• Korean Journal of Microbiology
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• v.40 no.2
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• pp.65-72
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• 2004

Instability of some eukaryotic sequence propagated in prokaryotic hosts is a frequently observed phenomenon. It is well documented that long inverted repeats, AT-rich sequences with structures like Z-DNA are extremely unstable in E. coli. These sequences may either be under-represented or even lost when cloned in E. coli. When we analyzed the polymorphic pattern for several tandom repeat (TR) in human SCKI gene, we found some TR regions were frequently deleted from plasmids and had difficult problem for their sequencing. These regions may result in non-clonability of the DNA sequence. Here we have cloned two difficult TR regions under low temperature and made two library for DNA sequencing using a nebulizer or sonicator. This study will help to determine the unstable genomic elements in complex mammalian genome.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.139-139
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• 2017

The complete chloroplast genome sequence of Avena sterilis L., a dominant wild oat species in the family Poaceae, is first reported in this study. The complete cp genome sequence of A. sterilis is 135,887 bp in length with 38.5% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (21, 603 bp) separated by a small single-copy region (12,575 bp) and a large single-copy region (80,106). The A. sterilis cp genome encodes 111 unique genes, 76 of which are protein-coding genes, 4 rRNA genes, 30 tRNA genes and 18 duplicated genes in the inverted repeat region. Nine genes contain one or two introns. Pair-wise alignments of cp genome were performed for genome-wide comparison. This newly determined cp genome sequence of A. sterilis will provide valuable information for the future breeding programs of valuable cereal crops in the family Poaceae.

• Korean Journal of Plant Resources
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• v.32 no.6
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• pp.644-668
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• 2019

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

• Genomics & Informatics
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• v.12 no.3
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• pp.80-86
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• 2014

Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as $180^{\circ}$ and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 1995.06b
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• pp.1-19
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• 1995

The plasmid pJEL 101 contains a highly repetitive element from the genome of Xanthomonas oryae pv. oryzae that has properties of an insertional element. The insertional nature of the element, hereto referred to as IS203, was confirmed by molecular analyses of the element and three related elements that were isolated from X. oryzae. The related sequences were isolated on the basis of transposition to the transposon-trapping vector pL3SAC and hybridization with pJEL101. The trapped elements (IS203a, IS203b, and IS203c) were each composed of 1,055 base pairs with 25 base terminal inverted repeats. The elements caused a three base pair target site duplication at the site of insertion in the sacRB gene. The sequence of pJEL 101 has 96% base pair identity with IS203a and 99% identity with IS203a and IS203c but lacks three nucleotides of the consensus left terminal repeat. IS203b has the same DNA sequences as IS203c but is inserted ito the sacRB gene in the opposite orientation. The longest open reading frame of IS203a could code for a protein of 318 amino acids and molecular weight of 37, 151. A search of the Genbank database revealed that IS203 has 51% identity with 909 nucleotides of IS4551 from Escherichia coli. The predicted protein of ORF1 has 40% and 30% amino acid identity to the ORF1 of Tn4551 and the transposase of IS30, respectively.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.37-37
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• 2018

The genus Crepidiastrum (Asteraceae), containing ca. 20 species, is mainly distributed in Asia. Crepidiastrum denticulatum, an edible plant that commonly call "e-go-deulppae-gi" in Korean, distributes in Korea, Japan, and China. The complete chloroplast (cp) genome sequences of C. denticulatum was characterized from MiSeq2000 (Illumina Co.) pair-end sequencing data. The cp genome of C. denticulatum has a total sequence length of 152,689 bp and show a typical quadripartite structure. It consists of the large single copy (LSC: 84,022 bp), small single copy (SSC: 18,519 bp), separated by a pair of inverted repeats (IRs: 25,074 bp) and contains 110 unique genes and 18 genes duplicated in the IR regions. Our comparative analysis identified three cpDNA regions (matK, rbcL, and psbA-trnH) from three Crepidiastrum species, which may be useful for molecular identification of each species, and providing a guideline for its clear confirming about dried medical herb.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.41-41
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• 2019

The genus Ficus L., containing approximately 850 species, is by far the largest genus in the Moraceae. They are mainly distributed worldwide, mainly in tropical countries. In South Korea, there are three native Ficus (including F. erecta Thunb, F. sarmentosa var. nipponica (Franch. & Sav.) Corner, and F. thunbergii Maxim.). Among them, F. erecta is effectively natural resources for the improvement of senile cognitive impairment. However, the chloroplast (cp) genome sequences and information of F. erecta have not been addressed. Therefore, in this study, we provide the complete cp genome of F. erecta and its allied species using next-generation sequencing technology. The chloroplast of Ficus species has typical structure which includes large and small single copy regions and a pair of inverted repeats (IRs). The sizes of cp genomes range from 160,276 bp to 160,603 bp. To determine the phylogenetic positions of these species, we conducted a maximum likelihood analysis using common protein-coding genes in chloroplast sequences. Also, we describe a newly developed single nucleotide polymorphism (SNP) markers using multiplex PCR to identify F. erecta based on amplification-refractory mutation system (ARMS) technique. We analyzed matK, atpB of the chloroplast genes and ITS from F. erecta and three related taxa, F. carica, F. sarmentosa var. nipponica and F. thunbergii. It provides useful information for molecular identification between F. erecta and related Korean native species.

• Journal of Species Research
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• v.10 no.2
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• pp.154-158
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• 2021

An endemic endangered species, Aster altaicus var. uchiyamae (Danyang aster) B2015-0044, is cultivated at the Shingu Botanical Garden, which serves as the ex situ conservation institution for this species. In this work, we sequenced the chloroplast genome of A. altaicus var. uchiyamae B2015-0044. We found that the chloroplast (cp) genome of B2015-0044 was 152,457 base pairs(bps) in size: 84,247 bps of large single copy regions(LSC), 25,007 bps of inverted repeats(IRs), and 18,196 bps of small single copy regions. The B2015-0044 cp genome contains 79 protein-coding genes (PCGs), 4 RNA genes, 29 tRNA genes, and 3 pseudogenes. These results were identical to a previously reported cp genome (Park et al., 2017), except for two sites in introns and three in intergenic spacer (IGS) regions. For the intronic differences, we found that clpP.i1 had a 1-bp small simple repeat (SSR) (T) and petD.i had a 3-bp SSR (ATT). We found 1-bp SSRs in the IGSs of trnT_ggu~psbD and psbZ~trnG_gcc, C and A, respectively. The IGS of(ndhF)~rpl32 had a SNP. Based on our results, the cp genome of the A. altaicus var. uchiyamae can be classified into two genotypes, [C]¹-[A]¹²-[T]¹²-[ATT]⁴-C and [C]²-[A]¹¹-[T]¹¹-[ATT]²-A.

• Korean Journal of Plant Taxonomy
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• v.52 no.2
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• pp.114-117
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• 2022

Lindera angustifolia is mainly distributed in the temperate climate zone of China but shows an extraordinary distribution, disjunctively isolated on the western coastal islands of Korea. We therefore present the complete chloroplast genome of Korean L. angustifolia. The complete plastome was 152,836 bp in length, with an overall GC content of 39.2%. A large single copy (93,726 bp) and a small single copy (18,946 bp) of the genome were separated by a pair of inverted repeats (20,082 bp). The genome consists of 125 genes, including 81 protein-coding, eight ribosomal RNA, and 36 transfer RNA genes. While five RNA editing genes (psbL, rpl2, ndhB×2, and ndhD) were identified in L. angustifolia from China, the "ndhD" gene was not recognized as an RNA editing site in the corresponding Korean individual. A phylogenetic analysis revealed that Korean L. angustifolia is most closely related to the Chinese L. angustifolia with strong bootstrap support, forming a sister group of L. glauca.

• Korean Journal of Plant Taxonomy
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• v.53 no.3
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• pp.237-241
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• 2023

The genus Scrophularia L. (Scrophulariaceae) comprises 200-270 species worldwide and is a taxonomically challenging lineage, displaying morphological diversity and hybridization. S. kakudensis is morphologically similar to the closely related taxa S. kakudensis var. microphylla, S. pilosa, and S. cephalantha. Therefore, the purpose of this study was to sequence the chloroplast (cp) genome of S. kakudensis using next-generation sequencing and compare it to those of related taxa. The complete cp genome sequence of Scrophularia kakudensis was found to be 152,355 bp long, consisting of a pair of inverted repeats of 25,485 bp that separate a large single-copy (LSC) of 83,479 bp from small single-copy regions of 17,909 bp. The cp genome contained 78 protein-coding genes, 30 tRNAs, and four rRNAs. A phylogenetic analysis based on 78 protein-coding genes from six Scrophularia species showed S. kakudensis and S. cephalantha formed with 100% bootstrap values. We compared the complete cp genomes of S. kakudensis and S. cephalantha and identified seven sequence divergence regions: matK/rps16, rps16/trnQ, trnS/trnG, rpoB/trnC, trnS/trnG, rpl32/trnL, and ndhD/psaC. These regions may be useful for determining the phylogenetic relationships among S. kakudensis-related species.