A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum.

Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible and functional foods. In this study, we compared the plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that the PJ accessions were monophyletic within the genus Peucedanum.

Comparative chloroplast genome analyses of cultivated and wild Capsicum species shed light on evolution and phylogeny.

The chloroplast (cp.) genome, also known as plastome, plays crucial roles in plant survival, adaptation, and evolution. The stable genetic structure of cp.

A chromosome-level genome assembly of Korean mint (Agastache rugosa).

Agastache rugosa, also known as Korean mint, is a perennial plant from the Lamiaceae family that is traditionally used for various ailments and contains antioxidant and antibacterial phenolic compounds. Molecular breeding of A. rugosa can enhance secondary metabolite production and improve agricultural traits, but progress in this field has been delayed due to the lack of chromosome-scale genome information.

Correction: Genetic and chemical markers for authentication of three Artemisia species: A. capillaris, A. gmelinii, and A. fukudo.

[This corrects the article DOI: 10.1371/journal.pone.

Multiplex genotyping of SNPs in genomic DNA via hydrogel-based assay mediated with MutS and polyethylene glycol.

The simultaneous genotyping of multiple single nucleotide polymorphisms (SNPs) in genomic DNA derived from organisms holds significant potential for applications such as precision medicine and food product authentication. However, conventional assay technologies including qPCR-based techniques, microarrays, and hydrogel-based assays face limitations in efficient multiplexing of SNPs, particularly for large-size DNA beyond kilobase scales, due to constraints in multiplex capability, specificity, or sensitivity. In this study, a hydrogel-based multiplex SNP genotyping platform specifically designed for genomic DNA is presented.

Comparative transcriptome and metabolome analyses of four species explore the dynamics of metabolite biosynthesis.

Background: The genus in the Araliaceae family has been used as traditional medicinal plants worldwide and is known to biosynthesize ginsenosides and phytosterols. However, genetic variation between species has influenced their biosynthetic pathways is not fully understood.

Methods: Simultaneous analysis of transcriptomes and metabolomes obtained from adventitious roots of two tetraploid species ( and ) and two diploid species ( and ) revealed the diversity of their metabolites and related gene expression profiles.

High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants.

Chimeric plants composed of green and albino tissues have great ornamental value. To unveil the functional genes responsible for albino phenotypes in chimeric plants, we inspected the complete plastid genomes (plastomes) in green and albino leaf tissues from 23 ornamental chimeric plants belonging to 20 species, including monocots, dicots, and gymnosperms. In nine chimeric plants, plastomes were identical between green and albino tissues.

A comparative phytochemical study of nine Lauraceae species by using chemometric data analysis.

The diversity of secondary metabolites of individual plants results from multiple enzymatic processes in planta and various environmental factors, such as temperature, moisture, and soil conditions. Chemical composition analysis of plants can lead to a new method to understand relationship among comparable plants along with biological classification such as genetic and anatomical method. In this study, the chemical diversity of nine different Lauraceae species was investigated, and the plant samples were chemically analyzed and classified.

Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin.

Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants.

The complete plastid genome sequence of Nakai (Apiaceae), an endemic and rare species in Korea.

Nakai is one of the rare species in the Korean Peninsula. This study characterized the complete plastid genome (plastome) sequence of by assembly with next-generation sequencing data. The complete plastome of 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.

Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes.

Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong.

Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F hybrid combinations.

Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F hybrids were analyzed using an next generation whole genome sequencing data.

The complete chloroplast genome sequence of a medicinal herb (Asparagaceae).

is herbaceous perennial plant belonging to the Asparagaceae family and widely used both as ornamental plant and herbal medicine. The complete chloroplast genome of 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.

Impact of Government Support on Performing Artists' Job and Life Satisfaction: Findings from The National Survey in Korea.

In this study, we aim to propose motives that can help increase the creative activities of Korean performing artists and discuss the policy implications for the sustainable management of Korean performing arts. First, we investigate the characteristics of Korean artists that receive subsidies as a form of government support for undertaking artistic activities. Second, we examine whether receipt of such grants influences the artists' job and life satisfaction.

Mitochondrial plastid DNA can cause DNA barcoding paradox in plants.

The transfer of ancestral plastid genomes into mitochondrial genomes to generate mitochondrial plastid DNA (MTPT) is known to occur in plants, but its impacts on mitochondrial genome complexity and the potential for causing a false-positive DNA barcoding paradox have been underestimated. Here, we assembled the organelle genomes of Cynanchum wilfordii and C. auriculatum, which are indigenous medicinal herbs in Korea and China, respectively.

Comprehensive comparative analysis of chloroplast genomes from seven species and development of an authentication system based on species-unique single nucleotide polymorphism markers.

Background: species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven species, two ( and ) from North America and five ( , , , , and ) from Asia.

Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven whole chloroplast genomes.

Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb "Bang-Poong".

Three Apiaceae species , , and 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 , , and were 147,467, 147,830, and 164,633 bp, respectively.

The complete chloroplast genome sequence of Magic Lily ().

Magic Lily (), 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 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 complete chloroplast genome sequence of (Koidz.) Nakai (Asparagaceae).

(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 was completed by assembly with whole genome sequence data.

The complete chloroplast genome sequence of Korean and intra-species diversity.

is a traditional medicinal plant well known for its anti-inflammatory effect. The complete chloroplast genome sequence of collected from Korea was obtained by 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).