Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution.

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

The complete chloroplast genome of Campanula takesimana Nakai from Dokdo Island in Korea (Campanulaceae).

Completed chloroplast genome of Campanula takesimana Nakai isolated from Dokdo island in Korea is 169,719 bp long (GC ratio is 38.8%) and has four subregions: 102,381 bp of large single-copy (37.8%) and 7,750 bp of small single-copy (32.6%) regions are separated by 29,794 bp of inverted repeat (41.3%) regions including 131 genes (87 protein-coding genes, eight rRNAs, and 36 tRNAs). Phylogenetic analyses suggested that C. takesimana from Dokdo Island form a clade with C. takesimana from Ulleungdo Island and that chloroplast genomes of the two accessions are diverged.

Complete chloroplast genomes of all six Hosta species occurring in Korea: molecular structures, comparative, and phylogenetic analyses.

BACKGROUND: The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. Due to considerable morphological variability, the genus has been well recognized as a group with taxonomic problems. Chloroplast is a cytoplasmic organelle with its own genome, which is the most commonly used for phylogenetic and genetic diversity analyses for land plants. To understand the genomic architecture of Hosta chloroplasts and examine the level of nucleotide and size variation, we newly sequenced four (H. clausa, H. jonesii, H. minor, and H. venusta) and analyzed six Hosta species (including the four, H. capitata and H. yingeri) distributed throughout South Korea. RESULTS: The average size of complete chloroplast genomes for the Hosta taxa was 156,642 bp with a maximum size difference of ~ 300 bp. The overall gene content and organization across the six Hosta were nearly identical with a few exceptions. There was a single tRNA gene deletion in H. jonesii and four genes were pseudogenized in three taxa (H. capitata, H. minor, and H. jonesii). We did not find major structural variation, but there were a minor expansion and contractions in IR region for three species (H. capitata, H. minor, and H. venusta). Sequence variations were higher in non-coding regions than in coding regions. Four genic and intergenic regions including two coding genes (psbA and ndhD) exhibited the largest sequence divergence showing potential as phylogenetic markers. We found compositional codon usage bias toward A/T at the third position. The Hosta plastomes had a comparable number of dispersed and tandem repeats (simple sequence repeats) to the ones identified in other angiosperm taxa. The phylogeny of 20 Agavoideae (Asparagaceae) taxa including the six Hosta species inferred from complete plastome data showed well resolved monophyletic clades for closely related taxa with high node supports. CONCLUSIONS: Our study provides detailed information on the chloroplast genome of the Hosta taxa. We identified nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in various research area.

Genetic diversity and population structure of Lychnis wilfordii (Caryophyllaceae) with newly developed 17 microsatellite markers.

Lychnis wilfordii (Regel) Maxim. is a perennial plant designated as an endangered species by the Korean government because of rapid reduction in its population size. Thus, a population genetic study of this species is needed to establish the strategy for management and conservation based on scientific evidences. The goals of this study were to develop useful microsatellite markers for L. wilfordii and to understand current genetic status of L. wilfordii in Korean peninsula. Seventeen microsatellite markers were identified using next-generation sequencing and bioinformatic analysis and then analyzed genetic diversity in one hundred forty-five individuals from Korea (KI1, KI2, and KP), China (CX, CF) and Russia (RP). Analysis of molecular variance (AMOVA), principal coordinates analysis (PCoA) and STRUCTURE results consistently showed discontinuity among L. wilfordii populations. AMOVA showed that the percentage of variation among populations was 53%, which was higher than the variation within populations (19%). PCoA showed that the populations were divided into three genetic clusters, (1) Chinese (CX, CF), (2) Russian (RP) populations and Korean populations (KI1, KI2) excluding KP, and (3) the KP population. In particular, KP, the most southern population on the Korean peninsula, showed significantly lower observed and expected heterozygosity, number of effective alleles, and Shannon index (I) than those of KI1 and KI2. L. wilfordii showed high differentiation between populations with low genetic diversity within populations. Among Korean populations, KP is likely to be affected by genetic drift due to small population size, low genetic diversity and limited gene flow.

The complete chloroplast genome sequence of Lychnis kiusiana (Caryophyllaceae).

The complete chloroplast genome sequence of Lychnis kiusiana Makino (Caryophyllaceae) was determined. The genome was 151,831 bp long, consisting of a large single-copy region (83,875 bp) and a small single-copy region (17,591 bp) separated by two inverted repeats (25,331 bp). The plastome contained 124 genes; 82 encode proteins, 34 encode tRNA, and eight encode rRNA. The gene quantity and order resembled those of a typical Caryophyllaceae plastome. Phylogenetic analysis using 79 gene sequences from 14 previously reported genomes of Caryophyllaceae showed that Lychnis clades were nested within the Silene genus, suggesting that Lychnis is a lower taxonomic rank than genus.

Genetic diversity and structure of an endangered medicinal herb: implications for conservation.

Human-driven habitat fragmentation leads to spatial isolation of endangered plant species increasing extinction risk. Understanding genetic variability and population structure of rare and isolated plant species is of great importance for assessing extinction risk and setting up conservation plans. Aconitum austrokoreense, an endangered and endemic species in Korea, is a perennial herb commonly used for medicinal purposes. We used five nuclear microsatellites and one chloroplast marker to investigate genetic diversity and population structure for 479 individuals of A. austrokoreense from seven populations throughout South Korea. A multivariate approach, discriminant analysis of principal components analysis, revealed broad-scale spatial patterns of A. austrokoreense populations across three major mountains that were composed of seven genetically distinct subgroups. High pairwise FST values (mean FST = 0.35; highest FST = 0.55) suggested significant differentiation among populations. Overall within population genetic variation was low. Based on Mantel test, there was significant correlation between geographical and genetic distances indicating pattern of isolation by distance. Our results suggest that A. austrokoreense populations may have undergone recent population bottlenecks. Given the limited dispersal ability of the species and ongoing habitat fragmentation, population isolation may further be exacerbated leading to increased extinction risk.

The complete chloroplast genome sequence of Asarum sieboldii Miq. (Aristolochiaceae), a medicinal plant in Korea.

Asarum sieboldii is a medicinal plant belonging to the Aristolochiaceae family. In this study, complete chloroplast genome sequence of A. sieboldii was characterized through de novo assembly with next generation sequencing data. The chloroplast genome is 193,356 bp long and has the stereotypical tripartite organization consisting of large single copy region and a pair of inverted repeats. The genome contains 78 protein-coding genes, 30 rRNA genes, and 4 tRNA genes. Phylogenetic analysis revealed that A. sieboldii has close relationship with Piper coenoclatum (Piperaceae, Piperales).

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

The complete chloroplast genome of a Korean endemic ornamental plant Hosta yingeri S. B. Jones (Asparagaceae).

Hosta yingeri is a perennial herbal ornamental plant belonging to the Asparagaceae family and an endemic species distributed in islands of Korea. In this study, complete chloroplast genome sequence of H. yingeri was characterized through de novo assembly with next generation sequencing data. The chloroplast genome is 156,756 bp in length and contains four rRNA genes, 30 tRNA genes, and 77 protein-coding genes. Phylogenetic analysis demonstrated a close relationship of H. yingeri with other species belonging to the subfamily Agavoideae in Asparagaceae.

Complete chloroplast genome sequence of Patrinia saniculifolia hemsl. (Disacales: Caprifoliaceae), an endemic plant in Korea.

Patrinia saniculifolia Hemsl. is a Korean endemic plant belongs to the family Caprifoliaceae s. l. In this study, we report the complete chloroplast genome of P. saniculifolia. The chloroplast genome was 153,775 bp with LSC (87,529 bp) and SSC (17,236 bp) regions, separated by two IRs regions 23,806 bp, and overall GC content was 38.48%. It contains total of 111 genes, including 78 protein-coding genes, 29 tRNA genes, and 4 rRNA genes.

Copper(I)-taniaphos catalyzed enantiodivergent hydroboration of bicyclic alkenes.

In this study, highly enantioselective copper(I)-catalyzed hydroboration of bicyclic alkenes is reported. Using a copper-taniaphos complex, excellent enantioselectivities up to >99% ee were obtained for bicyclic alkenes including oxa- and azabicyclic alkenes. Furthermore, copper-catalyzed enantiodivergent hydroboration methods with the same chiral ligand-copper precursors were developed using different boron sources based on alternative mechanistic pathways.

Analysis of traditional knowledge of medicinal plants from residents in Gayasan National Park (Korea).

BACKGROUND: The purpose of this study is to investigate and analyze the traditional knowledge of medicinal plants used by residents in Gayasan National Park in order to obtain basic data regarding the sustainable conservation of its natural plant ecosystem. METHODS: Data was collected using participatory observations and in-depth interviews, as the informants also become investigators themselves through attending informal meetings, open and group discussions, and overt observations with semi-structured questionnaires. Quantitative analyses were accomplished through the informant consensus factor (ICF), fidelity level, and inter-network analysis (INA). RESULTS: In total, 200 species of vascular plants belonging to 168 genera and 87 families were utilized traditionally in 1,682 ethnomedicianal practices. The representative families were Rosaceae (6.5%) followed by Asteraceae (5.5%), Poaceae (4.5%), and Fabaceae (4.0%). On the whole, 27 kinds of plant-parts were used and prepared in 51 various ways by the residents for medicinal purposes. The ICF values in the ailment categories were muscular-skeletal disorders (0.98), pains (0.97), respiratory system disorders (0.97), liver complaints (0.97), and cuts and wounds (0.96). In terms of fidelity levels, 57 plant species showed fidelities levels of 100%. Regarding the inter-network analysis (INA) between ailments and medicinal plants within all communities of this study, the position of ailments is distributed into four main groups. CONCLUSION: The results of the inter-network analysis will provide a suitable plan for sustainable preservation of the national park through a continued study of the data. Particular species of medicinal plants need to be protected for a balanced plant ecosystem within the park. Consequently, through further studies using these results, proper steps need to be established for preparing a wise alternative to create a sustainable natural plant ecosystem for Gayasan National Park and other national parks.

Insights into Korean red fox (Vulpes vulpes) based on mitochondrial cytochrome b sequence variation in East Asia.

The red fox (Vulpes vulpes) is the most widely distributed terrestrial carnivore in the world, occurring throughout most of North America, Europe, Asia, and North Africa. In South Korea, however, this species has been drastically reduced due to habitat loss and poaching. Consequently, it is classified as an endangered species in Korea. As a first step of a planned red fox restoration project, preserved red fox museum specimens were used to determine the genetic status of red foxes that had previously inhabited South Korea against red foxes from neighboring countries. Total eighty three mtDNA cytochrome b sequences, including 22 newly obtained East Asian red fox sequences and worldwide red fox sequences from NCBI, were clustered into three clades (i.e., I, II, and III) based on haplotype network and neighbor-joining trees. The mean genetic distance between clades was 2.0%. Clade III contained South Korean and other East Asian samples in addition to Eurasian and North Pacific individuals. In clade III, South Korean individuals were separated into two lineages of Eurasian and North Pacific groups, showing unclear phylogeographic structuring and admixture. This suggests that South Korean red fox populations may have been composed of individuals from these two different genetic lineages.

Effect of preparation method of multi-walled carbon nanotube/poly(methyl methacrylate) nanocomposite on its characteristics.

Multi-walled carbon nanotube (MWNTs)/poly(methyl methacrylate) (PMMA) nanocomposites were prepared by both coagulation and solvent casting methods in this study. Dispersibility of the MWNTs in the PMMA matrix was compared with each other using both scanning electron microscopy (SEM) and photograph. MWNTs from the solvent casting method were found to be dispersed better in the matrix, indicating that the dispersion state of the MWNTs depends on the preparation procedure. Moreover, using a stress-controlled rotational rheometer we investigated their rheological properties under small amplitude oscillation in their melt state. Well dispersed MWNTs in the PMMA matrix prepared by the solvent casting method efficiently blocked energy dissipation and relaxation of the PMMA chains, resulting in a lower tan delta with increased solid-like property.