• Journal of Plant Biotechnology
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• v.47 no.4
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• pp.289-297
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• 2020

The genetic diversity of two subpopulations of Corynandra chelidonii, one of terrestrial and the other of aquatic environments, was measured with molecular markers, such as start codon targeted (SCoT), inter simple sequence repeats (ISSR), and random amplification of polymorphic DNA (RAPD). The traditional morphological traits such as habitat, habit, leaf morphology, the colour of the sepals and petals, number of stamens, and seed morphology formed the base for their realization as two varieties, C. chelidonii var. pallae and C. chelidonii var. chelidonii. The polymorphism between the two variants was 100% with the primers SCoT-2 and OPA-1 and 4, while maximum polymorphism was detected with ISSR-2, SCoT-3, and OPA-3. The study used, for the first time, more than one molecular marker to assess the genetic variation underscoring the morphological variation in Corynandra chelidonii (L.f.) Cochrane & Iltis. The study justifies the recognition of the two subpopulations of Corynandra chelidonii from aquatic and terrestrial environments as two distinct varieties, C. chelidonii var. pallae (Reddy & Raju) V.S.Raju and C. chelidonii var. chelidonii, respectively, based on the traditional taxonomic evidence.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.656-659
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• 2005

Small peptides synthesized by nonribosomal peptide synthetases (NRPSs) genes are found in bacteria and fungi. While some microbial taxa have few, others make a large number and variety. However, biochemical characterization of the products synthesized by NPRS demands a great deal of efforts. Since the completion of genome projects of numerous microorganisms, the numbers of available NRPSs genes are being expanded. Prediction of the peptides encoded by NRPS could save time and efforts. We chose the NRPS gene from Bradyrhizobium japonicum as a model to predict the peptide structure encoded by NRPS genes. Using computational analyses, the domain structure of this gene was defined, and the structure of a peptide synthesized by this NRPS was deduced. It was found that it encoded a tripeptide consisting of proline-serine-phenylalanine. This method would be helpful to predict the structure of small peptides with various NPRS genes from the genome sequence.

• Environmental Analysis Health and Toxicology
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• v.26
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• pp.10.1-10.7
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• 2011

Objects: Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing. Method: To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C.ripairus using pyrosequencing method. Results: Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value${\leq}1^{-5}$) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest. Conclusions: The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.

• The Plant Pathology Journal
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• v.29 no.4
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• pp.397-409
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• 2013

The full-genome sequences of fourteen isolates of Broad bean wilt virus 2 (BBWV2), collected from broad bean, pea, spinach, bell pepper and paprika plants in Korea during the years 2006-2012, were determined and analyzed comparatively along with fifteen previously reported BBWV2 genome sequences. Sequence analyses showed that RNA-1 and RNA-2 sequences of BBWV2 Korean isolates consisted of 5950-5956 and 3568-3604 nucleotides, respectively. Full-length genome sequence-based phylogenetic analyses revealed that the BBWV2 Korean isolates could be divided into three major groups comprising GS-I (isolates BB2 and RP7) along with isolate IP, GS-II (isolates BB5, P2, P3 and RP3) along with isolate B935, and GS-III including 16 BBWV2 Korean isolates. Interestingly, GS-III appears to be newly emerged and predominant in Korea. Recombination analyses identified two recombination events in the analyzed BBWV2 population: one in the RNA-1 of isolate K and another one in the RNA-2 of isolate XJ14-3. However, no recombination events were detected in the other 21 Korean isolates. On the other hand, out of 29 BBWV2 isolates, 16 isolates were found to be re-assortants, of which each RNA segment (i.e. RNA1 and RNA2) was originated from different parental isolates. Our findings suggested that reassortment rather than recombination is a major evolutionary force in the genetic diversification of BBWV population in Korea.

• The Plant Pathology Journal
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• v.31 no.4
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• pp.388-401
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• 2015

Sweet potatoes (Ipomea batatas L.) are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), and Sweet potato latent virus (SPLV), have been detected in sweet potato fields at a high (~95%) incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88%) nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.

• The Plant Pathology Journal
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• v.18 no.3
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• pp.130-137
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• 2002

Potato virus Y (PVY) is one of the most important viruses in many field crops in Korea. In this study, 31 PVY isolates were isolated from infected potato (Solanum tuberosum), tobacco (Nicotiana tabacum), pea (Pisum sativum), and weeds (Veronica persica, Lamium amplexicause and Capsella bursa-pastoris) showing different mosaic symptoms in Jeonbuk, Chungnam, Gangwon, and Gyeongbuk areas in Korea. The 640 nucleotide region containing the C-terminal portion of coat protein (CP) gene and 3'non-translated region (NTR) was amplified by reverse transcription-polymerase chain reaction (RT-PCR) using PVY-specific oligonucleotide primers. Sequence analyses of the amplified DNA fragments showed that the C-terminal portion of CP gene was not significantly different from that of previously reported PVY strains from potato (PVY-OK and -T) and tobacco (PVY-VN) in Korea. Homologies of the deduced CP amino acid sequences were 93.3-99.0% to corresponding regions of the other PVY strains including PV $Y^{N}$, PV $Y^{o}$ , PV $Y^{OK}$ , PV $Y^{T}$ , and PV $Y^{VN}$ . In contrast the sequences located at the 3'-NTR showed more diverse sequence homologies (76.4-99.7%). These results indicate that the C-terminal portion of the CP gene was relatively conserved while sequences at the 3'NTR were more diverse and variable over the host species and the regions where they were isolated.e isolated.

• Molecules and Cells
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• v.27 no.4
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• pp.459-465
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• 2009

MUG1 is a MULE transposon-related domesticated gene in plants. We assessed the sequence diversity, neutrality, expression, and phylogenetics of the MUG1 gene among Oryza ssp. We found MUG1 expression in all tissues analyzed, with different levels in O. sativa. There were 408 variation sites in the 3886 bp of MUG1 locus. The nucleotide diversity of the MUG1 was higher than functionally known genes in rice. The nucleotide diversity (${\pi}$) in the domains was lower than the average nucleotide diversity in whole coding region. The ${\pi}$ values in nonsynonymous sites were lower than those of synonymous sites. Tajima D and Fu and Li $D^*$ values were mostly negative values, suggesting purifying selection in MUG1 sequences of Oryza ssp. Genome-specific variation and phylogenetic analyses show a general grouping of MUG1 sequences congruent with Oryza ssp. biogeography; however, our MUG1 phylogenetic results, in combination with separate B and D genome studies, might suggest an early divergence of the Oryza ssp. by continental drift of Gondwanaland. O. long-istaminata MUG1 divergence from other AA diploids suggests that it might not be a direct ancestor of the African rice species.

• Korean Journal of Environmental Biology
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• v.35 no.3
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• pp.354-360
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• 2017

Bryopsis africana and Pyropia kinositae are reported for the first time on the list of Korean marine algal flora based on integrated morphological-molecular study. Bryopsis africana from Korea is recognized with distinct main axes, robust thalli, pinnately and radially branched above, and basally denuded. Phylogenetic analyses revealed that B. africana was placed within a clade of Bryopsis. Bryopsis africana differs from B. corymbosa by 2.7% gene sequence divergence. Pyropia kinositae is characterized by oblong to lanceolate thalli, entire margin, purplish red in color, twice as long as broad cells in transversal section view. Phylogenetic analyses revealed that P. kinositae was placed within a clade of Pyropia. Pyropia kinositae differs from P. tenera by 1.5-1.8%, P. ishigecola by 1.2-1.3%, and P. yezoensis by 1.5-1.8% gene sequence divergence respectively.

• ALGAE
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• v.31 no.4
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• pp.303-315
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• 2016

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

• Journal of Microbiology
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• v.41 no.1
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• pp.16-21
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• 2003

We have collected eight high-level streptomycin-resistant strains of Pseudomonas marginalis and P. syringae pv. actinidiae which were isolated from kiwifruit orchards in Korea and Japan, The molecular mechanisms of resistance were investigated by the PCR, susceptibility tests, and nucleotide sequence analysis. Of the eight high-level streptomycin-resistant strains, four harbored strA-strB genes, which encode streptomycin-inactivating enzymes. While the three Korean strains of R marginalis did not have plasmid and carried the resistant genes in the chromosomes, the Japanese strain of P. syringae pv. actinidiae had a plasmid containing strA-strB genes. The myomycin susceptibility test demonstrated that the high-level resistance to streptomycin of the remaining four strains is associated with mutations in the rpsL gene. Nucleotide sequence analyses revealed that they contain a single base-pair mutation in codon 43 of their rpsL gene.