship together with available Cirsium chloroplast genomes: whether Cirsium species in Korean peninsula, as refugia in glacial epoch, have been evolved divergently in comparison to other continents or not.

Figure 1.

Neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1000) phylogenetic trees of six Cirsium including C. rhinoceros, two Cynara, one Centaurea, and one Saussurea from Asteraceae: Cirsium rhinoceros (MK922360 in this study), Cirsium arvense (NC_036965), Cirsium eriophorum (NC_036966), Cirsium vulgare (NC_036967), Cirsium japonicum var. maackii (MF034024), Cirsium japonicum var. spinosissimum (MF034025), Cynara cardunculus var. scolymus (KM035764), Cynara humilis (NC_027113), Centaurea diffusa (NC_024286), and Saussurea involucrata (NC_029465). Phylogenetic tree was drawn based on neighbor joining tree. The numbers above branches indicate bootstrap support values of maximum likelihood and neighbor joining phylogenetic tree, respectively.