• Korean Journal of Microbiology
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• v.48 no.4
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• pp.319-324
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• 2012

In this study, we investigated molecular divergences and phylogenetic characteristics of the 16S ribosomal RNA (rRNA) and RNA polymerase beta subunit (rpoB) gene sequences from the order Oscillatoriales (Cyanobacteria). The rpoB of Oscillatoriales showed higher genetic divergence when compared with those of 16S rRNA (p-distance: rpoB=0.270, 16S=0.109), and these differences were statistically significant (Student t-test, p<0.001). Phylogenetic trees of 16S rRNA and rpoB were generally compatible; however, rpoB tree clearly separated the compared Oscillatoriales taxa, with higher phylogenetic resolution. In addition, parsimony analyses showed that rpoB gene evolved 2.40-fold faster than 16S rRNA. These results suggest that the rpoB is a useful gene for the molecular phylogenetics and species discrimination in the order Oscillatoriales.

• Journal of Life Science
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• v.21 no.9
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• pp.1281-1287
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• 2011

Phyllostachys consists of high and fast growing trees and is a genus in the family Gramineae. The genus has many species in Asia, with main distribution being in India and China. One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. We evaluated four taxa with the ITS region to estimate phenotypic relationships within the genus Phyllostachys in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within the Phyllostachys was mostly due to natural selection, although several indels and inserts were found. Within the genus Phyllostachys, P. nigra and P. nigra var. henonis were the relatives in the three phylogenetic analyses (MP, ML, and NJ). However, some external nodes were poorly supported. Morphological traits and simple repeats (ISSR) represented the result of a relationship similar to the that of ITS sequences in the genus Phyllostachys. This suggests that ITS sequences are very informative for identification of these taxa.

• Journal of Life Science
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• v.24 no.6
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• pp.626-632
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• 2014

The genetic structure and phylogenetic relationship were investigated in Korean red spotted grouper populations using the nucleotide sequence polymorphisms of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene. The COI gene was sequenced showed 99.1-99.8% identity with the EF607565 sequence previously reported. A total of twenty haplotypes were found, and the Korean population showed nineteen haplotypes. Among those, Hap_03 and Hap_08 showed Jeju-do and China-specific COI sequences, respectively. However, Hap_07 had twelve COI sequences from South Korea and records from Hong Kong and Taiwan. Neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COI haplotypes showed a monophyletic branching pattern within the genus Epinephelus. This indicated that the red spotted grouper populations had evolved from common maternal ancestors. In addition, the Hap_08, which had the COI sequence recorded only from China Sea, was found in the middle of the NJ tree nearby Hap_07 and showed a close relationship with Hap_07. This indicates that Chinese red spotted grouper is also maternally related to other populations in East Asia. Consequently, East Asian red spotted grouper populations are maternally related, as well as sharing the same evolutionary history, and are still affected by the East Asian ocean current (Kuroshio). These findings help to explain the genetic structure and phylogenetic relationship of red spotted grouper and also contribute to research on artificial breeding and industrialization.

• The Plant Pathology Journal
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• v.33 no.3
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• pp.307-317
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• 2017

Satsuma dwarf virus (SDV) or Citrus mosaic sadwavirus (CiMV) were not consistently detected in RTPCR assay with the primer sets based on gene of Japan isolates. SDV and CiMV isolates were distinctively divided into two groups based on phylogenetic analysis of PP2 gene cloned from 22 Korean isolates, and the Korean CiMV and SDV isolates shared 95.5-96.2% and 97.1-97.7% sequence identity with Japanese isolate, respectively. We developed PP2-1 primer set based on the PP2 gene sequence of Korean isolates to simultaneously and effectively detect SDV and CiMV. And CTLV-2013 and CTV-po primer sets were newly designed for detection of Citrus tatter leaf virus (CTLV) and Citrus tristeza virus (CTV), respectively. Using these primer sets, a new multiplex PCR assay was developed as a means to simultaneously detect 4 citrus viruses, CTV, CTLV, SDV, and CiMV. The degree of detection by the multiplex PCR were consistent with those of uniplex RT-PCR for detection of each of the viruses. Therefore, the new multiplex PCR provides an efficient method for detecting 4 citrus viruses, which will help diagnose many citrus plants at the same time. We verified that 35.2% and 72.1% of 775 trees in 155 orchards were infected with SDV or CiMV (SDV/CiMV) and CTV by the multiplex-PCR assay, respectively, and CTLV was not detected in any of the trees tested.

• Research in Plant Disease
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• v.25 no.1
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• pp.8-15
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• 2019

Plum pox virus (PPV) is a significant viral disease in Prunus spp. worldwide. A nationwide survey was started in Prunus spp. orchards, since PPV was first detected from peach in Korea, 2015. During 2016-2017, samples were collected from 30,333 trees in 1,985 orchards of stone fruits in 8 provinces and 4 cities, Korea and tested by RT-PCR using specific PPV primer set. As a result, 21 trees including peach (9 trees), Japanese apricot (4 trees), plum (1 tree), apricot (7 trees) in 10 orchards were infected and controlled by eradication program. Amplicons of the expected size (547 bp) were obtained from total RNA of seven peach trees in 2016, and directly sequenced. BLAST analysis revealed the highest nucleotide (NT) identity (99%) with a PPV D isolates (LC331298, LT600782) in Genbank. The seven isolates from shared nt sequence identities of 98 to 100% with one another. Phylogenetic analysis showed the isolates in peach clustered closely with the PPV-D isolates from Korea, Japan, USA, and Canada. This is, to our knowledge, the first report of the presence of PPV in Prunus spp. orchards in Korea, 2016-2017, we hope that our results and efforts will contribute to effective measures for eradication of PPV.

• ALGAE
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• v.19 no.4
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• pp.283-292
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• 2004

Psilothallia is a ceramiaceous red algal. genus that includes three species worldwide: P. dentate, P. siliculosa, and P. striate. The latter two species are limited to Australian waters, and P. dentate occurs in Japan. We here report the detailed morphology of P. dentate, and also determined plastid protein-coding psbA in P. dentate and putative relatives. Psilothallia dentate is distinguished by compressed thalli with alternate-distichous determinate branchlets, six periaxial cells, rhizoidal filaments in axes, cystocarps with 7-8 involucral filaments, spermatangia on branched filaments, and tetrahedrally divided tetrasporangia on branched filaments. Psilothallia dentate is also unusual in that cystocarps, spermatangial clusters, and tetrasporangial tufts are formed on short adventitious indeterminate branches arising on axils of determinate branchlets. The phylogenetic trees of psbA sequences show that P. dentata was nested in a monophyletic Glade comprising Ptilota, Neoptilota, and Plumaria. This result suggests that the taxonomic position of P. dentate may be transferred from the tribe Rhodocallideae to the Ptiloteae.

• Korean Journal of Plant Taxonomy
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• v.41 no.3
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• pp.209-214
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• 2011

The taxonomy of the umbelliferous species Angelica amurensis and its allies was reviewed on the basis of molecular phylogenies derived from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) regions. Strict consensus of six minimal length 119-step trees derived from equally weighted maximum parsimony analysis of combined nuclear rDNA ITS1 and ITS2 sequences from 29 accessions of Angelica and outgroups indicated that Angelica purpuraefolia, known to be endemic to Korea, is the same species as A. amurensis. Comparisons of sequence pairs across both spacer regions revealed identity or 1-2 bp differences between A. purpuraefolia and A. amurensis. These results indicated that the two taxa are not distinguished taxonomically. Also, nuclear rDNA ITS regions are discussed as potential barcoding loci for identifying Korean Angelica.

• The Korean Journal of Mycology
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• v.44 no.4
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• pp.338-341
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• 2016

A dark septate endophytic fungal strain 13E043 was isolated from the needle leaves of Thuja koraiensis from a forest in Korea. Morphological characteristics of conidia and phialids. Along with a molecular phylogenetic analysis based on the internal transcribed spacer region of rDNA, the isolate was identified as Phialocephala piceae (also known as Phaeomollisia piceae). This is the first report of a dark septate endophyte isolated from the foliage of conifer trees in Korea.

• Mycobiology
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• v.39 no.4
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• pp.266-271
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• 2011

Species of Phoma and its allies were isolated during a survey on the diversity of endophytic fungi associated with pine trees in Korea. Based on the phylogenetic analyses of internal transcribed spacer and ${\beta}$-tubulin gene sequences, two Phoma-like species from the needles of Pinus koraiensis were identified as Peyronellaea calorpreferens and P. glomerata. They were also morphologically identified based on the previous descriptions. Here, we report P. calorpreferens and P. glomerata being present in Korea as endophytic fungi in Pinus koraiensis.

• The Korean Journal of Mycology
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• v.49 no.3
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• pp.417-423
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• 2021

Apple decline symptoms were frequently observed on cv. Fuji apple orchards located in Gyeonggi, Gyeongbuk, and Gangwon provinces during surveys conducted from May until the end of September 2020. Three fungal strains were isolated from the margins of internal lesions of diseased apple trees, and their morphological characteristics were considered similar to Botryosphaeria sinensis. Phylogenetic analysis using internal transcribed spacer (ITS) regions, translation elongation factor 1-alpha (tef1), beta-tubulin (tub2), and the second largest subunit of RNA polymerase II (rpb2) gene sequences confirmed the closest relationship of isolates with B. sinensis at the species level. According to a pathogenicity test, the appearance of dark-brown discolorations and vascular necrosis on apple branches inoculated with the isolated strain KNUF-20-014 was observed. To the best of our knowledge, this is the first report of B. sinensis as the causal agent of apple disease in Korea.