• Korean Journal of Plant Taxonomy
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• v.53 no.1
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• pp.32-37
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• 2023

Spiraea prunifolia f. simpliciflora Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of S. prunifolia f. simpliciflora, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus Spiraea was monophyletic and sister to the clade of Sibiraea angustata, Petrophytum caespitosum and Kelseya uniflora. Within the genus Spiraea, the sections Calospira and Spiraea were monophyletic, but the sect. Glomerati was nested within the sect. Chamaedryon. In the sect. Glomerati, S. prunifolia f. simpliciflora formed a subclade with S. media, and the subclade was sister to S. thunbergii and S. mongolica. The close relationship between S. prunifolia f. simpliciflora and S. media was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus Spiraea. The newly reported complete plastome and nrDNA transcription unit sequences of S. prunifolia f. simpliciflora provide useful information for further phylogenetic and evolutionary studies of the genus Spiraea, as well as the family Rosaceae.

• Korean Journal of Plant Tissue Culture
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• v.25 no.6
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• pp.477-485
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• 1998

To underatand in vitro regulation of differentiation, the effects of growth regulators and nitrogen source on metabolism of cell wall polysaccharides in suspension culture of kidney bean (Phaseolus vulgaris L.) were investigated. The suspension cells (cell clusters) were directly induced from the epicotyl segments of the seedlings, which were cultivated in MS medium supplemented with 1.0mg/L of 2,4-D and 0.5 mg/L of kinetin. When compared with cell wall sugar contents of the epicotyl segments, the cellulose content of the suspension-cultured cells decreased; while the pectin and hemicellulose content increased; suggesting increases of rhamnogalacturonan I and arabinogalactan IIduring the dedifferentiation, respectively, The effects of growth regulators(2,4-D, 1.0mg/L and kinetin, 0.5mg/L) and nitrogen source (potasium nitrate, 19.0mg/L and ammonium nitrate, 16.5 g/L) in the medium on the proliferation and the turnover of the cell wall polysaccharides were investigated for 30 days. In the medium with growth regulators and without nitrogen source, the proliferation rate was extremely high (16 folds). Growth regulators and nitrogen source increased the pectin content. Analysis of neutral sugar composition of pectin fraction showed that nitrogen source enhanced rhamnose level remarkably, suggesting that rhamnogalacturonan I was the one most likely synthesized. In hemicellulose fraction, growth regulators reduced arabinose level, suggesting that arabinogalactan II was degraded. And nitrogen source reduced galactose level, suggesting that xyloglucan was also degraded.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.343-343
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• 2005

• 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.

• Journal of Plant Biotechnology
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• v.37 no.1
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• pp.77-83
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• 2010

Eighteen cultivars of tomato were tested for their regeneration response. Lycopersicon esculentum cv. 2001-58 showed a very high frequency of regeneration (93%). We evaluated the effect of two compounds with known antioxidant activity (ascorbic acid and cystein). The use of ascorbic acid ($200\;-\;300\;{\mu}M/L$) has a positive effect on shoot regeneration. To develope a system for plastid transformation in tomato via homologous recombination, we constructed the tomato plastid expression vector (pKRT22-AG) harboring 2.2 kb flanking sequences cloned from intact plastid genome and gfp gene. To investigate the factors affecting the delivery system of the pKRT22-AG into chloroplast using bombardment, We assessed the optimal DNA concentration, gold particle volume and target distance. Expression of the GFP protein was observed within chloroplast on protoplast of cotyledon explant by confocal laser scanning microscopy, which indicates that the protocol developed in this study be useful for the production of plastid transgenic plants in tomato.

• Proceedings of the Botanical Society of Korea Conference
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• 1999.07a
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• pp.51-56
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• 1999

Plastids, which are organelles unique to plant cells, bear their own genome that is organized into DNA-protein complexes (nucleoids). Regulation of gene expression in the plastid has been extensively investigated because this organelle plays an important role in photosynthesis. Few attempts, however, have been made to characterize the regulation of plastid gene expression at the chromosomal structure, using plastid nucleoids. In this report, we summarize the recent progress in the characterization of DNA-binding proteins in plastids, with special emphasis on CND41, a DNA binding protein, which we recently identified in the choloroplast nucleoids from photomixotrophically cultured tobacco cells. CND41 is a protein of 502 amino acids which consisted of a transit peptide of 120 amino acids and a mature protein of 382 amino acids. The N-terminal of the 'mature' protein has lysine-rich region which is essential for DNA-binding. CNA41 also showed significant identities to some aspartyl proteases. Protease activity of purified CND41 has been recently confirmed and characterized. On the other hand, characterization of accumulation of CND41 both in wild type and transgenic tobacco with reduced amount of CND41 suggests that CND41 is a negative regulator in chloroplast gene expression. Further investigation indicated that gene expression of CND41 is cell-specifically and developmentally regulated as well as sugar-induced expression. The reduction of CND41 expression in transgenic tobacco also brought the stunted plant growth due to the reduced cell length in stem. GA3 treatment on apical meristem reversed the dwarf phenotype in the transformants. Effects of CND41 expression on GA biosynthesis will be discussed.

• Korean Journal of Plant Taxonomy
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• v.53 no.2
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• pp.157-165
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• 2023

Paraphlomis koreana (Lamiaceae) was newly named and added to Korean flora in 2014. Paraphlomis belongs to the tribe Paraphlomideae, along with Ajugoides and Matsumurella. However, a recent study has suggested that P. koreana is morphologically similar to Matsumurella chinensis, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of P. koreana within the tribe and compare its genetic relationship with M. chinensis. We sequenced an additional complete plastid genome for an individual of P. koreana and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of P. koreana. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (rpl16 intron, rpl32-trnL, rps16 intron, and trnL-F) covering 13 Paraphlomis species and M. chinensis were conducted. Phylogenetic analyses concordantly supported that P. koreana forms a monophyletic group with M. chinensis. Moreover, our study revealed that P. koreana includes nrDNA sequences of M. chinensis as minor intra-individual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of P. koreana within Paraphlomis should be reconsidered.

• Journal of Applied Biological Chemistry
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• v.44 no.1
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• pp.6-11
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• 2001

An ${\omega}-3$ fatty acid desaturase gene which is involved in de novo synthesis of -Iinolenate was isolated from cDNA library of Perilla frutescens. A cDNA library was constructed with mRNA extracted from perilla seeds of 12 DAF. The cDNA clone consisting of 1317-bp open reading frame encoding 438 amino acids with a relative MW of 50kDa, was isolated and showed 65-83% similarities to other known genes. This cDNA is deduced to encode a plastidal ${\omega}-3$ fatty acid desaturase based on the fact that it has higher homology to plastidal ones than to microsomal ones and its N-terminal sequence shares several characteristics of transit peptides of chloroplast proteins. Southern blot analysis of genomic DNA indicated that more than one gene or alleles for ${\omega}-3$ fatty acid desaturase are present in the genome of perilla. Northern blot analysis showed that the ${\omega}-3$ fatty acid desaturase gene is mainly revealed in early developing seeds and has different expression patterns depending on tissue types compared to the microsomal ones.

• BMB Reports
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• v.34 no.6
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• pp.496-501
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• 2001

Lincomycin, an inhibitor of plastid protein synthesis, was found to block the synthesis of apoprotein P700 with a molecular mass of 72 kDa and the assembly of the Chl a-protein of PS I. Synthesis of the polypeptides of 48, 43.5, and 32 kDa of the PS II complex is also suppressed. This process is accompanied by the disappearance of the PS Two reaction center Chl a at 683 nm, and of the PS One reaction center Chl a at 690, 696, and 705 nm on the fourth derivative of the absorption spectra at 77K. Lincomycin does not affect the synthesis of LHC subunits. It increases the content of the two main Chl forms of LHC at 648 nm (Chl b) and 676 nm (Chl a). The low-temperature fluorescence ratio F736/F685 is also increased. However, the effect of cycloheximide (an inhibitor of cytoplasmic protein synthesis) leads to the reduction of polypeptides of the light-harvesting Chl a/b-protein complex in the range of 29.5-22 kDa. Under these conditions, the relative amount of Chl b and the F736/ F685 fluorescence ratio decrease significantly. This is obviously the result of blocking the LHC I and LHC II synthesis. At the same time rifampicin and actinomycin D (inhibitors which block transcription in chloroplast and nuclear genome, respectively) inessentially affect the characteristics of these complexes.

• Journal of Plant Biotechnology
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• v.49 no.3
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• pp.178-186
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• 2022

The tetraploid Solanum acaule is a wild potato species from Bolivia widely used for potato breeding because of its diverse attractive traits, including resistance to frost, late blight, potato virus X, potato virus Y, potato leafroll virus, potato spindle tuber viroid, and cyst nematode. However, the introgression of useful traits into cultivated potatoes via crossing has been limited by differences in endosperm balance number between species. Somatic fusion could be used to overcome sexual reproduction barriers and the development of molecular markers is essential to select proper fusion products. The chloroplast genome of S. acaule was sequenced using next-generation sequencing technology and specific markers for S. acaule were developed by comparing the obtained sequence with those of seven other Solanum species. The total length of the chloroplast genome is 155,570 bp, and 158 genes were annotated. Structure and gene content were very similar to other Solanum species and maximum likelihood phylogenetic analysis with 12 other species belonging to the Solanaceae family revealed that S. acaule is very closely related to other Solanum species. Sequence alignment with the chloroplast genome of seven other Solanum species revealed four InDels and 79 SNPs specific to S. acaule. Based on these InDel and SNP regions, one SCAR marker and one CAPS marker were developed to discriminate S. acaule from other Solanum species. These results will aid in exploring evolutionary aspects of Solanum species and accelerating potato breeding using S. acaule.