• Mycobiology
• /
• v.51 no.2
• /
• pp.109-113
• /
• 2023

Auricularia is one of the broadly cultivated edible mushrooms in Korea. Most of the Korean Auricularia strains used for cultivation and breeding are known as A. auricula-judae. Recently, this species has been reported to belong to a species complex. Therefore, this study was carried out to genetically clarify the bred and cultivated Korean A. auricula-judae strains. The internal transcribed spacer (ITS) and IGS1 rDNA region sequences were determined from 10 A. auricula-judae strains by PCR and sequencing. Variation in the nucleotide sequence and sequence length of the two rDNA regions were found among the seven A. auricula-judae strains. A maximum-likelihood (ML) phylogenetic tree based on the ITS sequences clearly placed all the 10 Korean A. auricula-judae strains in the A. heimuer clade of the A. auriculajudae complex. A. heimuer is diverged from A. auricula-judae. An ML phylogenetic tree based on the IGS1 sequences revealed the close relationship between Korean A. heimuer strains to Chinese A. heimuer strains. But each strain could be distinguishable by the IGS1 sequence. Furthermore, progeny strains in the seven Korean strains could be differentiated from their parental strains by the IGS1 sequence based phylogenetic tree. Our results are expected to be used to complement the distinction of domestic Auricularia cultivars.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.142-143
• /
• 2003

Ammi majus (white lace flower, Unbelliferae) is an ornamental plant used for cut-flower arrangements worldwide. A potyvirus was isolated from its leaves with mosaic and chlorotic symptoms in the cultivated field of Chiba, Japan. Compared with Japanese homuort mosaic virus (JHMV) previously isolated from Cryptotaenia japonica, it showed similar characteristics in host reactions and molecular properties. The nucleotide sequences of coat protein and 3'- nontranslated region were highly homologous and shared 87％ and 91％ identities with those of JHMV, respectively. This virus was thus supposed to be an isolate of JHMV and designated as JHMV-Am. Phylogenetic tree was constructed using CP nucleotide sequences of the two isolates and other potyviruses previously reported. JHMV-Am and JHMV fell into a cluster with Korean strain of Zantedeschia mosaic virus (ZaMV-KR). However, low identity in amino acid sequences was found in the termini of CP genes between the two isolates of JHMV and ZaMV-KR.

• Journal of Life Science
• /
• v.13 no.6
• /
• pp.958-969
• /
• 2003

The human Y chromosome is strictly paternally inherited and does not X-Y crossing over during male meiosis in most of its length. Although this region came to be known as the non-recombining region Y (NRY), it was renamed as male-specific region Y (MSY) due to abundant recombination. The MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerated and ampliconic. The X-transposed sequences exhibit 99% identity to the X chromosomal sequences. The X-degenerate sequences are remnants of ancient autosomes from which the modem X and Y chromosomes evolved. Eight palindromes of the ampliconic comprise one-quarter of the euchromatic DNA of the male-specific region of the human Y chromosome. They contain many testis-specific genes and typically exhibit 99.97% intra-palindromic (arm-to-arm) sequence identity. The arms of these palindromes must have subsequently engaged in gene conversion, driving the pair arms to evolve it concert. Averages of approximately 600 nucleotides per newborn male have undergone Y-Y gene conversion, which has had an important role in the evolution of multi-copy testis gene families in the MSY.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.2 no.1
• /
• pp.87-89
• /
• 2001

The nucleotide sequence of the domestic silkworm (Bombyx mori) mitochondrial (mt) control region and its flanking genes was determined from PCR clones. The control region of the silkworm mt genome was located between the small ribosomal RNA gene and transfer RN $A^{Met}$. This 499 bp control region hale 95.4% A+T content. Extensive comparative analysis studies performed with similar control region of other insect genomes could not reveal a highly conserved region containing conserved motifs of animal mito-chondrial genome. The remarkable feature that found in this control region was the presence of tandem motifs containing nine repetitive sequences. The potential usefulness of this motif sequences for Bombyx species or their taxonomically related species is enhanced by its unique localization in the maternally inheritance mitochondrial molecule.e.

• 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.

• Korean Journal of Veterinary Service
• /
• v.42 no.3
• /
• pp.161-167
• /
• 2019

The poultry red mite (PRM), Dermanyssus gallinae, causes great economic losses to poultry industries in Korea. The molecular epidemiological characterization of PRM has been investigated in some countries, but those analysis has been not conducted yet in Korea. The aim of this study is to determine the genetic diversity of PRMs in Korea compared with those from other countries. Here, 13 PRM samples collected from Korea were analyzed with a part of the mitochondrial cytochrome oxidase subunit I (COI) gene and nuclear internal transcribed spacers (ITS) region. All the samples showed an identical COI sequence, which has also been reported in European countries and Japan. Phylogenetic diversity analysis showed that the mites from Korea were genetically related to those in other countries. The nuclear ITS region sequences were classified into three sequence types. Additionally, one of the ITS sequences was an intermediate type, implying that a hybridization event occurred among the mite populations in Korea. These findings suggested PRMs from Korea showed low genetic diversity with respect to mitochondrial COI gene, but three different populations inhabited in Korea with respect to nuclear ITS region sequences.

• 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 Resources
• /
• v.34 no.1
• /
• pp.1-16
• /
• 2021

The phylogenetic relationships among thirty-two strains (P1~P32; including Cordyceps sp., Paecilomyces sp., Beauveria sp., Aranthomyces sp., Isaria sp. and Himenostilbe sp.) in Miryang region located in the southern part of Korea, were investigated based on internal transcribed spacer (ITS) sequences of ribosomal DNA. A fragment of ITS region was amplified by polymerase chain reaction (PCR) using the specific primer pairs ITS1 and ITS4. After obtained same size of PCR products from various strains, we cloned them into a pGEM-T easy vector to determine their sequences. BLAST analyses of the nucleotide sequence ITS1, 5.8S and ITS2 gene fragments revealed the identity and their phylogenetic relationship. Among 32 strains isolated from Miryang region, Cordyceps militaris was shared 100% sequences with Genbank (AY49191, EU825999, AY491992), while some species are not shared perfectly with reported sequences. For example, strain P17 (P. tenuipes in Ulju-gun Gaji Mountain) has some differences among the other strains of P. tenuipes (Miryang-si Jocheon-eup, Miryang-si Gaji Mountain) and those of gene bank. We conclude that ITS analyses with strains in the suburbs of Miryang in this study can be effectively used as a tool for classification, evaluation and collection of the natural eco-type genetic resources.

• Journal of Mushroom
• /
• v.10 no.2
• /
• pp.93-99
• /
• 2012

This study was carried to identify a correct species and asses genetic diversity within the same species of Grifola spp. preserved in Division of applied Microbiology. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Grifola spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that four strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Grifola clustered into one group, most of which correlated with species-groups identified by RAPD method. Eight isolates included strain GM01 showed high similarity with Grifola frondosa. All isolates were collected in the Japan(GM01, GM02, GM03) was identified as Grifola frondosa and isolates of the China(GM05, GM06, GM08) was identified as Bjerkandera fumosa, Grifola frondosa and Dichomitus squalens, respectively. RAPD analysis of genetic polymorphisms of genus Grifola showed a very different band patterns on the isolat. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 4 isolates of Grifola spp. may be need to reclassify or eliminate from preserved catalogue.

• Journal of Mushroom
• /
• v.9 no.1
• /
• pp.27-33
• /
• 2011

This study was carried to identify a correct species and asses genetic diversity within the same species of Trametes spp. preserved in Division of applied Microbiology The morphological and cultural characteristics of preserved strains were observed through microscope and investigated on PDA, respectively. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Trametes spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that five strains were different species and six strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Trametes clustered into four distinct group, most of which correlated with species-groups identified by RAPD method. Seven isolates included TM 01 strain showed high similarity with Trametes versicolr, TM 07 and TM 10 high similarity with Trametes gibbosa, and TM 05 high similarity with Trametes elegans. But isolates collected in the United States was identified as T. junipericola. T. gibbosa and T. versicolor by RAPD analysis of genetic polymorphisms showed a very different band patterns and these strains showed different band patterns on areas. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 11 isolates of Trametes spp. may be need to reclassify or eliminate from preserved catalogue.