• Genomics & Informatics
• /
• v.20 no.4
• /
• pp.43.1-43.18
• /
• 2022

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformatic methodologies were used to examine the pattern of coding sequences and the factors that might influence codon usage bias in the chloroplast genome of Atropa belladonna and other nightshade genomes. The chloroplast engineering being a promising field in modern biotechnology, the characterization of chloroplast genome is very important. The results revealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanum tuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, we observed a weak codon usage bias. According to the correspondence analysis, the genesis of the codon use bias in these chloroplast genes might be explained by natural selection, directed mutational pressure, and other factors. GC12 and GC3S were shown to have no meaningful relationship. Further research revealed that natural selection primarily shaped the codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful for future research on medicinal plants.

• Journal of Plant Biotechnology
• /
• v.2 no.2
• /
• pp.101-108
• /
• 2000

The liverwort Pellia borealis is a diploid, monoecious, allopolypliod species (n=18) that as it was postulated, originated after hybridization and duplication of chromosome sets of two cryptic species: Pellia epiphylta-species N (n=9) and Pellia epiphylla-species 5 (n=9). Our recent results have supported the allopolyploid origin of P.borealis. We have shown that the nuclear genome of P.borealis consists of two nuclear genomes: one derived from P.epiphylla-species N and the other from P.epiphylla-species 5. In this paper we show the origin of chloroplast and mitochondrial genomes in an allopolyploid species P.borealis. To our knowledge there is no information concerning the way of mitochondria and chloroplast inheritance in Brophyta. Using an allopolyploid species of p. borealis as a model species we have decided to look into chloroplast and mitochondrial genomes of P.borealis, P.epiphylla-species N and P.epiphylla-species S for nucleotide sequences that would allow us to differentiate between both cryptic species and to identify the origin of organelle genomes in the alloploid species. We have amplified and sequenced a chloroplast $tRNA^{Leu}$ gene (anticodon UAA) containing an intron that has shown to be highly variable in a nucleotide sequence and used for plant population genetics. Unfortunately these sequences were identical in all three liverwort species tested. The analysis of the nucleotide sequence of chloroplast, an intron containing $tRNA^{Gly}$ (anticodon UCC) genes, gave expected results: the intron nucleotide sequence was identical in the case of both P.borealis and P.epiphyllaspecies N, while the sequence obtained from P.epiphyllasperies S was different in several nucleotide positions. These results were confirmed by the nucleotide sequence of another chloroplast molecular marker the chloroplast, an intron-contaning $tRNA^{Lys}$ gene (anticodon UUU). We have also sequenced mitochondrial, an intron-containing $tRNA^{Ser}$ gene (anticodon GCU) in all three liverwort species. In this case we found that, as in the case of the chloroplast genome, P.borealis mitochondrial genome was inherited from P.epiphylla-species N. On the basis of our results we claim that both organelle genomes of P.borealis derived from P.epiphylla-species N.

• Korean Journal of Plant Taxonomy
• /
• v.51 no.4
• /
• pp.353-362
• /
• 2021

The chloroplast genome of Glycyrrhiza uralensis Fisch was sequenced to investigate intraspecific variations on the chloroplast genome. Its length is 127,689 bp long (34.3% GC ratio) with atypical structure of chloroplast genome, which is congruent to those of Glycyrrhiza genus. It includes 110 genes (76 protein-coding genes, four rRNAs, and 30 tRNAs). Intronic region of ndhA presented the highest nucleotide diversity based on the six G. uralenesis chloroplast genomes. A total of 150 single nucleotide polymorphisms and 10 insertion and deletion (INDEL) regions were identified from the six G. uralensis chloroplast genomes. Phylogenetic trees show that the six chloroplast genomes of G. uralensis formed the two clades, requiring additional studies to understand it.

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

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

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

• Korean Journal of Plant Taxonomy
• /
• v.50 no.1
• /
• pp.8-16
• /
• 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 Plant Resources
• /
• v.32 no.6
• /
• pp.644-668
• /
• 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.

• Korean Journal of Plant Taxonomy
• /
• v.51 no.3
• /
• pp.326-331
• /
• 2021

The complete chloroplast genome of Zoysia macrostachya Franch. & Sav. isolated in Korea is 135,902 bp long (GC ratio is 38.4%) and has four subregions; 81,546 bp of large single-copy (36.3%) and 12,586 bp of small single-copy (32.7%) regions are separated by 20,885 bp of inverted repeat (44.1%) regions, including 130 genes (83 protein-coding genes, eight rRNAs, and 39 tRNAs). Thirty-nine single nucleotide polymorphisms and 11 insertions and deletion (INDEL) regions were identified from two Z. macrostachya chloroplast genomes, the smallest among other Zoysia species. Phylogenetic trees show that two Z. macrostachya chloroplast genomes are clustered into a single clade. However, we found some incongruency with regard to the phylogenetic position of the Z. macrostachya clade. Our chloroplast genome provides insights into intraspecific variations and species delimitation issues pertaining to the Zoysia species.

• Korean Journal of Plant Taxonomy
• /
• v.51 no.4
• /
• pp.345-352
• /
• 2021

Diarthron linifolium Turcz. is an annual herb usually found in sandy soil or limestone areas. Plants in the genus Diarthron are known to have toxic chemicals that may, however, be potentially useful as an anticancer treatment. Diarthron linifolium is a unique species among the species of the genus distributed in Korea. Here, we determine the genetic variation of D. linifolium collected in Korea with a full chloroplast genome and investigate its evolutionary status by means of a phylogenetic analysis. The chloroplast genome of Korean D. linifolium has a total length of 172,644 bp with four subregions; 86,158 bp of large single copy and 2,858 bp of small single copy (SSC) regions are separated by 41,814 bp of inverted repeat (IR) regions. We found that the SSC region of D. linifolium is considerably short but that IRs are relatively long in comparison with other chloroplast genomes. Various simple sequence repeats were identified, and our nucleotide diversity analysis suggested potential marker regions near ndhF. The phylogenetic analysis indicated that D. linifolium from Korea is a sister to the group of Daphne species.