• The Korean Journal of Ecology
• /
• v.24 no.6
• /
• pp.359-364
• /
• 2001

Regional variations of Dictyostelid cellular slime molds were examined using molecular data. The intertranscribed spacer regions including the 5.8S ribosomal DNA of 2 species(D. purpureum, P. violaceum) of Cellular Slime Molds were sequenced and analyzed. Among 13 strains of D. purpureum and 12 strains of P. violaceum analyzed, each two strains were obtained from ATCC and the others were isolated from the forest soils in Korea. The sequences of the 5.8S ribosomal DNA were conserved among the strains of the same species, but unexpectedly highly variable among species. A high level of genetic diversity was found which was best resolved at the genus/species level as well as the family level by sequence data from the ITS 1 and ITS 2 regions. According to the sequence alignments by CLUSTAL X and the phylogeographic analyses by PAUP, 12 strains of P. violaceum were divided into three groups among which there were no difference of the morphological characteristics. Among 13 strains of D. purpureum, genetic variations were related to two morphological types, the temperate and subtropical type. There was no variation pattern according to geography in Korea, but there were some variations between Korea and other countries.

• Journal of Mushroom
• /
• v.4 no.2
• /
• pp.43-47
• /
• 2006

PMO-P4, being cultivated as "Sanghwang" in Korea, was proved to be P. baumii based on ITS (internal transcribed spacer) sequencing and RFLP (Restriction Fragment Length Polymorphism) patterns along with some Phellinus species including P. linteus. The similaraty of ITS sequencing between PMO-P4 and other Phellinus species was given the range of 48.6%~72.2%, showing the highest homology from P. linteus and the lowest from P. gilvus.

• Journal of Mushroom
• /
• v.8 no.1
• /
• pp.27-32
• /
• 2010

This study was carried out to analyze the genetic relationships among 22 strains of Sparassis crispa, which were collected from various regions of worldwide. The cleaved amplified polymorphic sequence were obtained from the ribosomal DNA ITS regions of each strain. Based on the sequence analysis, the presence of five different groups were observed. Most strains shared the high nucleotide sequence similarity (about 90%) to each other, except only one strain, KACC50866. Nucleotide sequence similarity of KACC50866 was below 10% to other strains, indicating the genetic relatedness of strain KACC50866 was low compared to other strains. More works such as mitochondria genome analysis should help to determine the precise genetic diversity of S. crispa strains.

• Korean Journal of Plant Resources
• /
• v.25 no.6
• /
• pp.753-761
• /
• 2012

We performed phylogenetic analyses of a total of 21 acessions covering 5 species in the Korean Trigonotis and one outgroup species using nuclear ribosomal ITS and chloroplast rbcL, matK, ndhF sequences. Outgroup were chosen from the closely related genus Lithospermum zollingeri. Both parsimony and Bayesian Inference methods were used to reconstruct the evolutionary history of the group. The evidence collected indicated that phylogenetic relationships among Korean Trigonotis species are unresolved based on nuclear marker (ITS), as the same as based on separated chloroplast sequences. While the phylogenetic relationships of Korean Trigonotis species almost clearly were resolved in combined chloroplast sequences. Thus, the members of Trigonotis coreana can be distinguished to the members of Trigonotis peduncularis in combined cpDNA sequences and Trigonotis nakaii was treated as a synonymed to Trigonotis radicans var. sericea. In addition, the MP and BI analysis showed Trigonotis icumae as sister of the remained Korean Trigonotis species based on combined molecular markers (BI: PP = 1).

• Journal of Ecology and Environment
• /
• v.34 no.3
• /
• pp.323-331
• /
• 2011

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

• Mycobiology
• /
• v.28 no.1
• /
• pp.11-16
• /
• 2000

The nucleotide sequences of the internal transcribed spacer (ITS) regions of the ribosomal DNA including the 5.8S ribosomal RNA gene (rDNA) have been determined for 11 species in order to analyze their intrageneric relationships. The total length of these sequences ranged from 530 nucleotides for Trichoderma reesei KCTC 1286 to 553 nucleotide for Trichoderma koningii IAM 12534. Generally speaking, the length of ITS1 region was about 30 nucleotides longer than that of the ITS2 region. Also, the sequences of 5.8S rDNA were more conserved in length and variation than those of ITS regions. Although the variable ITS sequences were often ambiguously aligned, the conserved sites were also found. Thus, a neighbor-joining tree was constructed using the full sequence data of the ITS regions and the 5.8S rDNA. The Trichoderma genus used to be grouped on the basis of the morphological features and especially the shape of phialides needs to be reexamined. The phylogenetic tree displayed the presence of monophylogeny in the species of Trichoderma. Therefore, it was difficult to distinguish the intrageneric relationships in the Trichoderma genus.

• Journal of Plant Biotechnology
• /
• v.38 no.3
• /
• pp.234-240
• /
• 2011

The genus Paeonia belongs to the family Paeoniaceae having significant medicinal and ornamental importance. The present investigation was undertaken with an aim to understand phylogenetic relationships of three Paeonia species (P. lactiflora, P. obovata, and P. suffruticosa) that are widely distributed in China, Korea, and Japan, using nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequence and to compare the phylogeny results with investigations reported earlier using existed sequences of the same species. The size variation obtained among sequenced nrDNA ITS region was narrow and ranged from 722 to 726 bp. The highest interspecific genetic distance (GD) was found between P. lactiflora and P. suffruticosa or P. obovata. The phylogram obtained using our nrDNA ITS sequences showed non-congruence with previous hypothesis of the phylogeny between section Paeonia and section Moutan of genus Paeonia. This result was supported by the phylogenetic relations showed in the phylogram constructed with existed sequences in NCBI. The present study suggested that P. obovata belonging to section Paeonia was phylogenetically closer to P. suffruticosa representing section Moutan of genus Paeonia than P. lactiflora belonging to section Paeonia. The main reason of the paraphyly of section Paeonia is thought to be nucleotide additivity directly caused by origin hybridization. This study provides more sequence sources of genus Paeonia, and will help for further studies in intraspecies population, and their phylogentic analysis and molecular evolution.

• Journal of Life Science
• /
• v.23 no.6
• /
• pp.770-778
• /
• 2013

To determine the seasonal variation of bacterial community in the seawater of Gwangyang Bay, three hundred thirty six bacterial strains were isolated on February, May, July and October 2011. Amplified Ribosomal DNA Restriction Analysis (ARDRA) was used to construct the phylotyes of the isolates using the restriction endonuclease, Hae III. Diversity indices of ARDRA patterns were calculated. One hundred and one phylotypes including 40 unique pylotypes were found at the 80% similarity level. Partial 16S rRNA genes of one hundred thirty nine strains representing each phylotypes were sequenced and compared. Bacterial community composed of 4 different phyla which include Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. Proteobacteria was the prevailing phylum in all seasons, followed by Bacteroidetes in winter, spring and autumn while Actinobacteria in summer. At the family level, Flavobacteriaceae dominated in winter and spring and Pseudoalteromonadaceae did in summer and autumn. Genera Altererythrobacter, Loktanella, Pseudoalteromonas and Vibrio were encountered in all seasons. The most diverse bacterial community was found in autumn followed by the order of spring, winter and summer.

• Animal cells and systems
• /
• v.5 no.4
• /
• pp.283-290
• /
• 2001

Phylogenetic relationships among the Korean taxa of the genus Allium subgenus Rhizirideum and some related taxa were assessed on the basis of in sequences of nuclear ribosomal DNA. Twenty-eight accessions of the genus Allium L. consisting of subgenera Rhizirideum (19 taxa), Allium (5 taxa) and Amerallium (one taxon) were analyzed. The variation in the ITS region was informative at the levels of section except for sect. Reticulato- bulbosa which is known to be of multiple origin. The ITS 2 region was longer than the ITS 1 region, and all of the investigated Allium taxa were the same in length in the 5.8S region except for A. monanthum. Allium cyaneum var. cyaneum was the shortest (635 bp) and A. victorialis the longest (646 bp) among the investigated Korean taxa. The three morphologically similar taxa, A. thunbergii, A. sacculiferum that has been included in A. thunbergii, and A. deltoid- fistulosum, had the same ITS lengths of 641 bp, but were clearly distinguished in the phylogenetic analysis of their ITS sequences.

• Mycobiology
• /
• v.30 no.1
• /
• pp.13-17
• /
• 2002

The genomic DNAs were extracted from roots of Glycine max and Sorghum bicolor, and compared with those from spores of two arbuscular mycorrhizal(AM) fungi, Glomus mosseae and Scutellospora heterogama. The partial small subunit(SSU) of ribosomal RNA genes were synthesized and amplified by polymerase chain reaction with the fungal specific primers, AM1 and NS31. By the recent molecular techniques, the presence of another AM fungal DNA were confirmed in the roots of two plants, and three sequences of rDNA fragments amplified were identified to be close to those of G. caledonium, G. fasiculatum and G. proliferum. The two AM fungi, both, were found to colonize at the cortical layers of plant roots collected in the fields, together.