The second complete chloroplast genome of Dysphania pumilio (R.Br.) mosyakin & clemants (Amranthaceae): intraspecies variation of invasive weeds

Abstract

We completed chloroplast genome of Dysphania pumilio (R.Br.) Mosyakin & Clemants isolated in Anyang city in Korea. Its length is 151,960 bp consisting four subregions: 83,756 bp of large single copy (LSC) and 17,742 bp of small single copy (SSC) regions are separated by 25,231 bp of inverted repeat (IR) region. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content is 36.9% and those in LSC, SSC, and IR regions are 34.8%, 30.4%, and 42.7%, respectively. 25 single nucleotide polymorphisms and two insertions and deletions suggest multiple invasive origins in Korea.

Keywords:

• Dysphania pumilio
• chloroplast genome
• intraspecies variation
• Amaranthaceae
• invasive origin

Genus Dysphania R. Br., consisting of up to 45 species among which 7 ∼ 10 species were endemic to Australia, contains aromatic plant species (Aellen 1930; Scott 1978; Wilson et al. 1983). Since Dysphana pumilio (R.Br.) Mosyakin & Clemants was introduced to Korea in 1992 (Chung et al. 2001), it has been spread out (Kang and Shim 2002). Usually, genetic diversity of invasive species ranges from low to high based on invasion patterns (Tsutsui et al. 2000; Stepien et al. 2005). Based on previous D. pumilio chloroplast genome (Kim et al. 2019b), another individual isolated in Anyang City in Gyounggi province, which is at a distance of 16 km from where the first individual was isolated (Kim et al. 2019b) was used for whole chloroplast genome sequences.

Total DNA of D. pumilio (Voucher in InfoBoss Cyber Herbarium (IN); Y Kim, IB-00594) was extracted from fresh leaves by using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome sequencing was performed using HiSeq4000 at Macrogen Inc., Korea, and de novo assembly and sequence confirmations were done 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 D. pumilio chloroplast complete genome (MH936550; Kim et al. 2019b).

Chloroplast genome length of D. pumilio (Genbank accession is MK541016) is 151,960 bp (GC ratio is 36.9%) and has four subregions: 83,756 bp of large single copy (LSC; 34.8%) and 17,742 bp of small single copy (SSC; 30.4%) regions are separated by 25,231 bp of inverted repeat (IR; 42.7%). It contained 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs); 17 genes (6 protein-coding genes, 4 rRNAs, and 7 tRNAs) are duplicated in IR regions.

By comparing with D. pumilio chloroplast genome (Kim et al. 2019b), 25 single nucleotide polymorphisms (SNPs) and two insertions and deletions (INDELs) are identified. This amount of variations is larger than those of Coffea (Park, Kim, Xi, et al. 2019), Liriodendron, Camellia, Marchantia, smaller than those of Pseudostellaria, Illicium, Duchesnea (Park, Kim, Lee 2019), and Rehmannia (Jeon et al. 2019), and similar to that of Camellia. It partially supports that D. pumilio chloroplast contains enough variations to support multiple invasive origins in Korea. Three SNPs are non-synonymous in matK, rpoC2, and ycf1, and five SNPs are synonymous in psbE, psbB, petD, ndhH, and ycf1.

Two complete Dysphania (Kim et al. 2019b), six Cheopodium (Devi and Thongam 2017; Hong et al. 2017; Wang et al. 2017; Kim et al. 2019a), and five Amranthaceae chloroplast genomes were used for constructing bootstrapped neighborjoining, maximum likelihood, and minimum evolution phylogenetic trees using MEGA X (Kumar et al. 2018) based on whole chloroplast genome alignment calculated by MAFFT 7.388 (Katoh and Standley 2013). Phylogenetic trees show the phylogenetic position of Dysphania genus is the same as previous phylogenetic study (Figure 1; Fuentes-Bazan et al. 2012).

Figure 1. Neighbor joining (bootstrap repeat is 10,000), maximum likelihood (bootstrap repeat is 1,000), and minimum evolution (bootstrap repeat is 10,000) phylogenetic trees of fourteen Amranthaceae complete chloroplast genomes: Dysphania pumilio (MK541016, in this study and MH936550), Chenopodium ficipolium (MK182725), Chenopodium quinoa ‘Real Blanca’ (CM008430), Chenopodium quinoa (NC_034949, MF805727, and KY635884), Chenopodium album (NC_034950 and MF418659), Spinacia oleracea (NC_002202), Beta vulgaris (EF534108), Salicornia brachiata (NC_027224), Bienertia sinuspersici (KU726550), and Suaeda malacosperma (NC_039180). Phylogenetic tree was drawn based on neighbor joining tree. The numbers above branches indicate bootstrap support values of neighbor joining, maximum likelihood, and minimum evolution phylogenetic trees, respectively.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by InfoBoss Research Grant [IBG-0001].