Identification of the Plant Family Caryophyllaceae in Korea Using DNA Barcoding.

Caryophyllaceae is a large angiosperm family, with many species being utilized as ornamental or medicinal plants in Korea, in addition to several endangered species that are managed by the government. In this study, we used DNA barcoding for the accurate identification of Korean Caryophyllaceae. A total of 78 taxa (n = 215) were sequenced based on three chloroplast regions (rbcL, matK, and psbA-trnH) and nuclear ribosomal internal transcribed spacers (ITS). In the neighbor-joining tree, a higher accuracy of identification was generally observed when using ITS (>73%) rather than chloroplast regions (<62%). The highest resolution was found for rbcL + ITS (77.6%), although resolution varied according to the genus. Among the genera that included two and more species, five genera (Eremogone, Minuartia, Pseudostellaria, Sagina, and Stellaria) were successfully identified. However, the species of five other genera (Cerastium, Gypsophila, Dianthus, Silene, and Spergularia) showed relatively low resolutions (0-61.1%). In the cases of Cerastium, Dianthus, and Silene, ambiguous taxonomic relationships among unidentified species may have been a factor contributing to such low resolutions. However, in contrast to these results, Gypsophila and Spergularia have been identified well in previous studies. Our findings indicate the need of taxonomic reconsideration in Korea.

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications.

BACKGROUND: Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge. RESULTS: To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power. CONCLUSIONS: The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

The complete chloroplast genome sequence of Aristolochia manshuriensis Kom. (Aristolochiaceae).

Aristolochia manshuriensis is a medicinal plant belonging to the family Aristolichiaceae. In this study, complete chloroplast (cp) genome sequence of A. manshuriensis was characterized through de novo assembly with next-generation sequencing data. The cp genome is 160,182 bp long and has a typical quadripartite organization consisting of a large single-copy (LSC), a small single-copy (SSC), and a pair of inverted repeats (IRs). The cp genome harboured 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis revealed that A. manshuriensis has close relationship with Aristolochia macrophylla.

Determining the scope of control underlying the congruency sequence effect: roles of stimulus-response mapping and response mode.

Sequential modulation between two task congruencies has been examined to investigate the nature of the cognitive control mechanism underlying the congruency sequence effect (CSE). Previous results regarding what consecutive tasks must have in common to engender the cross-task CSE are inconsistent. The present study examined the roles of stimulus-response (S-R) mappings and response mode as critical factors in determining the scope of control. Two flanker-compatibility tasks having different stimulus and response sets alternated in turn, and the arbitrariness of S-R mappings alone (Experiment 1) or the arbitrariness of stimulus set and the distinctiveness of response modes (Experiment 2) were manipulated. Experiment 1 showed that non-arbitrary S-R mappings engendered a cross-task CSE even when the response modes were different. However, when S-R mappings were arbitrary in Experiment 2, sequential modulation was evident across two tasks only when their response modes were same, irrespective of the arbitrariness of the stimulus set. These results suggest that the arbitrariness of S-R mappings and response mode are salient task features that reconfigure task representation and consequently determine the scope of the control underlying the CSE.

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 of Artemisia hallaisanensis Nakai (Asteraceae), an endemic medicinal herb in Korea.

We determined the complete chloroplast DNA sequence of Artemisia hallaisanensis Nakai, an endemic herbal species distributed on Jeju Island, Korea. The chloroplast DNA is 151,015 bp in length and encodes 4 rRNA, 30 tRNA, and 80 protein-coding genes. Phylogenetic analysis and sequence comparison of protein-coding genes with other Artemisa chloroplast DNAs revealed that the chloroplast genome of A. hallaisanensis is closely related to that of A. capillaris. Additionally, a unique 9 bp deletion in ycf1 gene is specific to A. hallaisanensis.