• Journal of Plant Biotechnology
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• v.43 no.4
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• pp.417-421
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• 2016

The complete chloroplast genome sequence of Panax ginseng breeding line 'G07006', showing higher salt tolerance, was confirmed by de novo assembly using whole genome next-generation sequences. The complete chloroplast (CP) genome size is 156,356 bp, including two inverted repeats (IRs) of 52,060 bp, separated by the large single-copy (LSC 86,174 bp) and the small single-copy (SSC 18,122 bp) regions. One hundred fourteen genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 18 sites were duplicated in the inverted repeat regions. By comparative analyses of the previously identified CP genome sequences of nine cultivars of P. ginseng and that of G07006, five useful SNPs were defined in this study. Since three of the five SNPs were cultivar-specific to Chunpoong and Sunhyang, they could be easily used for distinguishing from other ginseng accessions. However, on arranging SNPs according to their gene location, the G07006 genotype was 'GTGGA', which was distinct from other accessions. This complete chloroplast DNA sequence could be conducive to discrimination of the line G07006 (salt-tolerant) and further enhancement of the genetic improvement program for this important medicinal plant.

• Horticultural Science & Technology
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• v.30 no.6
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• pp.751-756
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• 2012

Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA sequences in the specific region of the chromosomes. As well as for the integrated physical mapping, FISH karyotype analysis has to be preceded. Karyotype of Raphanus sativus 'Wonkyo 10039' was analyzed by a dual-color FISH technique; using various repetitive DNA probes, including 5S rDNA, 45S rDNA, and centromere retrotransposon. The length of the somatic metaphase chromosome ranged from 1.35 to $2.06{\mu}m$ with a total length of $15.29{\mu}m$. The chromosome complements comprised of eight pairs of metacentrics and one pair of submetacentric. Bleached DAPI Band analysis revealed a heterochromatin region, covering 28.6% to 50.4% each chromosomes. 5S and 45S rDNA sequences were located on two and three pairs of chromosomes, respectively. The centromere retrotransposon of Brassica (CRB) is a major component in Brassica related species that has been maintained as a common centromere component. CRB signals were detected on the centromere and pericentromeric region of R. sativus 'Wonkyo 10039' and three basic Brassica species (B. rapa, B. nigra, and B. oleracea). These results will provide a valuable background for physical mapping and elucidation of the evolutionary relationship among the Brassica related species.

• Journal of Microbiology and Biotechnology
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• v.3 no.3
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• pp.146-155
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• 1993

A DNA fragment from an alkali-tolerent Bacillus sp., conferring strong promoter activity, was subcloned into the promoter probe plasmid pPL703 and the nucleotide sequence of this promoter region was determined. The sequence analysis suggested that this highly efficient promoter region containing the complex clustered promoters comprised three kinds of promoters (P1, P2 and P3), which are transcribed by $\sigma^B (formerly \sigma^{37}), \sigma^E(formerly \sigma^{29}) and \sigma^A (formerly \sigma^{43})$ RNA polymerase holoenzymes which play major rules at the onset of endospore formation, during sporulation and at the vegetative phase of growth, respectively. S1 nuclease mapping experiments showed that all three promoters had staggered transcription initiation points. The results of chloramphenicol acetyltransferase assay after the subcloning experiments also indicated that the expression of these clustered promoters was correlated with the programs of growth and endospore development. Promoter P1, P2 and P3 were preceded by 75% AT, 79% AT and 81% AT regions, respectively, and a partial deletion of AT-rich region prevented transcription from promoter P1 in vivo. Two sets of 5 -AGTGTT-3 sequences and inverted repeat sequences located around the promoter P1 were speculated as the possible cis acting sites for the catabolite repression in B. subtilis. In vivo transcripts from these sequence regions may be able to form a secondary structure, however, the possibility that a regulatory protein induced by the excess amount of glucose could be bound to such a domain for crucial action remains to be determined.

• Fisheries and Aquatic Sciences
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• v.6 no.4
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• pp.180-186
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• 2003

The full-length cDNA encoding the pre-protein growth hormone (sfGH) from spotted flounder (Verasper variegatus) was amplified by the rapid amplification of cDNA ends (RACE) using degenerated oligonucleotide primers derived from conserved growth hormone sequences. It consists of 901 nucleotides in length, including the coding region of 609 nucleotides, 111 nucleotides of a 5' untranslated region, and 181 nucleotides of a 3' untranslated region. The conserved polyadenylation signal (AATAAA) lies 12 bases upstream from the poly (A) tail. The deduced amino acid sequence shows an open reading frame encoding a pre-protein of 203 amino acids and a putative signal peptide of 17 amino acids, suggesting that the mature hormone consists of 186 amino acids. The analyses of sfGH reveal some unique structural features. The repetitive sequences are located in the 5' untranslated region of sfGH cDNA and consist of tandem arrays of imperfect direct repeat monomers. Moreover, sfGH contains six Cys residues, as opposed to four or five in other GHs, and it is clearly distinguishable from olive flounder (Paralichthys olivaceus) GH, which lacks a region corresponding to residues 175-188 in alignment positions. It has important implications from an evolutionary standpoint, suggesting possible divergence among flatfishes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.57-57
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• 2017

Chrysanthemum is one of the most important floral crop in Korea produced about 7 billion dollars (1 billion for pot and 6 billion for cutting) in 2013. However, it is difficult to breed and to do genetic study because 1) it is highly self-incompatible, 2) it is outcrossing crop having heterozygotes, and 3) commercial cultvars are hexaploid (2n = 6x = 54). Although low-density genetic map and QTL study were reported, it is not enough to apply for the marker assisted selection and other genetic studies. Therefore, we are trying to make high-density genetic mapping using GBS with about 100 $F_1s$ of C. boreale that is oHohhfd diploid (2n = 2x = 18, about 2.8Gb) instead of commercial culitvars. Since Chrysanthemum is outcrossing, two-way pseudo-testcross model would be used to construct genetic map. Also, genotype-by-sequencing (GBS) would be utilized to generate sufficient number of markers and to maximize genomic representation in a cost effective manner. Those completed sequences would be analyzed with TASSEL-GBS pipeline. In order to reduce sequence error, only first 64 sequences, which have almost zero percent error, would be incorporated in the pipeline for the analysis. In addition, to reduce errors that is common in heterozygotes crops caused by low coverage, two rare cutters (NsiI and MseI) were used to increase sequence depth. Maskov algorithm would also used to deal with missing data. Further, sparsely placed markers on the physical map would be used as anchors to overcome problems caused by low coverage. For this purpose, were generated from transcriptome of Chrysanthemum using MISA program. Among those, 10 simple sequence repeat (SSR) markers, which are evenly distributed along each chromosome and polymorphic between two parents, would be selected.

• Molecules and Cells
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• v.22 no.3
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• pp.300-307
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• 2006

Brassica rapa ssp. pekinensis (Chinese cabbage) is an economically important crop and a model plant for studies on polyploidization and phenotypic evolution. To gain an insight into the structure of the B. rapa genome we analyzed 12,017 BAC-end sequences for the presence of transposable elements (TEs), SSRs, centromeric satellite repeats and genes, and similarity to the closely related genome of Arabidopsis thaliana. TEs were estimated to occupy 14% of the genome, with 12.3% of the genome represented by retrotransposons. It was estimated that the B. rapa genome contains 43,000 genes, 1.6 times greater than the genome of A. thaliana. A number of centromeric satellite sequences, representing variations of a 176-bp consensus sequence, were identified. This sequence has undergone rapid evolution within the B. rapa genome and has diverged among the related species of Brassicaceae. A study of SSRs demonstrated a non-random distribution with a greater abundance within predicted intergenic regions. Our results provide an initial characterization of the genome of B. rapa and provide the basis for detailed analysis through whole-genome sequencing.

• Korean Journal of Breeding Science
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• v.41 no.3
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• pp.194-204
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• 2009

Cytoplasmic male sterility (CMS) and fertility restoration have been utilized as valuable tools for $F_1$-hybrid seed production in many crops despite laborious breeding processes. Molecular markers for the selection of CMS-related genes help reduce the expenses and breeding times. A previously reported genomic region containing the Ppr-B gene, which is responsible for restoration of fertility and corresponds to the Rfo locus, was used to develop gene-based or so-called "functional" markers for allelic selection of the restorer-of-fertility gene (Rfo) in $F_1$-hybrid breeding of radish (Raphanus sativus L.) Polymorphic sequences among Rfo alleles of diverse breeding lines of radish were examined by sequencing the Ppr-B alleles. However, presence of Ppr-B homolog, designated as Ppr-D, interferes on specific PCR amplification of Ppr-B in certain breeding lines. The organization of Ppr-D, resolved by genome walking, revealed extended homology with Ppr-B even in the promoter region. Interestingly, PCR amplification of Ppr-D was repeatedly unsuccessful in certain breeding lines implying the lack of Ppr-D in these radishes. Ppr-B could only be successfully amplified for analysis through designing primers based on the sequences unique to Ppr-B that exclude interference from Ppr-D gene. Four variants of Rfo alleles were identified from 20 breeding lines. A combination of three molecular markers was developed in order to genotype the Rfo locus based on polymorphisms among four different variants. These markers will be useful in facilitating $F_1$-hybrid cultivar development in radish.

• Genomics & Informatics
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• v.19 no.3
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• pp.33.1-33.10
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• 2021

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

• International Journal of Industrial Entomology and Biomaterials
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• v.46 no.2
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• pp.41-54
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• 2023

The blue-tailed damselfly, Ischnura elegans Van der Linden, 1820 (Odonata: Coenagrionidae), is a climate-sensitive indicator species in South Korea. In this study, we sequenced the complete mitochondrial genome (mitogenome) of I. elegans collected from South Korea for subsequent population genetic analysis, particularly to trace population movements in response to climate change. The 15,963 base pair (bp)-long complete mitogenome of I. elegans has typical sets of genes including a major non-coding region (the A+T-rich region), and an arrangement identical to that observed in ancestral insect species. The ATP6, ND3 and ND1 genes have the TTG start codon, which, although rare, is the canonical start codon for animal mitochondrial tRNA. The A/T content was 71.4% in protein-coding genes, 72.1% in tRNAs, 72.9% in the whole genome, 74.7% in srRNA, 75.3% in lrRNA, and 83.8% in the A+T-rich region. The A+T-rich region is unusually long (1,196 bp) and contains two subunits (192 bp and 176-165 bp), each of which is tandemly triplicated and surrounded by non-repeat sequences. Comparison of the sequence divergence among available mitogenomes of I. elegans, including the one from the current study, revealed ND2 as the most variable gene, followed by COII and COI, suggesting that ND2 should be targeted first in subsequent population-level studies. Phylogenetic reconstruction based on all available mitogenome sequences of Coenagrionidae showed a strong sister relationship between I. elegans and I. senegalensis.

• Journal of Microbiology
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• v.35 no.4
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• pp.264-270
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• 1997

The structure of plasmid mlp1, a linear 10.2kb mitochondrial plasmid of Pleurotus ostreatus NFF A2 was determined by restriction enzyme mapping and partial sequencing. The plasmid encodes at least two proteins; a putative RNA polymerase showing homology to yeast mitochondrial RNA polymerase and to viral-encoded RNA polymerases, and a putative DNA polymerase showing significant homology to the family B thpe DNA polymerases. It also contains terminal inverted repeat sequences at both ends which are longer than 274 bp. A 1.6 kb EcoRI restriction fragment of m1p1 containing the putative RNA polymerase gene did not hybridize to the nuclear or motochondrial genomes from P. ostreatus, suggesting that it may encode plasmidspecific RNA polymerase. The gene fragment also did not hybridize with the RNA polymerase gene (RPO41) from Saccaromyces cerevisiae. The relationship between genes in m1p1 and those in another linear plasmid pC1K1 of Claviceps purpurea was examined by DNA hybridization. The result indicates that the genes for DNA and RNA polymerases are not closely related with those in C. purpurea.