The complete chloroplast genome sequence of Pseudostellaria palibiniana (Takeda) Ohwi (Caryophyllaceae)

Abstract

Pseudostellaria palibiniana (Takeda) Ohwi which belongs to Caryophyllaceae is distributed in Korea and Japan. In this study, we present the complete chloroplast genome of P. palibiniana which is 149,668 bp long and has four subregions: 81,313 bp of large single copy (LSC) and 16,958 bp of small single copy (SSC) regions are separated by 25,709 bp of inverted repeat (IR) regions including 126 genes (81 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.5% and those in the LSC, SSC, and IR regions are 34.3%, 29.4%, and 42.4%, respectively.

Keywords:

• Pseudostellaria
• chloroplast genome
• Pseudostellaria palibiniana
• Caryophyllaceae

Pseudostellaria palibiniana (Takeda) Ohwi is a perennial and herbaceous plant which is only distributed in the Korean peninsula and Honshu in Japan (Ōi et al. 1965; Park 2007). It also contains secondary metabolites which have pharmacological effect (Yang and Kim 1984) like Pseudostellaria heterophylla (Han et al. 2008; Chen et al. 2018; Deng et al. 2018). It lives mainly in foothills and forests. This species adopts a mixed-mating system which has both open-pollinated chasmogamous and permanently closed self-pollinating cleistogamous flowers (Culley and Klooster 2007). P. palibiniana was classified in series Mamillatae by its seed coat and in subseries Verticillatae by leaf arrangement (pseudo whorl; Ohwi 1937). Despite obvious morphological differences among four species in subseries Verticillatae, P. palibiniana is unresolved with the other species, named as P. palibiniana species complex (Kim et al., in preparation).

We sequence complete chloroplast genome of P. palibiniana to understand the phylogenic relationship of Pseudostellaria species with the already published two chloroplast genomes of Pseudostellaria genus (Kim and Park 2009; Kim et al. 2018). Pseudostellaria palibiniana was collected in Mt. Gwangdeok, Gangwon Province, Korea (N38°7'18.68", E 127°26'14.23"). The voucher and its DNA are deposited in InfoBoss Cyber Herbarium (IN; Y. Kim, IB-00588). Total DNA was extracted from fresh leaves of P. palibiniana by using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome sequencing was performed using HiSeq2000 at Macrogen Inc., Korea, and de novo assembly was done by Velvet 1.2.10 (Zerbino and Birney 2008) and confirmed all assembled bases using BWA 0.7.17 and SAMtools 1.9 (Li et al. 2009; Li 2013). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for chloroplast genome annotation based on Pseudostellaria longipedicellata (Kim et al. 2018).

The chloroplast genome of P. palibiniana (Genbank accession is MK120981) is 149,626 bp long and has four subregions: 81,313 bp of large single copy (LSC) and 16,958 bp of small single copy (SSC) regions are separated by 25,709 bp of the inverted repeat (IR). It contains 126 genes (81 protein-coding genes, eight rRNAs, and 37 tRNAs); 18 genes (seven protein-coding genes, four rRNAs, and seven tRNAs) are duplicated in IR regions. The overall GC content of P. palibiniana is 36.5% and those in the LSC, SSC, and IR regions are 34.3%, 29.4%, and 42.4%, respectively.

Nine complete chloroplast genomes of Caryophyllaceae including three Pseudostellaria species and two species from Amaranthaceae were used for constructing maximum likelihood phylogenetic tree. Alignment was conducted by MAFFT 7.388 (Katoh and Standley 2013) and a phylogenetic tree was constructed by IQ-TREE 1.6.6 (Nguyen et al. 2015). The phylogenetic tree shows that three Pseudostellaria species belonging to P. palibiniana species complex (Kim et al., in preparation) is resolved clearly with monophyletic manner (Figure 1). The tree also presents that Alsinoideae, containing Alsineae and Sagineae, is paraphyletic, which is different from the previous molecular phylogenic study (Greenberg and Donoghue 2011; Figure 1). In consequence, Caryophylloideae and Alsinoideae are monophyletic (Greenberg and Donoghue 2011); while the tree shows that Caryophylloideae is monophyletic but Alsinoideae is paraphyletic (Figure 1). Our results indicate that Pseudostellaria chloroplast genomes can provide additional information on phylogenetic relationships in Caryophyllaceae.

Figure 1. Maximum likelihood phylogenetic tree of Caryophyllaceae based on 11 complete chloroplast genomes: Pseudostellaria palibiniana (MK120981; in this study), Pseudostellaria okamotoi (MH879018); Pseudostellaria longipedicellata (MH373593), Beta vulgaris subsp. vulgaris (KR230391), Chenopodium album (NC_034950), Gymnocarpos przewalskii (NC_036812), Colobanthus quitensis (NC_028080), Dianthus longicalyx (KM668208), Agrostemma githago (NC_023357), Lychnis wilfordii (NC_035225), and Silene conoidea (NC_023358). The numbers above branches indicate bootstrap support values.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIP) (No. NRF-2014R1A1A1008723).