• Korean Journal of Agricultural Science
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• v.43 no.1
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• pp.21-27
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• 2016

Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV), and Apple stem pitting virus (ASPV) have been known to induce top working disease causing economical damage in apple. Occurrences of these three viruses in pome fruit trees, including apple, have been reported around the world. The transmission of the three viruses was reported by grafting, and there was no report of transmission through mechanical contact, insect vector, or seed except some herbaceous hosts of ASGV. As RNA extraction methods for fruit trees, Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and multiplex RT-PCR techniques have been improved for reliability and stability, and low titer viruses that could not be detected in the past have become detectable. We studied the seed transmission ability of three apple viruses through apple seedling diagnosis using RT-PCR. Nineteen seeds obtained from commercially grown apple were germinated and two of the resulting plants were ASGV positive. Seven clones of the amplified ASGV coat protein (CP) genes of these isolates were sequenced. Overall sequence identities were 99.84% (nucleotide) and 99.76% (amino acid). Presence of a previously unreported single nucleotide and amino acid variation conserved in all of these clones suggests a possible association with seed transmission of these 'S' isolates. A phylogenetic tree constructed using ASGV CP nucleotide sequences showed that isolate S sequences were grouped with Korean, Chinese, Indian isolates from apple and Indian isolates from kiwi.

• Molecules and Cells
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• v.27 no.3
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• pp.365-381
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• 2009

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast MatK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.

• Parasites, Hosts and Diseases
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• v.54 no.4
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• pp.455-460
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• 2016

Blastocystis is a common zoonotic enteric protozoan that has been classified into 17 distinct subtypes (STs). A cross-sectional study was conducted to determine the prevalence and subtype distributions of Blastocystis in villagers living along the Chao Phraya River, Ayutthaya Province, Thailand, and to assess the risk of zoonotic infection. In total, 220 stool samples were collected, and DNA was extracted. PCR and sequencing were performed with primers targeting the small-subunit ribosomal RNA (SSU rRNA) genes. Blastocystis was present in 5.9% (13/220) of samples, and ST3 (5.0%; 11/220) was the predominant subtype, followed by ST2 (0.45%; 1/220) and ST6 (0.45%; 1/220). Phylogenetic trees were constructed with the maximum-likelihood method based on the Hasegawa-Kishino-Yano + G + I model, neighbor-joining, and maximum parsimony methods. The percentage of bootstrapped trees in which the associated taxa clustered together was relatively high. All the sequences of the Blastocystis-positive samples (KU051524-KU051536) were closely related to those from animals (pig, cattle, and chicken), indicating a zoonotic risk. Therefore, the villagers require proper health education, especially regarding the prevention of parasitic infection, to improve their personal hygiene and community health. Further studies are required to investigate the Blastocystis STs in the animals living in these villages.

• Korean Journal of Plant Taxonomy
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• v.32 no.4
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• pp.449-465
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• 2002

A systematic review for Korean Liliopsida was carried out with rbcL and atpB sequence data. Congruent phylogenetic trees were obtained from two different data sets. Korean Liliopsida consists of the three orders, Asparagales, Liliales, and Dioscoreales sensu Dahlgren et al. Members of Dioscoreales were used as an outgroup for inferring relationships among Asparagales and Liliales in the molecular studies. Iridaceae showed close relationship to Asparagales both in the rbcL and atpB sequence trees rather than to Liliales. Family Nartheciaceae (previously included within Melanthiaceae s. lat.) appeared as a paraphyletic assemblage basal within Liliales, but did not show relationships to other orders. Genera of Ruscaceae (previously Convallariaceae) like Disporum, Clintonia, and Streptopus had to be transferred to Colchicaceae, Liliaceae, and Calochortaceae, respectively. A revised list of families for Korean members of Liliopsida is suggested.

• The Plant Pathology Journal
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• v.35 no.3
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• pp.243-256
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• 2019

Field surveys for Plum pox virus (PPV) infection were conducted in stone fruit orchards all over Bulgaria. In total, 1168 out of 3020 leaf samples from cultivated Prunus spp. and wildly growing P. cerasifera trees reacted positive for PPV in DASI-ELISA with the universal monoclonal antibody (MAb) 5B. Further ELISA analyses showed that 987 and 127 isolates belonged to PPV-M and PPV-D serotypes, respectively. The plum and P. cerasifera showed 82.0% and 50.5% levels of infection, respectively followed by the peach (40.0%) and the apricot (32.0%). Five hundred fifty one PPV isolates were further typed by IC-RT-PCR with PPV-Rec, -M and -D-specific primers, targeting (Cter)NIb-(Nter) CP genome region, as 125 isolates were sequenced. The results revealed the presence of PPV-Rec, PPV-M and PPV-D and mixed infections of these strains. PPV-Rec was the most prevalent strain (49.0%), followed by PPV-M (40.1%), while PPV-D was the less spread strain (8.2%). PPV-Rec was the most common strain in plums, including the eight "old-aged" trees from the region of the first Sharka discovery. PPV-M was the most prevalent strain in peach and apricot. Phylogenetic analyses on (Cter)NIb-(Nter)CP of the isolates were performed. PPV-Rec isolates formed a homogeneous group, while PPV-M isolates split into PPV-Ma and PPV-Mb subgroups. Five separated clades were formed by the analyzed PPV-D isolates. Nucleotide sequences of the partial CP coding region of the analyzed isolates revealed a slightly higher intra-strain genetic variability in PPV-Rec and PPV-M isolates, while that of PPV-D strain isolates was higher from the reported for these strains.

• Korean Journal of Plant Taxonomy
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• v.46 no.3
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• pp.314-325
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• 2016

Multiple changes of the photosynthesis pathway are independent evolutionary events occurring in the phylogeny of flowering plants, and such changes have occurred more than five times in Cyperaceae. In the tribe Cypereae, the C4 photosynthetic pathway appeared only once and is regarded as a synapomorphy of the C4 plants within this tribe. The morphological delimitation of genera within Cypereae does not correspond to their molecular phylogenetic relationships. In this study, the molecular phylogeny was compared with the photosynthetic pathways of Korean Cypereae (18 species of Cyperus, 1 species of Kyllinga, and 1 species of Lipocarpha). The photosynthetic pathways were determined by observing the leaf anatomy. The phylogenetic analysis was performed using three DNA regions (nrITS, rbcL, and trnL-F). According to the position of the photosynthetic tissue, 4 species (C. difformis, C. flaccidus, C. haspan, and C. tenuispica) and 16 species (14 Cyperus species, K. brevifolia var. leiolepis, and L. microcephala) were confirmed as C3 and C4 plants, respectively. Tribe Cypereae was divided into the CYPERUS and FICINIA clades, and all species of Korean Cypereae plants belonged to the CYPERUS clade in the phylogenetic analysis. Within the CYPERUS clade, C4 plants were monophyletic but their phylogenetic relationships were unclear. The genera Kyllinga and Lipocarpha were not supported as an independent genus in either case because they were nested by the Cyperus species in the molecular phylogenetic trees in the present and in previous studies. To determine the classification within the CYPERUS clade, a detailed morphological study and a molecular phylogenetic analysis at a high resolution will be necessary.

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

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.2
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• pp.103-109
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• 2000

Complete senuences of the mitochondrial rRNA Benes were determined among six salmonines in Korean Waters (Brachpmystax lenok, Onoorhpchus keta, O. masou mason, O. mason ishikawae, O. mykiss, and albino mutant of O. mykiss). The purposes of this study were to provide the basic information on levels of mtDNA polymorphism among these species for genetic characterization; discuss phylogentic relationships among three Oncorhynchus sepecies; demonstrate the utility of rRNA gene sequence data as a genetic marker for disringuishinf among Korean salmonines. PCR/direct sequencing data indicated the following consistent results; 1) 12S rRNA genes was 945 bases long in Oncorhynchus species, and 946 bases in B. lenot including one insertion. 2) Of sequence variation in mitochondrial rRNA regions, transitional substitutions were superior to transversion. 3) The significant differences were not shown in the intraspecific variation values in these gene regions. The percentage sequence divergence values were ranged from $0.066 to 0.212{\%}$. 4) The interspecific divergences were greater than the intraspecific variation. Nevertheless, ribosomal RMh genes were more conserved among species than the other mitochondrial genes, and they showed potentiality as an intergenic marker for systematics. In addition, phylogenetic trees, constructed from this data, supported that cherry salmon was closer to chum salmon than to rainbow trout, and that lenok was most distantly related species in six salmonid species.

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