• Korean Journal of Plant Taxonomy
• /
• v.45 no.4
• /
• pp.306-317
• /
• 2015

This study was conducted to address the taxonomic status of the Korean endemic species Saxifraga octopetala, which is sometimes considered conspecific to Micranthes manchuriensis. Extensive molecular phylogenetic analysis using nrITS sequences as well as morphological examination of type specimens of the two species were undertaken to ascertain the phylogenetic position and species delimitation of S. octopetala. In the resulting nrITS trees, a total of 65 accessions representing S. octopetala grouped together and nested within the Micranthes clade, exhibiting a close relationship with M. nelsoniana and M. manchuriensis. Multiple accessions of M. manchuriensis collected from China and Russia also formed a clade, showing a sister group relationship with M. nelsoniana var. pacifica and M. fusca. The ambiguous species entity of S. octopetala is thought to have originated from Nakai's misinterpretation of Wilford's collection (type specimens of M. manchuriensis), which is a complex collection including an inflorescence of M. nelsoniana. In spite of apparent morphological similarity between S. octopetala and M. manchuriensis, they differ in the presence and absence of underground stolons. The distinct position of S. octopetala within the Micranthes clade on the nrITS tree suggests that it should retain species status in Micranthes. Thus a new combination (Micranthes octopetala) is proposed.

• Korean Journal of Plant Taxonomy
• /
• v.39 no.1
• /
• pp.35-41
• /
• 2009

Astilbe (Saxifragaceae) is a genus well known for its disjunctive distribution in Asia and eastern North America. In this study, we reconstructed a molecular phylogeny of the genus using the sequences of ITS regions of nuclear ribosomal DNA. A total of 17 species representing major lineage of Astilbe and closely related taxa were included in the phylogenetic analyses. We obtained a Bayesian phylogenetic tree in which Saxifragopsis was positioned as a sister group to Astilbe. The Japanese endemic species, A.platyphylla was the most basal lineage within the genus. This species is well known for its distinct morphological features such as unisexual flowers, apetaly, and calyx with 7-11 lobes. Two species, A. biternata, a New World representative of the genus, and A. rivularis widely distributed in S. Asia, branched off early in the evolution of Astilbe. The remaining species formed a strongly supported core clade, which diverged into two robust geographical lineages: the first ("Japonica" clade) of species distributed in Japan, Taiwan, and Philippines and the other ("Rubra" clade), of taxa in China and Korea. The ITS phylogeny indicates that the Bering land bridges were the major route for the origin and dispersal of A. biternata. The two Taiwanese taxa and A. philippinensis were found to derive from the Japanese member, as the genus advanced southwards. The ITS phylogeny suggests that apetaly originated independently at least two times within the genus. Our results do not support Engler's classification system of the genus based on the leaf type (simple vs. compound), but reaffirm Hara's taxonomic idea which primarily considered the features of calyx.

• Korean Journal of Plant Taxonomy
• /
• v.36 no.3
• /
• pp.189-207
• /
• 2006

Goodyera rosulacea, which is morphologically similar to G. repens, is described recently as a new species based on its distinct morphological characters such as rosette-formed leaves, short rhizome and habitat. To verify the taxonomic identity of G. rosulacea and its taxonomic relationship within Korean Goodyera taxa, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and the trnL region of cpDNA from 24 accessions including 1 outgroup accession were analyzed. Aligned sequences were analyzed using maximum parsimony and distance method, and the taxonomic identity and the taxonomic relationships among the related taxa were estimated by the existence of private marker gene and the phylogenetic tree of the aligned sequences. Molecular data indicate that G. rosulacea gas several private marker genes and shows monophyly in phylogenetic trees of both ITS and trnL sequences. the pairwise distance between G. rosulacea and the orher taxa of Korean Goodyera was 3.49-6.68% for ITS region and 5.05-9.53% for trnL region, indicating that G. rosulacea could be treated as an independent species. Therefore, our molecular data support the taxonomic of G. rosulacea as a distinct species of Korea. In phylogenetic trees, G. rosulacea formed same clade with G. repens, which has similar morphological characters with G. rosulacea, and showed the lowest pairwise distance with G. repens among Korean Goodyera taxa. These molecular data sugguested that G. rosulacea and G. repens are closely related taxa.

• Korean Journal of Plant Taxonomy
• /
• v.46 no.1
• /
• pp.1-12
• /
• 2016

DNA sequences of nrITS regions obtained from 49 accessions representing 12 species and one variety within the section Adonanthe of the genus Adonis were analyzed to test the previous intra-sectional classification system and to determine their phylogenetic relationships. The results showed that the seven accessions of A. amurensis Regel et Radde included in the present study did not form a monophyletic group, as some of the accessions showed a close relationship with the Japanese endemic species A. ramosa Franch., which implies that the current species delimitation and identification of A. amurensis is problematic. Adonis pseudoamurensis W. T. Wang, which is frequently misidentified as A. ramosa in Korea, formed a segregated group, which suggests that they should not be considered as conspecific taxa. Accessions from A. shikokuensis Nishikawa et Koji Ito, A. multiflora Nishikawa et Koji Ito, and A. pseudoamurensis formed a clade, but monophyly of each species was not evident. The nrITS data did not support the classification system proposed by Wang, who classified sect. Adonanthe into four series, as most of these were found to be either polyphyletic or paraphyletic.

• Korean Journal of Microbiology
• /
• v.49 no.4
• /
• pp.383-390
• /
• 2013

Lateral gene transfer (LGT) of genes from other bacteria into Vibrio cholerae is expectable because of the pronounced natural competence of the bacterium. In this study, quantitative aspects of LGT among the three species of Vibrio pathogenic to humans were characterized. Genome sequences of V. cholerae N16961, V. parahaemolyticus RIMD2210633, V. vulnificus CMCP6, and Escherichia coli K12 substrain MG1655 were analyzed to determine orthologous quartets of protein coding genes present in all four genomes. Phylogenetic analyses on the quartets were conducted to resolve vertical versus lateral patterns of gene polymorphisms based on congruence versus incongruence of phylogenetic trees. About 70% of the quartets could be resolved as either cohesive topology (75%) or LGT tree topologies (25%). The amount of LGT genes in Vibrio spp. appeared to be abnormally high for a genus and comparable to those of families. Patched distributions of LGT from different donors were observed on a chromosome. In the small chromosome of V. cholerae, physical linkages among LGT loci spanned half the length of the chromosome. Either accumulative selection for the donor alleles in LGT or presence of large-scale LGT events was hypothesized. These findings warrant further studies on the nature of donor-specificity of LGT alleles and its influence on evolution of Vibrio virulence to humans.

• Journal of Mushroom
• /
• v.11 no.2
• /
• pp.69-76
• /
• 2013

Pholiota species were collected from different geographical regions of the world. Genetic diversity and phylogenetic relationships were analyzed by rDNA-ITS sequences and RAPD polymorphism. The sizes of rDNA-ITS PCR amplicons of Pholiota spp. varied from 233~271, 158~223 and 174~219 bp, respectively. A phylogenetic tree was constructed on the ITS region sequences and Pholiota strains were classified into 8 clusters. Twenty strains in seven Pholiota spp. were classified into seven clusters by RAPD polymorphism using 15 arbitrary primers. Our experimental results suggested that rDN-ITS and RAPD analysis are useful tool for classifying Pholiota spp. and strains.

• Journal of Life Science
• /
• v.22 no.1
• /
• pp.62-73
• /
• 2012

This study was carried out to investigate the genetic relationship of Flammulina velutipes with other species. The ribosomal DNA cluster containing 4 rRNA genes from F. velutipes 4154 were sequenced. The length of the rDNA cluster sequence was estimated at 7,403 bp long and consisted of 1,806 bp of SSU rDNA, 245 bp of ITS 1 region, 159 bp of 5.8S rDNA, 308 bp of ITS 2 region, 3,402 bp of LSU rDNA, 1,400 bp of IGS 1 region, and 83 bp of 5S rDNA. The F. velutipes 4154 genes were contained in the rDNA cluster of F. velutipes in the order of SSU rDNA - ITS 1 - 5.8S rDNA - ITS 2 - LSU rDNA - IGS 1 - 5S rDNA. The phylogenetic relationships of 20 strains of Tricholomataceae and Physalacriaceae were analyzed by conducting distance analysis using the Neighbor-joining (NJ) method. The 20 strains used in this study were divided into three groups and the strains of the genus Flammulina were related very closely to strains of Physalacria bambusae.

• Korean Journal of Plant Taxonomy
• /
• v.45 no.3
• /
• pp.243-253
• /
• 2015

Series Chinensis, Genus Iris, endemic to the far regions of East Asia, consists of four species and related varieties. This series is divided into two major groups (I. rossii and I. minutiaurea complex). In this study, the ITS region and matK gene sequences within nuclear ribosomal DNA and plastid DNA were analyzed in order to investigate the phylogenetic relationships among the I. minutiaurea complex (I. minutiaurea, I. odaesanensis, and I. koreana) and the taxonomic identities of a putative hybrid in Mt. Palgong. In the internal transcribed spacer (ITS1, 5.8S, and ITS2) region, a total of 106 cloned genomic sequences from three taxa were obtained to study the intragenomic polymorphisms of the ITS regions. Three taxa revealed high levels of intragenomic polymorphisms, indicative of incomplete nrDNA concerted evolution. This incomplete ITS concerted evolution in the series Chinensis may be linked to the recent species divergence and frequent interspecies hybridization of the series Chinensis. In the matK gene, three taxa were fairly separated by eleven variable sites. In eight individuals collected on Mt. Palgong, putative hybrids between I. odaesanensis and I. minutiaurea were clustered in the I. minutiaurea clade in the NJ (neighbor-joining) tree based on the matK gene. However, in the ITS tree, some of them were clustered in the I. odaesanensis clade and others were clustered in the I. minutiaurea clade. Therefore, the individuals on Mt. Palgong were formed by the hybridization between two taxa (I. odaesanensis and I. minutiaurea) and not through the lineage of I. koreana.

• Korean Journal of Plant Taxonomy
• /
• v.44 no.1
• /
• pp.39-50
• /
• 2014

Phylogenetic positions of Sedirea and Neofinetia were addressed using the chloroplast matK and the nuclear ITS sequences. We also evaluate the usefulness of the makers for the identification of species and localities. Sedirea and Neofinetia form an independent monophyletic genus, respectively, in both matK and nuclear ITS trees. The sister genus of the Neofinetia was Vanda in both trees. In addition, our trees support the separate recognition of the Neofinetia from Vanda rather than the inclusion of Neofinetia into Vanda. The sister group of the Sedirea was (Dimorphorchis(Pteroceras(Saccolabiun+Phalaeonopsis))) clade. The Dimorphorchis was one of the most probable sister genus to the Sedirea. The sister group relationship between Sedirea and Aerides was suggested by their similar morphology, but not supported in molecular trees. The identification of species and localities of Neofinetia was possible using our two molecular markers. However, several pseudo-gene sequences are discovered from the public data base. In addition, the horizontal gene transfer of chloroplast genomes is frequent events in orchid hybrids. Therefore, we need a careful evaluation for the data prior to systematic use. Generation of sequence data from multiple accessions of a species may helpful to reduce these types of error.

• Korean Journal of Plant Taxonomy
• /
• v.34 no.4
• /
• pp.335-358
• /
• 2004

To investigate molecular phylogenetic relationships and to test hypothesis of hybrid origin of Ranunculus cantoniensis (Ranunculaceae), the sequences of nrDNA and chloroplast DNA were analyzed for 8 taxa and 25 accessions including 5 accessions of outgroup. In the phylogenetic trees by analyses of maximum parsimony and maximum likelihood for ITS nrDNA sequences and combined data of psbA-trnH, rps16 and trnL sequences of cpDNA, R. cantoniensis was most closely related to R. chinensis, and then to R. taciroi and R. silerifolius. The molecular phylogenetic relationships were not congruent with the previous report that R. cantoniensis was most closely related to R. silerifolius. In the sequence analysis of ITS and psbA-trnH, rps16, trnL for R. cantoniensis and the related taxa, R. cantoniensis showed polymorphism. It supported that the polymorphism also was reported in chromosome number and karyotype of R. cantoniensis. Ranunculus cantoniensis shared the marker gene of R. chinensis and R. silerifolius in ITS, and one of R. silerifolius in cpDNA. These results supported the hypothesis that R. cantoniensis was caused by hybridization between R. chinensis and R. silerifolius based on chromosome number and karyotype, and also estimated that R. silerifolius might be of maternal origin and R. chinensis be paternal.