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We report complete sequences of chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) for 11 Panax ginseng cultivars. We have obtained complete sequences of cp and 45S nrDNA, the representative barcoding target sequences for cytoplasm and nuclear genome, respectively, based on low coverage NGS sequence of each cultivar. The cp genomes sizes ranged from 156,241 to 156,425 bp and the major size variation was derived from differences in copy number of tandem repeats in the ycf1 gene and in the intergenic regions of rps16-trnUUG and rpl32-trnUAG. The complete 45S nrDNA unit sequences were 11,091 bp, representing a consensus single transcriptional unit with an intergenic spacer region. Comparative analysis of these sequences as well as those previously reported for three Chinese accessions identified very rare but unique polymorphism in the cp genome within P. ginseng cultivars. There were 12 intra-species polymorphisms (six SNPs and six InDels) among 14 cultivars. We also identified five SNPs from 45S nrDNA of 11 Korean ginseng cultivars. From the 17 unique informative polymorphic sites, we developed six reliable markers for analysis of ginseng diversity and cultivar authentication. [ABSTRACT FROM AUTHOR]

The twoBrassicaspecies,Brassica nigraandBrassica oleracea,are important agronomic crops. The chloroplast genome sequences were generated byde novoassembly using whole genome next-generation sequences. The chloroplast genomes ofB. nigraandB. oleraceawere 153 633 bp and 153 366 bp in size, respectively, and showed conserved typical chloroplast structure. The both chloroplast genomes contained a total of 114 genes including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis revealed thatB. oleraceais closely related toB. rapaandB. napusbutB. nigrais more diverse than the neighbor speciesRaphanus sativus. [ABSTRACT FROM PUBLISHER]

Three Apiaceae species Ledebouriella seseloides, Peucedanum japonicum, and Glehnia littoralis are used as Asian herbal medicines, with the confusingly similar common name "Bang-poong". We characterized the complete chloroplast (cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences of two accessions for each species. The complete cp genomes of G. littoralis, L. seseloides, and P. japonicum were 147,467, 147,830, and 164,633 bp, respectively. Compared to the other species, the P. japonicum cp genome had a huge inverted repeat expansion and a segmental inversion. The 45S nrDNA cistron sequences of the three species were almost identical in size and structure. Despite the structural variation in the P. japonicum cp genome, phylogenetic analysis revealed that G. littoralis diverged 5–6 million years ago (Mya), while P. japonicum diverged from L. seseloides only 2–3 Mya. Abundant copy number variations including tandem repeats, insertion/deletions, and single nucleotide polymorphisms, were found at the interspecies level. Intraspecies-level polymorphism was also found for L. seseloides and G. littoralis. We developed nine PCR barcode markers to authenticate all three species. This study characterizes the genomic differences between L. seseloides, P. japonicum, and G. littoralis; provides a method of species identification; and sheds light on the evolutionary history of these three species. [ABSTRACT FROM AUTHOR]

Perilla citriodorais a diploid and an aromatic herb species belonging to the family Lamiaceae and widely distributed in East Asia. The complete chloroplast genome sequence ofP. citriodorawas generated byde novoassembly using whole genome next-generation sequences. The assembled chloroplast genome ofP. citriodorawas 152 588 bp in length and structurally divided into four distinct regions; large single copy region (83 699 bp), small single copy region (17 537 bp), and a pair of inverted repeat regions (25 676  bp). A total of 115 genes were annotated including 81 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationship with previously reported chloroplast genomes revealed thatP. citriodorais most closely related toP. frutescens, a tetraploidPerillaspecies. [ABSTRACT FROM PUBLISHER]

The complete chloroplast genome sequence ofPanax vietnamensis, a medicinal herb belonging to Araliaceae family, was generated byde novoassembly using whole genome next-generation sequences. The chloroplast genome was a circular form of 155 992 bp long and showed typical chloroplast genome structure consisting of a large single-copy region of 86 177 bp, a small single copy region of 17 935 bp and a pair of inverted repeats of 25 940 bp. The chloroplast genome had 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes. The phylogenetic analysis with the reported chloroplast genomes revealed that fourPanaxspecies were grouped in the same clade andP. vietnamensisis more closely related toP. notoginsengthanP. ginsengandP. quinquefolius. [ABSTRACT FROM PUBLISHER]

The complete chloroplast genome ofIris sanguineawas sequenced newly in this study. The total chloroplast genome size ofI. sanguineawas 152 408 bp, its structure and gene contents were well conserved as typical chloroplast characteristics. Large single copy (LSC) and small single copy (SSC) of 82 340 bp and 18 016 bp, respectively, were separated from a pair of inverted repeats (IRA and IRB) of 26 026 bp. A total of 112 genes, i.e. 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, were encoded in the chloroplast genome ofI. sanguinea. Overall GC content ofI. sanguineawas 36.83%. Phylogenetic analysis with the reported chloroplast genomes revealed thatI. sanguineais most closely related toI. gatesii. [ABSTRACT FROM PUBLISHER]

Lilium tsingtauense,known as ‘Korean wheel lily’ and ‘Twilight lily’, is a lily species naturally distributed in Korea. The complete chloroplast genome sequences ofL. tsingtauensewas obtained byde novoassembly using whole-genome next-generation sequencing data. The chloroplast genome ofL. tsingtauensewas 152,710 bp in length and consisted of four distinct regions, such as large single-copy region (82,059 bp), small single-copy region (17,619 bp) and a pair of inverted repeat regions (26,516 bp). The genome contained a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed thatL. tsingtauenseis most closely related toLilium hansonii, a lily species native to Korea. [ABSTRACT FROM PUBLISHER]

Artemisia argyi, called wormwood, is widely distributed in northeastern Asia. The complete chloroplast genome sequence ofA.argyiwas generated byde novoassembly using whole genome next generation sequences. The complete chloroplast genome sequence ofA.argyiis 151 192 bp in size. It is composed of a large single-copy (LSC), a small single-copy (SSC) and two inverted repeat (IR) regions of 82 930 bp, 18 344 bp and 24 959 bp, respectively. Overall GC contents of the genome were 37.46%. TheA.argyichloroplast genome has a total of 114 genes including 80 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on the chloroplast genome demonstrated thatA.argyiis most closely related toArtemisia montana. [ABSTRACT FROM PUBLISHER]

Solanum commersoniiDunal is a well-known wild potato belonging to Solanaceae family and commonly used as materials for somatic hybridization due to various biotic and abiotic stress resistances. The complete chloroplast genome ofS. commersoniiwas constituted byde novoassembly using a small amount of whole genome sequencing data. The chloroplast genome ofS. commersoniiwas 155 525 bp in length, consisted of 86 013 bp of large single copy, 18 366 bp of small single copy region and 25 573 bp of a pair of inverted repeats. A total of 113 genes were annotated including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Maximum likelihood phylogenetic analysis with 14 Solanaceae species revealed thatS. commersoniiis much closely related toSolanum tuberosumandS. bulbocastanum. [ABSTRACT FROM PUBLISHER]

Wisteria floribundaandWisteria sinensisare ornamental woody vines in the Fabaceae. The complete chloroplast genome sequences of the two species were generated byde novoassembly using whole genome next generation sequences. The chloroplast genomes ofW. floribundaandW. sinensiswere 130 960 bp and 130 561 bp long, respectively, and showed inverted repeat (IR)-lacking structures as those reported in IRLC in the Fabaceae. The chloroplast genomes of both species contained same number of protein-coding sequences (77), tRNA genes (30), and rRNA genes (4). The phylogenetic analysis with the reported chloroplast genomes confirmed close taxonomical relationship ofW. floribundaandW. sinensis. [ABSTRACT FROM AUTHOR]

Epimedium koreanumis a perennial medicinal plant distributed in Eastern Asia. The complete chloroplast genome sequences ofE. koreanumwas obtained byde novoassembly using whole genome next-generation sequences. The chloroplast genome ofE. koreanumwas 157 218 bp in length and separated into four distinct regions such as large single copy region (89 600 bp), small single copy region (17 222 bp) and a pair of inverted repeat regions (25 198 bp). The genome contained a total of 112 genes including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed thatE. koreanumis most closely related toBerberis bealei, a traditional medicinal plant in the Berberidaceae family. [ABSTRACT FROM AUTHOR]

Lilium distichumis a native lily species in Korea, northeastern China and far eastern Russia. The complete chloroplast genome sequence ofL. distichumwas generated byde novoassembly using whole genome next generation sequences. The chloroplast genome ofL. distichumwas 152 598 bp in length and divided into four distinct regions, such as large single copy region (82 031 bp), small single copy region (17 487 bp) and a pair of inverted repeat regions (26 540 bp). The genome annotation predicted a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes,and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed thatL. distichumis most closely related toL. superbum(Turk’s-cap lily). [ABSTRACT FROM AUTHOR]

Cynanchum auriculatumis a climbing vine belonging to the Apocynaceae family and shows very similar morphology toCynanchum wilfordii,a medicinal plant. The complete chloroplast genome ofC. auriculatumwas generated byde novoassembly using the small amount of whole genome sequencing data. The chloroplast genome ofC. auriculatumwas 160 840 bp in length and consisted of four distinct regions, such as large single copy region (91 973 bp), small single copy region (19 667 bp), and a pair of inverted repeat regions (24 600 bp). The overall GC contents of the chloroplast genome were 37.8%. A total of 114 genes were predicted and included 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed thatC. auriculatumis most closely related toCynanchum wilfordii,a medicinal plant. [ABSTRACT FROM AUTHOR]

The complete chloroplast (cp) genomes of twoMiscanthusspecies,M. sinensisandM. sacchariflorus, were sequenced and investigated for genes, genome size variation, and polymorphisms. There are 170 genes in both cp genomes, consisting of 122 mRNA genes (84 protein-coding genes and 38 hypothetical genes), 40 tRNA genes, and 8 rRNA genes. The cp genome contains two inverted repeat (IR) regions, separated by large single copy (LSC) region and small single copy (SSC) region. Indels were responsible for 40 bp difference in cp genome size in two species. In addition, we established phylogenetic relationship with other monocot cp genomes, and estimated divergence time. The twoMiscanthusspecies clustered together among other C4monocot species and the divergence time of twoMiscanthusspecies was approximately 0.5 1–0.84 Mya. [ABSTRACT FROM AUTHOR]

The complete chloroplast (cp) genomes of threeEchinochloa crus-galliaccessions (KR822684, KR822685, and KR822686) are reported in this work. The cp genome size is similar in three accessions, ranging from 139 846 bp to 139 860 bp. All three genomes have two inverted repeats (IR) of 22 748 bp per each IR with a large single copy (LSC) region of 81 833–81 844 bp and a small single copy (SSC) region of 12 517–12 520 bp. The total of 131 genes was identified in individual accession. Phylogenetic analysis revealed three KoreanEchinochloaaccessions belonged toE. crus-galli, and diverged less than 0.1 million years ago (Mya). [ABSTRACT FROM AUTHOR]

Eleutherococcus gracilistylusis a plant species that is close toE. senticosus,a famous medicinal plant called Siberian ginseng. The complete chloroplast genome sequence of theE. gracilistyluswas determined byde novoassembly using whole genome next generation sequences. The chloroplast genome ofE. gracilistyluswas 156 770 bp long and showed distinct four partite structures such as a large single copy region of 86 729 bp, a small single copy region of 18 175 bp, and a pair of inverted repeat regions of 25 933 bp. The overall GC contents of the genome sequence were 36.8%. The chloroplast genome ofE. gracilistyluscontains 79 protein-coding sequences, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis with the reported chloroplast genomes confirmed close taxonomical relationship ofE. gracilistyluswithE. senticosus. [ABSTRACT FROM AUTHOR]

Lilium hansoniiis a lily species native to Korea and an important wild species for lily breeding. The chloroplast genome ofL. hansoniiwas completed byde novoassembly using the small amount of whole genome sequencing data. The chloroplast genome ofL. hansoniiwas 152 655 bp long and consisted of large single copy region (82 051 bp), small single copy region (17 620 bp) and a pair of inverted repeat regions (26 492 bp). A total of 115 genes were annotated, which included 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed thatL. hansoniiis most closely related toL. superbum(Turk’s-cap lily) andL. longiflorum(Easter lily). [ABSTRACT FROM AUTHOR]

Ledebouriella seseloides(Hoffm.) H.Wolff is a traditional medicinal herb belonging to Apiaceae family, whose dried roots and rhizomes have been used as traditional medicine in East Asian countries. The complete chloroplast genome ofL. seseloideswas obtained byde novoassembly using the small amount of whole genome sequencing data. The chloroplast genome ofL. seseloideswas 147 880 bp in length, which consisted of large single copy region (93 222 bp), small single copy region (17 324 bp), and a pair of inverted repeat regions (18 667 bp). The overall GC contents of the chloroplast genome were 37.5%. A total of 113 genes were annotated, which included 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed thatL. seseloidesis most closely related toPetroselinum crispum(parsley), an herb widely used in cooking. [ABSTRACT FROM AUTHOR]

Cynanchum wilfordii(Maxim.) Hemsl. is a traditional medicinal herb belonging to the Asclepiadoideae subfamily, whose dried roots have been used as traditional medicine in Asia. The complete chloroplast genome ofC. wilfordiiwas generated byde novoassembly using the small amount of whole genome sequencing data. The chloroplast genome ofC. wilfordiiwas 161 241 bp long, composed of large single copy region (91 995 bp), small single copy region (19 930 bp) and a pair of inverted repeat regions (24 658 bp). The overall GC contents of the chloroplast genome was 37.8%. A total of 114 genes were annotated, which included 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed thatC. wilfordiiis most closely related toAsclepias nivea(Caribbean milkweed) andAsclepias syriaca(common milkweed) within the Asclepiadoideae subfamily. [ABSTRACT FROM AUTHOR]

Glehnia littoralisF. Schmidt ex Miq is an oriental medicinal herb belonging to Apiaceae family, and its dried roots and rhizomes are known to show various pharmacological effects. The complete chlorplast genome ofG. littoraliswas generated byde novoassembly using whole genome sequencing data. The chloroplast genome ofG. littoraliswas 147 467 bp in length and divided into four distinct regions: large single copy region (93 493 bp), small single copy region (17 546 bp) and a pair of inverted repeat regions (18 214 bp). A total of 114 genes including 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes were predicted and accounted for 57.1% of the chloroplast genome. Phylogenetic analysis with the reported chloroplast genomes revealed thatG. littoralisis an herbal species closely related toLedebouriella seseloides, an herbal medicinal plant. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome sequence ofZanthoxylum piperitum, a plant species with useful aromatic oils in family Rutaceae, was generated in this study byde novoassembly with whole-genome sequence data. The chloroplast genome was 158 154 bp in length with a typical quadripartite structure containing a pair of inverted repeats of 27 644 bp, separated by large single copy and small single copy of 85 340 bp and 17 526 bp, respectively. The chloroplast genome harbored 112 genes consisting of 78 protein-coding genes 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the complete chloroplast genome sequences with those of known relatives revealed thatZ. piperitumis most closely related to theCitrusspecies. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome sequence ofPanax quinquefolius, an important medicinal herb, was generated byde novoassembly with low-coverage whole-genome sequence data and manual correction. A circular 156 088-bp chloroplast genome showed typical chloroplast genome structure comprising a large single copy region of 86 095 bp, a small single copy region of 17 993 bp, and a pair of inverted repeats of 26 000 bp. The chloroplast genome had 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis with the chloroplast genome revealed thatP. quinquefoliusis much closer toP. ginsengthanP. notoginseng. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome sequence ofDendropanax morbifera, an economically and medicinally important endemic tree species in Korea, was obtained byde novoassembly with whole-genome sequence data and manual correction. A circular 156 366-bp chloroplast genome showed typical chloroplast genome structure comprising a large single copy region of 86 475 bp, a small single copy region of 18 125 bp, and a pair of inverted repeats of 25 883 bp. The chloroplast genome harbored 87 protein-coding genes. Phylogenetic analysis with the chloroplast genome revealed thatD. morbiferais most closely related toDendropanax dentiger, an evergreen tree species in China and Southeastern Asia. [ABSTRACT FROM AUTHOR]