• 식물분류학회지
• /
• 제51권3호
• /
• pp.332-336
• /
• 2021

The complete chloroplast (cp) genome sequence of Neolitsea sericea was determined by Illumina sequencing. The complete cp genome was 152,446bp in length, containing a large single-copy region of 93,796 bp and a small single-copy region of 18,506bp, which were separated by a pair of 20,072bp inverted repeats. A total of 112 unique genes were annotated, including 78 protein-coding genes (PCGs), 30 transfer RNAs, and four ribosomal RNAs. Among the PCGs, 18 genes contained one or two introns. A very low level of sequence variation between two cp genomes of N. sericea was found with seven insertions or deletions and only one single nucleotide polymorphism. An analysis using the maximum likelihood method showed that N. sericea was closely related to Actinodaphne trichocarpa.

• 대한본초학회지
• /
• 제26권3호
• /
• pp.15-21
• /
• 2011

Objectives : The application of polymerase chain reaction (PCR) for the discrimination of the herbal medicine Leonuri Herba (Leonurus japonicus) was evaluated by the comparison of the DNA sequence with Lamiaceae herbal medicine. Method : Genetic analysis showed that phylogenetic tree and comparing sequences through the DNA analysis of rbcL (ribulose-1, 5-bisphosphatecarboxylase) region and trnL-F (tRNA-Leu, trnL-trnF intergeni cspacer, and tRNA-Phe) region of chloroplast DNA from six Lamiaceae sold in market. And we developed IMCF and IMCR primers in order to distinction Leonuri Herba in six Lamiaceae using rbcL and trnL-F sequences. Results : Genetic analysis showed that six Lamiaceae showed individual group on phylogenetic tree. PCR amplification product of Leonuri Herba and another five Lamiaceae were developed for amplification of a 281 bp sequence and the specific PCR amplification of a 460 bp sequence that was exclusive to Leonuri Herba was designed using IMCF and IMCR primers. Conclusion : PCR analysis based on the chloroplast DNA sequences allows the discrimination of Leonuri Herba-based medicine.

• Plant Breeding and Biotechnology
• /
• 제5권3호
• /
• pp.243-251
• /
• 2017

Rhus chinensis is a shrub widely distributed in Asia. It has been used for traditional medicine and ecological restoration. Here, we report the complete chloroplast genome sequence of two R. chinensis genotypes collected from China and Korea. The assembled chloroplast genome of Chinese R. chinensis is 149,094 bp long, consisting of a large single copy (97,246 bp), a small single copy (18,644 bp) and a pair of inverted repeats (16,602 bp). Gene annotation revealed 77 protein coding genes, 30 tRNA genes, and 4 rRNA genes. A phylogenomic analysis of the chloroplast genomes with 11 known complete chloroplast genomes clarified the relationship of R. chinensis with the other plant species in the Sapindales order. A comparative chloroplast genome analysis identified 170 SNPs and 85 InDels at intra-species level of R. chinensis between Chinese and Korean collections. Based on the sequence diversity between Korea and Chinese R. chinensis plants, we developed three DNA markers useful for genetic diversity and authentication system. The chloroplast genome information obtained in this study will contribute to enriching genetic resources and conservation of endemic Rhus species.

• 식물분류학회지
• /
• 제51권4호
• /
• 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.

• 대한본초학회지
• /
• 제34권6호
• /
• pp.91-97
• /
• 2019

Objective : To establish a reliable tool between for the distinction of original plants of Sanguisorbae Radix, we analyzed the complete chloroplast genome sequence of Sanguisorbae Radix and identified single nucleotide polymorphisms (SNPs). Materials and methods : The chloroplast genome sequence of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link obtained using next-generation sequencing technology were described and compared with those of other species to develop specific markers. Candidate genetic markers were identified to distinguish species from the chloroplast sequences of each species using Modified Phred Phrap Consed and CLC Genomics Workbench programs. Results : The structure of the chloroplast genome of each sample that had been assembled and verified was circular, and the length was about 155 kbp. Through comparative analysis of the chloroplast sequences, we found 220 nucleotides, 158 SNPs, and 62 Indel (insertion and/or deletion), to distinguish Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link. Finally, 15 specific SNP genetic markers were selected for the verification at positions. Avaliable primers for the dried herb, which is used as medicine, were used to develop the PCR amplification product of Sanguisorbae Radix to assess the applicability of PCR analysis. Conclusion : In this study, we found that Fendel-qPCR analysis based on the chloroplast DNA sequences can be an efficient tool for discrimination of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link.

• Applied Biological Chemistry
• /
• 제36권3호
• /
• pp.208-214
• /
• 1993

엽록체 DNA 내에서 반복 염기서열의 존재와 이들에 의한 유전자 재배열 현상을 고찰하기 위하여 151bp Repeated Sequence 갖는 이질적인 유전인자군의 존재를 여러가지 품종의 벼 엽록체 DNA에서 관찰 하였다. 또한 쌀 DNA를 벼의 생장과 조직부위에 따라 분리하고, rp12 probe를 이용하여 Southern blot 분석하여 엽록체의 발달에 따르는 엽록체 DNA의 재배열 현상을 관찰하였다. 아울러 유전자 재배열 현상을 유발하는 반복염기서열을 database로부터 검색하여 유전자의 상호 비교 분석하였다. 그 결과 151bp Repeated Sequence와 유사한 염기 서열을 같는 rp123유전자를 포함하는 이질적인 유전인자군은 어느 특정한 품종의 벼에 국한되는것이 아니고 본 실험에 사용된 다양한 품종의 벼에 일반적으로 나타나는 현상임이 확인되었으며 또한 이들의 양상은 벼의 조직 부위에 따라 다르게 나타나고 있음을 확인하였다. 이러한 실험적 결과와 함께 엽록체 유전자 database의 검색과 유전자의 상호비교분석을 통하여 151bp 반복 염기 저열에 의한 벼 엽록체 DNA의 유전자 재배열현상은 식물 특히 단자엽 식물의 진화와 함께 발달된 현상으로 특히 151bp반복 염기 서열은 매우 다양한 유전자 재배열을 유발하는 변이유발 위치로 발달되어 왔음을 확인할 수 있었다. 따라서 이러한 반복염기서열에 의한 유전자 재배열 현상은 특히 벼에 있어서 plastid의 발달에 밀접하게 관여하고 있음을 제시하고 있다.

• 식물분류학회지
• /
• 제52권4호
• /
• pp.269-274
• /
• 2022

Dracocephalum rupestre Hance is a perennial herb distributed across China, Mongolia, and Korea. This study reports the first complete chloroplast genome sequence of D. rupestre. The plastome is 151,230 bp long and exhibits a typical quadripartite structure comprising a large single-copy region of 82,536 bp, a small single-copy region of 17,408 bp, and a pair of identical inverted repeat regions of 25,643 bp each. It contains 130 genes, comprising 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of D. rupestre and related species of Lamiaceae showed that the genus Dracocephalum is a monophyletic group, and D. rupestre is most closely related to D. psammophilum.

• 식물분류학회지
• /
• 제52권4호
• /
• pp.262-268
• /
• 2022

The complete chloroplast genome (cp genome) sequence of Clematis calcicola J. S. Kim (Ranunculaceae) is 159,655 bp in length. It consists of large (79,451 bp) and small (18,126 bp) single-copy regions and a pair of identical inverted repeats (31,039 bp). The genome contains 92 protein-coding genes, 36 transfer RNA genes, eight ribosomal RNA genes, and two pseudogenes. A phylogenetic analysis based on the cp genome of 19 taxa showed high similarity between our cp genome and data published for C. calcicola, which is recognized as a species endemic to the Korean Peninsula. The complete cp genome sequence of C. calcicola reported here provides important information for future phylogenetic and evolutionary studies of Ranunculaceae.

• 식물분류학회지
• /
• 제51권1호
• /
• pp.109-114
• /
• 2021

Veronica nakaiana Ohwi (Plantaginaceae) is an endemic taxon on Ulleungdo Island, Korea. We report the second complete chloroplast genome sequence of V. nakaiana. Its genome size is 152,319 bp in length, comprising a large single-copy of 83,195 bp, a small single-copy of 17,702 bp, and a pair of inverted repeat regions of 25,711 bp. The complete genome contains 115 genes, including 51 protein-coding genes, four rRNA genes, and 31 tRNA genes. When comparing the two chloroplast genomes of V. nakaiana, 11 variable sites are recognized: seven SNPs and four indels. Two substitutions in the coding regions are recognized: rpoC2 (synonymous substitution) and rpl22 (nonsynonymous substitution). In nine noncoding regions, one is in the tRNA gene (trnK-UUU), one is in the intron of atpF, and seven are in the intergenic spacers (trnH-GUG~psbA, trnK-UUU, rps16~trnQ-UUG, trnC-GCA~petN, psbZ~trnG-GCC, ycf3~trnS-GGA, ycf4~cemA, and psbB~psbT). The data provide the level of genetic variation in V. nakaiana. This result will be a useful resource to formulate conservation strategies for V. nakaiana, which is a rare endemic species in Korea.

• 식물분류학회지
• /
• 제53권3호
• /
• pp.237-241
• /
• 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.