Search

The climbing plant Cynanchum rostellatum (Turcz.) Liede & Khanum is widely distributed throughout Korea and Northeast Asia as a member of the Apocynaceae family. Although this plant has a high value in medicinal and industrial purposes, genetic research on this plant is insufficient. This study announces the complete plastid genome (plastome) sequence of C. rostellatum with 663× mean coverage, which was assembled using 763 Mbp short-read data generated by the Illumina HiSeq X platform. The C. rostellatum plastome was 158,018 bp in length and displayed the typical quadripartite structure composed of the large single-copy (LSC) region (89,058 bp), the small single-copy (SSC) region (18,718 bp), and a pair of inverted repeat (IR) regions (25,116 bp). A total of 129 genes have been annotated, including 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis indicated the genus Cynanchum including 12 Cynanchum plastome sequences, was monophyletic and was located within the sub-family Asclepiadoideae. Two C. rostellatum plastomes, including the plastome assembled in this study, formed a subclade and were sister to the C. thesioides plastome, whereas the other C. rostellatum, which was previously reported one, was located within the clade of C. wilfordii and C. bungei.

Peucedanum hakuunense Nakai is one of the rare species in the Korean Peninsula. This study characterized the complete plastid genome (plastome) sequence of P. hakuunense by de novo assembly with next-generation sequencing data. The complete plastome of P. hakuunense is 147,426 bp in length with a typical quadripartite structure comprising a large single-copy region of 91,915 bp, a small single-copy region of 17,425 bp, and two inverted repeat regions of 19,043 bp in length. The plastome of P. hakuunense is composed of 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis revealed that two Peucedanum species formed an independent subclade, sister to the subclade of Angelica species within the tribe Selineae.

Complete plastid genome (plastome) and ribosomal DNA (rDNA) sequences of three Rubus accessions (two Rubus longisepalus and one R. hirsutus) were newly assembled using Illumina whole-genome sequences. Rubus longisepalus Nakai and R. longisepalus var. tozawai, described as different varieties, have identical plastomes and rDNA sequences. The plastomes are 155,957 bp and 156,005 bp and the 45S rDNA transcription unit sizes are 5809 bp and 5811 bp in R. longisepalus and R. hirsutus, respectively. The 5S rDNA transcription unit is an identical 121 bp in three Rubus accessions. We developed three DNA markers to authenticate R. longisepalus and R. hirsutus based on plastome diversity. Phylogenomic analysis revealed that the Rubus species classified as two clades and R. longisepalus, R. hirsutus, and R. chingii are the most closely related species in clade 1.

Epimedium pubescens Maxim. is a well-known traditional Chinese medicine herb. In this study, the complete chloroplast genome of E. pubescens was sequenced. The genome was 158 956 bp in length, with a large single-copy region of 86,345 bp, a small single-copy region of 17,075 bp, and 2 inverted repeat regions of 27,768 bp. The genome consisted of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC contents were 38.82%. Phylogenetic analysis showed that E. pubescens of series Brachyrcerae was firstly clustered with E. acumiantum Franch. of ser. Dolichocerae, but not with E. brevicornu Maxim. from the same series.

Mahonia eurybracteata subsp. ganpinensis (H.Lév.) T.S.Ying & Boufford. is an evergreen shrub of Berberidaceae and has the potentials for horticultural and medicinal development. In the present paper, the complete chloroplast genome of Mahonia eurybracteata subsp. ganpinensis (H.Lév.) T.S.Ying & Boufford. was sequenced. The complete chloroplast genome was 165,562 bp in length, containing a large single copy region (73,394 bp), a small single copy region (18,698 bp) and two inverted repeat regions (36,735 bp). The genome consisted of 113 genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis showed that M. eurybracteata subsp. ganpinensis and M. bealei were firstly clustered into a branch and the two Mahonia species were most closely related to the genus Berberis of Berberidaceae.

Liriope platyphylla is herbaceous perennial plant belonging to the Asparagaceae family and widely used both as ornamental plant and herbal medicine. The complete chloroplast genome of L. platyphylla was 156,754 bp in length, which was composed of four distinct parts; a large single copy (LSC) of 85,118 bp, a small single copy (SSC) of 18,680 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,478 bp. A total of 130 genes including 83 protein-coding genes, 39 tRNA genes and 8 rRNA genes were identified. The phylogenetic tree showed that L. platyphylla has a close relationship with other Nolinoideae plants, especially with Maianthemum dilatatum and Nolina atopocarpa.

Plagiorhegma dubia Maxim. is a traditional Chinese medicinal herb from Plagiorhegma, Berberidaceae, which is distributed in the northeast of China, Korea, Russia. The complete chloroplast genome is 152,468 bp in length, with large single copy (LSC 82,257 bp) and small single copy (SSC 16,599 bp) regions separated by a pair of inverted repeats (IR 26 805 bp). The genome has a total of 113 genes including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis shows that P. dubia is closely related with Sinopodophyllum hexandrum and Epimedium species. The results are of great implication for the development and utilization of P. dubia and the phylogenetic researches on Berberidaceae.

Lonicera maackii is native to Northeastern Asia and considered as an invasive plant in North America. In this study, the complete chloroplast genome of L. maackii was obtained by high-throughput next-generation sequencing technology. The chloroplast genome was 155,318 bp in length and had typical quadripartite structures comprising a large single copy, a small single copy, and a pair of inverted repeat regions of 89,202, 18,680, and 23,718 bp long, respectively. The genome contained 80 protein-coding genes, four rRNA genes and 30 tRNA genes. Phylogenetic tree revealed that L. maackii was grouped with other Caprifoliaceae species, L. japonica, Patrinia saniculifolia, and Kolkwitzia amabilis.

Wolfiporia cocos have been used as diuretic, sedative, and tonic medicine. Although its medicinal effects were reported, its genomic information is rare. In this paper, we report the complete mitochondrial genome of Wolfiporia cocos which is a 136,067 bp circular structure with 5 protein-coding genes, 25 tRNA genes, and 2 rRNA genes. Additional six protein-coding genes (cob, cox1, cox2, cox3, nad2, nad6) were truncated or pseudogenized by internal stop codons. Phylogenetic analysis of the mitochondrial genome of W. cocos showed the distinct relationship with other five mitochondrial genomes of Polyporales.

Rehmannia glutinosa is a plant used as traditional medicine for its various tonic effects in Korea and China. In this study, chloroplast genomes of two R. glutinosa were completed by de novo assembly using whole-genome Illumina sequence data. The length of chloroplast genomes of R. glutinosa collected from China and Korea was 153,680 bp and 153,499 bp, respectively. A total of 114 coding regions were predicted in both R. glutinosa including 80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. We identified abundant intra-species diversity of 87 InDels and 147 SNPs, among three R. glutinosa chloroplast genome sequences including one from GenBank. The phylogenetic analysis showed that these R. glutinosa were closely clustered with related Rehmannia species, separated from other Orobanchaceae and Scrophulariaceae species.

Lonicera japonica is a traditional medicinal plant well known for its anti-inflammatory effect. The complete chloroplast genome sequence of L. japonica collected from Korea was obtained by de novo assembly using whole genome sequence data. The chloroplast genome is 155,060 bp in length, containing 88,853 bp in a large single copy (LSC), 18,653 bp in a small single copy (SSC) and 23,777 bp in a pair of inverted repeats (IRs). A total of 112 genes including 78 protein-coding genes and 34 structural RNA genes were identified. The sequence comparison of two L. japonica collected from Korea and China revealed 48 single nucleotide polymorphisms (SNPs) and 45 insertions/deletions (InDels). In addition, phylogenetic analysis represented intraspecific diversity within L. japonica species collected in Korea and China.

Hosta capitata (Koidz.) Nakai is an herbaceous perennial plant belonging to the Asparagaceae family and has become a popular ornamental plant. In this study, the chloroplast genome sequence of H. capitata was completed by de novo assembly with whole genome sequence data. The chloroplast genome of H. capitata is 156,416 bp in length, which is composed of a large single-copy (LSC) of 84,788 bp, a small single-copy (SSC) of 18,206 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,711 bp, as four distinct parts. In total, 114 genes were identified including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis revealed that H. capitata has a close relationship with other Hosta species, H. minor and H. ventricosa, but is farther than the distance between them.

Magic Lily (Lycoris squamigera), belonging to the Amaryllidaceae family, is cultivated for ornamental and medicinal purposes. To characterize its genomic information, we obtained the complete chloroplast genome sequence of L. squamigera by assembling Illumina whole genome sequence data. The complete chloroplast genome is 158,482 bp in length which is composed of four unique regions, a large single copy region (LSC) of 86,454 bp, a small single copy region (SSC) of 18,500 bp, and a pair of inverted repeats (IR) of 26,764 bp. The genome annotation predicted 159 genes including 105 protein-coding genes, 46 tRNA genes, and 8 rRNA genes. Phylogenetic tree analysis revealed that L. squamigera clustered with Allium species belonging to the Amaryllidaceae family.

Cucumber (Cucumis sativus var. sativus) is one of the economically important vegetable crops. In this study, we characterized the complete chloroplast genome sequence of inbred line ID YHB bred from Korean solid green-type cucumber variety, through de novo assembly using next-generation sequencing. The chloroplast genome is 155,501 bp long and has typical quadripartite structures and gene contents as found in reported cucumber chloroplast genomes. Interestingly, sequence comparison revealed a novel 24-bp deletion present only in the chloroplast genome of the inbred line. Phylogenetic analysis confirmed that the inbred line was closely grouped with cucumber cultivars.