• Journal of Korean Society of Forest Science
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• v.104 no.4
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• pp.549-557
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• 2015

Novel cpSSR primers were developed based on the sequence information of the Pinus koraiensis chloroplast genome. A total of 30 cpSSR loci were detected in the chloroplast genome, and a total of 30 primer sets flanking those loci were designed. All primer sets were successfully amplified for chloroplast DNA in P. koraiensis. The cross-species transferability of the 30 primer sets was considerably high in P. pumila (100%) and P. paviflora (97%) belonging to the same Subgenus (Strobus) of P. koraiensis. Meanwhile, the transferability was relatively low (73%) in P. densiflora and P. sylvestris belonging to Subgenus Pinus. A total of 13 cpSSR loci out of the 30 loci were polymorphic in the Mt. Jumbong population of P. koraiensis. The mean of haploid diversity(H) was 0.512. The number of haplotypes(N) and the haplotype diversity($H_e$) were 25 and 0.992, respectively. Of the 25 haplotypes, 22 were unique in the analyzed population. The unique haplotypes differentiated 22 individuals (79%) from the total of 28 individuals. In conclusion, the novel cpSSR primers developed in this study would be applicable to other Pinus species, especially the subgenus Strobus, and provide a high level of polymorphism for the study of genetic variation of P. koraiensis.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.135-144
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• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.

• 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.

• ALGAE
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• v.17 no.1
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• pp.59-68
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• 2002

A phylogenetic affinity between charophytes and embryophytes (land plants) has been explained by a few chloroplast genomic characters including gene and intron (Manhart and Palmer 1990; Baldauf et al. 1990; Lew and Manhart 1993). Here we show that a charophyte, Spirogyra maxima, has the largest operon of angiosperm chloroplast genomes, rpl23 operon (trnⅠ-rpl23-rpl2-rps19-rpl22-rps3-rpl16-rpl14-rps8-infA-rpl36-rps11-rpoA) containing both embryophyte introns, rpl16.i and rpl2.i. The rpl23 gene cluster of Spirogyra contains a distinct eubacterial promoter sequence upstream of rpl23, which is the first gene of the green algal rpl23 gene cluster. This sequence is completely absent in angiosperms but is present in non-flowering plants. The results imply that, in the rpl23 gene cluster, early charophytes had at least two promoters, one upstream of trnⅠ and and another upstream of rpl23, which partially or completely lost its function in land plants. A comparison of gene clusters of prokaryotes, algal chloroplast DNAs and land plant cpDNAs indicated a loss of numerous genes in chlorophyll a+b eukaryotes. A phylogenetic analysis using presence/absence of genes and introns as characters produced trees with a strongly supported clade containing chlorophyll a+b eukaryotes. Spirogyra and embryophytes formed a clade characterized by the loss of rpl5 and rps9 and the gain of trnⅠ (CAU) and introns in rpl2 and rpl16. The analyses support the hypothesis that the rpl23 gene cluster and the rpl2 and rpl16 introns of land plants originated from a common ancestor of Spirogyra and land plants.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.82-90
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• 2016

Most Araliaceae plant species distributed in Korea are economically important because of their high medicinal values. This study was conducted to develop barcode markers from sequence analysis of chloroplast DNA in 14 taxa of Araliaceae species grown in South Korea. Sequencing of seven chloroplast DNA regions was performed to establish the DNA barcode markers, as suggested by the Consortium for the Barcode of Life (CBOL). From the sequence analysis of chloroplast DNA, we identified specific sequences and nucleotides that allowed us to discriminate among each other 14 Korean Araliaceae species. The sequence in the region of psbA-trnH revealed the most frequent DNA indels and substitutions of all 7 regions studied. This psbA-trnH marker alone can discriminate among all 14 species. There are no differences between Korean and Chinese Panax ginseng in all seven sequenced chloroplast DNA regions. A phylogenetic tree constructed using the seven chloroplast DNA regions revealed that Tetrapanax papyriferus should be classified as an independent clade. The Aralia and Panax genera showed a close phylogenetic relationship. Five species in the Eleutherococcus genus were more closely related to Kalopanax septemlobus than to any Panax species.

• Plant Breeding and Biotechnology
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• v.5 no.4
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• pp.334-343
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• 2017

Eclipta prostrata and E. alba are annual herbal medicinal plants and have been used as Chinese medicinal tonics. Both species are widely distributed in tropical and subtropical regions as well as in Korea. Both species have similar morphological features but E. alba has smoother leaf blade margins compared with E. prostrata. Although both species are utilized as oriental medicines, E. prostrata is more widely used than E. alba. Morphological semblances have confounded identification of either species. Here, we report the complete chloroplast genomes of both species to provide an authentication system between the two species and understand their diversity. Both chloroplast genomes were 151,733-151,757 bp long and composed of a large single copy (83,285-83,300 bp), a small single copy (18,283-18,346 bp), and a pair of inverted repeats (25,075-25,063 bp). Gene annotation revealed 80 protein coding genes, 30 tRNA genes and four rRNA genes. A phylogenetic analysis revealed that the genus Eclipta is grouped with Heliantheae tribe species in the Asteraceae family. A comparative analysis verified 29 InDels and 58 SNPs between chloroplast genomes of E. prostrata and E. alba. The low chloroplast genome sequence diversity indicates that both species are really close to each other and are not completely diverged yet. We developed six DNA markers that distinguish E. prostrata and E. alba based on the polymorphisms of chloroplast genomes between E. prostrata and E. alba. The chloroplast genome sequences and the molecular markers generated in this study will be useful for further research of Eclipta species and accurate classification of medicinal herbs.

• Molecules and Cells
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• v.19 no.1
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• pp.104-113
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• 2005

Large inversions are well characterized in the chloroplast genomes of land plants. In contrast, reports of small inversions are rare and involve limited plant groups. In this study, we report the widespread occurrence of small inversions ranging from 5 to 50 bp in fully and partially sequenced chloroplast genomes of both monocots and dicots. We found that small inversions were much more common than large inversions. The small inversions were scattered over the chloroplast genome including the IR, SSC, and LSC regions. Several small inversions were uncovered in chloroplast genomes even though they shared the same overall gene order. The majority of these small inversions were located within 100 bp downstream of the 3' ends of genes. All had inverted repeat sequences, ranging from 11 to 24 bp, at their ends. Such small inversions form stem-loop hairpin structures that usually have the function of stabilizing the corresponding mRNA molecules. Intra-molecular recombination between the inverted sequences in the stem-forming regions are responsible for generating flip-flop orientations of the loops. The presence of two different orientations of the stem-loop in the trnL-F noncoding region of a single species of Jasminum elegans suggests that a short inversion can be generated within a short period of time. Small inversions of non-coding sequences may influence sequence alignment and character interpretation in phylogeny reconstructions, as shown in nine species of Jasminum. Many small inversions may have been generated by parallel or back mutation events during chloroplast genome evolution. Our data indicate that caution is needed when using chloroplast non-coding sequences for phylogenetic analysis.

• 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 Taxonomy
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• v.50 no.1
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• pp.8-16
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• 2020

Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.

• Korean Journal of Environmental Biology
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• v.38 no.1
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• pp.160-164
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• 2020

Papenfussiella densa was described as Papenfussiella kuromo f. densa from Japan by Inagaki in 1958. P. densa has been recognized as an endemic and independent species based on the molecular analyses of type material without detailed morphological observations. In this study, Papenfussiella densa is reported as a new record from Dok-do, South Korea, based on morphological and molecular analyses. Papenfussiella densa is mainly characterized as having narrow, branched, slimy, and tomentose thalli with branchlets, partially hollow in the medulla of the middle part. The molecular analyses of the chloroplast rbcL-rbcS DNA sequence of the Papenfussiella densa sample from Korea revealed that it matched that of P. densa from Japan and was nested in the clade of Papenfussiella. There was only a 0.02% gene sequence divergence between the Korean and Japanese samples. We report P. densa as a new record from Korea and add this species to the list of Korean macroalgal flora.