Tae-Young Choi’s research while affiliated with Chosun University and other places

Phedimus individuals from Mt. Daeam, once referred to as Phedimus sikokianus, exhibit certain morphological characters that are unique within the genus. Phedimus is one of the most notorious groups for taxo-nomic problems due to the high morphological variation found in leaf shape, stem numbers, phyllotaxis and seed structure. Taxa in Phedimus also easily hybridize, further leading to taxonomic confusion. To carefully confirm the identity of the putative new species from Mt. Daeam, we examined morphological characters from ~100 herbarium sheets of six closely related Phedimus species. A molecular phylogenetic approach was also employed to delimit the species boundary and infer the phylogenetic relationships among the seven Phedimus species, including the species from Mt. Daeam. Both morphological and molecular phylogenetic results indicated that the species found on Mt. Daeam is a new species that is more closely related to P. middendorffianus and P. takeshimensis than to the remaining four Phedimus species. Here, we provided a full description of the new species P. daeamensis as well as an updated key for the seven Phedimus species examined.

The nomenclatural status of two Carex species described by Ohwi, are reviewed. We found typification errors in C. chosenica Ohwi and C. ochrochlamys Ohwi. Accordingly, proper lectotypifications for the two taxa are provided here. We desginated specimens from the Kyoto University Herbarium (KYO) as lectotype for the two Carex taxa.

Polygonatum falcatum is a perennial herb distributed in East Asia. We determined the characteristics of the complete chloroplast genome in P. falcatum for the first time, with a de novo assembly strategy. The chloroplast genome was 154,579bp in length harboring 87 protein coding genes, 38 tRNA genes and eight rRNA genes. It exhibits typical quadripartite structure comprising a large single-copy (LSC) (83,528bp), a small single-copy (SSC) (18,457bp) and a pair of inverted repeats (IRs) (26,297bp). Phylogenetic analysis of 16 chloroplast genomes from Asparagaceae reveals that the genus Polygonatum is a monophyletic group and that P. falcatum is clustered together with the congener, P. odoratum.

Monitoring intraspecific diversity offers invaluable insights on conservation practices as the variation is the product of species evolution. Accordingly, the role of population genetic diversity has drawn great attention over the last century responding to the biodiversity loss induced by a series of anthropogenic changes. Orchids are one of the most diverse, yet ironically most rapidly disappearing plant groups due to the specialized habitat preferences. Thus, population-level genetic diversity studies may offer a powerful tool for orchid conservation programs. Using the 3 restriction site-associated DNA (3RAD) approach, 2,734 genome-wide single nucleotide polymorphisms (SNPs) were isolated. With the 2,734 SNPs, we investigated genetic diversity and population structure on 72 individuals of Habenaria linearifolia and Habenaria cruciformis in South Korea. Overall, the genetic diversity was well maintained in South Korean Habenaria, but high FST values were estimated suggesting large population diversification with limited gene flow. Bayesian assignment analysis revealed a morphologically cryptic diversity pattern in Jeju Island populations, which might serve as an evolutionarily significant unit.

Success of a species invasion partly depends on the level of genetic variability, since the expected founder effect likely limit the amount of genetic variation harbored in the introduced range. Multiple introductions and admixture might amiliorate the complications following lowered genetic variability particularly in early stages of species invasion. During range expansion, landscape factors may take over and play more active role to the expansion potential and shape the pattern of distribution. Siscyos angulatus, a wide spread invasive plant in Korea introduced late 1900’s and expanded the distribution causing many ecological and economic problems. We examined the extent of genetic variability and the spatial structure employing 3-RAD approach, which isolated 2696 genome-wide SNPs. Throughout Korean peninsula, 346 samples from 24 populations were collected. Genetic diversity, population bottleneck test, assignment analyses were conducted. To determine the landscape contributors during the range expansion, we employed a correlation analysis with five landscape factors. Overall, the genetic diversity was low and the regional populations were largely diversified due partly to the multiple genetic sources. The results of genetic diversity and the assignment analyses also proposed a possibility of multiple introductions. Number of highways between a pair of populations acted as a corridor, whereas number of the protected areas seemed to be a barrier for Siscyos angulatus in Korea. Our findings suggest that the species is likely further expand the range. For the management of the species, solid monitoring plan should be built for the new introduction near ports, airports and highways.

Given the significant impact of molecular markers on the genetic diversity assessment, understanding genetic diversity pattern across diverse marker types in comparative manner is of great importance. In Korea, within the last 10 years population genetics studies of wild plants have drawn much attention as varying DNA markers have developed. To investigate pattern of among- and within-population level genetic diversity of wild plants in Korea, we reviewed the extent of population genetic parameters across four DNA markers (RAPD, AFLP, ISSR, SSR). We compiled 73 data sets from research papers published between 2010 and 2019. ISSR markers were the most frequently used in population genetics studies conducted on Korean wild plants. Overall, genetic diversity patterns greatly varied across the different marker types. On average, endangered species exhibited low within-population genetic variation and high among-population genetic diversity. Species with wide geographic distribution showed greater within-population diversity values than the ones residing restricted area except for AFLP data. Populations were genetically less differentiated in long distance dispersal species with the wide geographic ranges. Our review indicates that the studies on the genetic diversity of wild plants may be improved by expanding the scope and increasing the sample sizes.

Genus Polygonatum Mill. (Asparagaceae) is a diverse plant group that is particularly well appreciated in East Asia for the wide array of commercial uses and the species diversity. Despite the increased recognition for its value as the natural resources, knowledge on the taxonomy and phylogenetic relationships among congeners have been lacking. The paucity of taxonomic and phylogenetic information on Polygonatum is primarily be attributed to the global scale distribution and poor understanding on the species boundaries. Taxonomic monographs have offered a great tool for understanding species diversity, although, in the recent past, the method has been considered outdated and rather daunting with augmented herbarium data. Here, we propose a research design for a global scale taxonomic monograph of Polygonatum integrated with a phylogenomic approach. Through the study, we aim delimit species boundaries and understand the phylogenetic relationships among taxa. To address our objectives: 1) we will be newly listing names under International Code of Nomenclature by examining over 200 names; 2) we will provide typification if required, keys and descriptions of species of interests following by the morphological examinations of 12,000 herbarium specimen and 3) we will infer genome-scale phylogeny of ~70 taxa by employing 353-angiosperm single copy genes targeted capture. The study will expand our knowledge of Polygonatum taxonomy and offer important information of biodiversity in the Asiatic plant taxa.

Rosa kokanica is a deciduous shrub distributed in Central Asia. We determined the genomic characteristics of the complete chloroplast genome in R. kokanica with a de novo assembly strategy. The chloroplast genome was 156,802bp in length harboring 89 protein coding genes, 37 tRNA genes and eight rRNA genes. It exhibits typical quadripartite structure comprising a large single-copy (LSC) (85,899bp), a small single-copy (SSC) (18,773bp) and a pair of inverted repeats (IRs) (26,065bp). Phylogenetic analysis of 16 chloroplast genomes from Rosaceae revealed that the genus Rosa is a monophyletic group and the R. kokanica is clustered together with the congener, R. acicular.

As anthropogenic transports of biomaterials have rapidly escalated in the past century, biological invasions have been of great concern on a global scale. Given the exponential growth of alien species passing through the initial point of introduction, reporting an alien species on its initial appearance is important. Sisymbrium irio, an annual herb distributed widely throughout the northern hemisphere, is a notorious weed for its strong invasiveness. In 2016 S. irio was first reported in Korea. The plant was found along the urban expressway, Beonyeong-ro, connecting Busan trading port to Gyeongbu expressway. To properly identify the species, we collected ten S. irio samples from the reported site and examine their morphological characters. The identification key of Sisymbrium irio and its related species in the genus was constructed to clarify taxonomic confusions. We further determined the identity of the taxa by inferring the phylogeny of S. irio and the related taxa. To investigate the distribution changes for the past four years since the first observation in 2016, we monitored the area in late summer of 2020. Both morphological and molecular examinations indicated that the Sisymbrium species we found in Korea for the first time was S. irio. From our site monitoring, we newly found a second distribution site that is approximately 1.5 km away from the original site. Considering the geographical proximity of the introduction sites from the port, we hypothesize that S. irio might started expanding its range by the aid of roads. Given the role of roads as a corridor for alien species, further expansion of S. irio in Korea is expected.

Iris loczyi is a perennial rhizomatous herb distributed in Central Asia. We examined genomic architecture of the complete chloroplast genome in I. loczyi by assembling the Illumina MiSeq reads using de novo strategy. The chloroplast genome is 150,940 bp in length harboring 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. It exhibits typical quadripartite structure comprising LSC (80,907 bp), SSC (17,853 bp), and a pair of IRs (26,090 bp). Phylogenetic analysis of 20 chloroplast genomes from Asparagales revealed that Iridaceae is a monophyletic group and the I. loczyi is clustered together with the congener, I. sanguinea.