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Zhang E, Liu Y, Wang Y, Zhang X, Wei Y, Zhang L. Characterization of the complete chloroplast genome of Cynanchum acutum subsp. s ibiricum (Apocynaceae). Mitochondrial DNA B Resour 2023; 8:993-997. [PMID: 37746032 PMCID: PMC10512800 DOI: 10.1080/23802359.2023.2256496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
In this study, we assembled the complete chloroplast (cp) genome of Cynanchum acutum subsp. sibiricum using high-throughput Illumina sequencing reads. The resulting chloroplast genome assembly displayed a typical quadripartite structure with a total length of 158,283 bp, which contained a pair of inverted repeat regions (IRs) of 24,459 bp. These two IRs were separated by a large single-copy region (LSC) and a small single-copy region (SSC) of 89,424 bp and 19,941 bp in length, respectively. The C. acutum subsp. sibiricum cp genome contained 130 genes, and its overall GC content was 37.87%. Phylogenetic analysis among C. acutum subsp. sibiricum and nine other Cynanchum species demonstrated that C. acutum subsp. sibiricum was closely related to C. chinense. The C. acutum subsp. sibiricum cp genome presented in this study lays a good foundation for further genetic and genomic studies of the Cynanchum as well as Apocynaceae.
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Affiliation(s)
- Erdong Zhang
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, School of Biological Science & Engineering, North Minzu University, Yinchuan, Ningxia, P. R. China
| | - Yi Liu
- Operation Management Department, Yinchuan Hedong International Airport, Yinchuan, Ningxia, P. R. China
| | - Yan Wang
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, School of Biological Science & Engineering, North Minzu University, Yinchuan, Ningxia, P. R. China
| | - Xuedan Zhang
- Operation Management Department, Yinchuan Hedong International Airport, Yinchuan, Ningxia, P. R. China
| | - Yuqing Wei
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, School of Biological Science & Engineering, North Minzu University, Yinchuan, Ningxia, P. R. China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People’s Republic of China, School of Biological Science & Engineering, North Minzu University, Yinchuan, Ningxia, P. R. China
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Lee SH, Jang W, Kim E, Kim J, Gong H, Kang JS, Shim H, Park JY, Yang TJ. The complete plastome of Cynanchum rostellatum (Apocynaceae), an indigenous plant in Korea. Mitochondrial DNA B Resour 2022; 7:2035-2039. [PMCID: PMC9744207 DOI: 10.1080/23802359.2022.2148489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The climbing plant Cynanchum rostellatum (Turcz.) Liede & Khanum is widely distributed throughout Korea and Northeast Asia as a member of the Apocynaceae family. Although this plant has a high value in medicinal and industrial purposes, genetic research on this plant is insufficient. This study announces the complete plastid genome (plastome) sequence of C. rostellatum with 663× mean coverage, which was assembled using 763 Mbp short-read data generated by the Illumina HiSeq X platform. The C. rostellatum plastome was 158,018 bp in length and displayed the typical quadripartite structure composed of the large single-copy (LSC) region (89,058 bp), the small single-copy (SSC) region (18,718 bp), and a pair of inverted repeat (IR) regions (25,116 bp). A total of 129 genes have been annotated, including 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis indicated the genus Cynanchum including 12 Cynanchum plastome sequences, was monophyletic and was located within the sub-family Asclepiadoideae. Two C. rostellatum plastomes, including the plastome assembled in this study, formed a subclade and were sister to the C. thesioides plastome, whereas the other C. rostellatum, which was previously reported one, was located within the clade of C. wilfordii and C. bungei.
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Affiliation(s)
- Sae Hyun Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Woojong Jang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea,National Institute of Horticultural and Herbal Science, RDA, Eumseong, Republic of Korea
| | - Eunbi Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jiseok Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Haiguang Gong
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea,Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea,CONTACT Tae-Jin Yang Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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Bailly C, Xiang C, Zhang JH. Traditional uses and phytochemical constituents of Cynanchum otophyllum C. K. Schneid (Qingyangshen). WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.353189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Wang L, Cai F, Zhao W, Tian J, Kong D, Sun X, Liu Q, Chen Y, An Y, Wang F, Liu X, Wu Y, Zhou H. Cynanchum auriculatum Royle ex Wight., Cynanchum bungei Decne. and Cynanchum wilfordii (Maxim.) Hemsl.: Current Research and Prospects. Molecules 2021; 26:7065. [PMID: 34885647 PMCID: PMC8658831 DOI: 10.3390/molecules26237065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 01/12/2023] Open
Abstract
Cynanchum auriculatum Royle ex Wight. (CA), Cynanchum bungei Decne. (CB) and Cynanchum wilfordii (Maxim.) Hemsl. (CW) are three close species belonging to the Asclepiadaceous family, and their dry roots as the bioactive part have been revealed to exhibit anti-tumor, neuroprotection, organ protection, reducing liver lipid and blood lipid, immunomodulatory, anti-inflammatory, and other activities. Until 2021, phytochemistry investigations have uncovered 232 compounds isolated from three species, which could be classified into C21-steroids, acetophenones, terpenoids, and alkaloids. In this review, the morphology characteristics, species identification, and the relationship of botany, extraction, and the separation of chemical constituents, along with the molecular mechanism and pharmacokinetics of bioactive constituents of three species, are summarized for the first time, and their phytochemistry, pharmacology, and clinical safety are also updated. Moreover, the direction and limitation of current research on three species is also discussed.
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Affiliation(s)
- Lu Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Fujie Cai
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Wei Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Jinli Tian
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Degang Kong
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Xiaohui Sun
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Qing Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Yueru Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Ying An
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Fulin Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Xue Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
| | - Yi Wu
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
| | - Honglei Zhou
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (L.W.); (F.C.); (W.Z.); (J.T.); (D.K.); (X.S.); (Q.L.); (Y.C.); (Y.A.); (F.W.); (X.L.)
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Park HS, Lee WK, Lee SC, Lee HO, Joh HJ, Park JY, Kim S, Song K, Yang TJ. Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F 1 hybrid combinations. Sci Rep 2021; 11:2506. [PMID: 33510273 PMCID: PMC7843999 DOI: 10.1038/s41598-021-81988-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 01/13/2021] [Indexed: 11/19/2022] Open
Abstract
Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.
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Affiliation(s)
- Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Won Kyung Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sang-Choon Lee
- Phyzen Genomics Institute, Seongnam, Gyeonggi-do, 13558, Republic of Korea
| | - Hyun Oh Lee
- Phyzen Genomics Institute, Seongnam, Gyeonggi-do, 13558, Republic of Korea
| | - Ho Jun Joh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Kihwan Song
- Department of Bioresources Engineering, College of Life Sciences, Sejong University, Seoul, 05006, Republic of Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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6
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Park HS, Jayakodi M, Lee SH, Jeon JH, Lee HO, Park JY, Moon BC, Kim CK, Wing RA, Newmaster SG, Kim JY, Yang TJ. Mitochondrial plastid DNA can cause DNA barcoding paradox in plants. Sci Rep 2020; 10:6112. [PMID: 32273595 PMCID: PMC7145815 DOI: 10.1038/s41598-020-63233-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 03/24/2020] [Indexed: 01/18/2023] Open
Abstract
The transfer of ancestral plastid genomes into mitochondrial genomes to generate mitochondrial plastid DNA (MTPT) is known to occur in plants, but its impacts on mitochondrial genome complexity and the potential for causing a false-positive DNA barcoding paradox have been underestimated. Here, we assembled the organelle genomes of Cynanchum wilfordii and C. auriculatum, which are indigenous medicinal herbs in Korea and China, respectively. In both species, it is estimated that 35% of the ancestral plastid genomes were transferred to mitochondrial genomes over the past 10 million years and remain conserved in these genomes. Some plastid barcoding markers co-amplified the conserved MTPTs and caused a barcoding paradox, resulting in mis-authentication of botanical ingredients and/or taxonomic mis-positioning. We identified dynamic and lineage-specific MTPTs that have contributed to mitochondrial genome complexity and might cause a putative barcoding paradox across 81 plant species. We suggest that a DNA barcoding guidelines should be developed involving the use of multiple markers to help regulate economically motivated adulteration.
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Affiliation(s)
- Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sae Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Hyeon Jeon
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Oh Lee
- Phyzen Genomics Institute, Seongnam, 13558, Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byeong Cheol Moon
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Ji Yeon Kim
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul, 01811, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Zhang M, Hong LZ, Gu MF, Wu CD, Zhang G. Transcriptome analyses revealed molecular responses of Cynanchum auriculatum leaves to saline stress. Sci Rep 2020; 10:449. [PMID: 31949203 PMCID: PMC6965089 DOI: 10.1038/s41598-019-57219-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/24/2019] [Indexed: 11/25/2022] Open
Abstract
Cynanchum auriculatum is a traditional herbal medicine in China and can grow in saline soils. However, little is known in relation to the underlying molecular mechanisms. In the present study, C. auriculatum seedlings were exposed to 3.75‰ and 7.5‰ salinity. Next, transcriptome profiles of leaves were compared. Transcriptome sequencing showed 35,593 and 58,046 differentially expressed genes (DEGs) in treatments with 3.75‰ and 7.5‰, compared with the control, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these DEGs enriched various defense-related biological pathways, including ROS scavenging, ion transportation, lipid metabolism and plant hormone signaling. Further analyses suggested that C. auriculatum up-regulated Na+/H+ exchanger and V-type proton ATPase to avoid accumulation of Na+. The flavonoid and phenylpropanoids biosynthesis pathways were activated, which might increase antioxidant capacity in response to saline stress. The auxin and ethylene signaling pathways were upregulated in response to saline treatments, both of which are important plant hormones. Overall, these results raised new insights to further investigate molecular mechanisms underlying resistance of C. auriculatum to saline stress.
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Affiliation(s)
- Ming Zhang
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Province, 224045, P.R. China
| | - Li-Zhou Hong
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Province, 224045, P.R. China
| | - Min-Feng Gu
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Province, 224045, P.R. China
| | - Cheng-Dong Wu
- Xinyang Agricultural Experiment Station of Yancheng City, Jiangsu Province, 224045, P.R. China.
| | - Gen Zhang
- Shenzhen GenProMetab Biotechnology Company Limited., Shenzhen, Guangdong Province, 51800, P.R. China.
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Kim Y, Choi H, Shin J, Jo A, Lee KE, Cho SS, Hwang YP, Choi C. Molecular Discrimination of Cynanchum wilfordii and Cynanchum auriculatum by InDel Markers of Chloroplast DNA. Molecules 2018; 23:molecules23061337. [PMID: 29865213 PMCID: PMC6100574 DOI: 10.3390/molecules23061337] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 05/25/2018] [Accepted: 05/30/2018] [Indexed: 11/16/2022] Open
Abstract
The tuber of Cynanchum wilfordii (Baekshuoh Radix in Korean) is an important medicinal herb in Korea and China; however, it is difficult to differentiate C. wilfordii from a related medicinal herb, C. auriculatum (Baishouwu Radix in Chinese). We sought to develop a molecular method that could be used to distinguish between the tubers of C. wilfordii and C. auriculatum. We aligned the chloroplast genome sequences (available in the NCBI database) of the two species and identified three species-specific insertion and deletion (InDel) sites in the trnQ-psbK, rps2-rpoC2, and psaJ-rpl33 intergenic spacer (IGS) regions. To confirm the presence of these three InDels and validate their use as markers, we designed three primer pairs to amplify the trnQ-psbK, rps2-rpoC2, and psaJ-rpl33 IGS regions. Polymerase chain reaction (PCR) amplification of the trnQ-psbK IGS region yielded a 249 bp fragment for C. wilfordii, and 419 bp fragment for C. auriculatum, whereas the rps2-rpoC2 IGS primers produced a 629 bp fragment from C. wilfordii and a 282 bp fragment from C. auriculatum. In the psaJ-rpl33 IGS region, allele fragments of 342 and 360 bp in length were amplified from C. wilfordii, whereas 249 and 250 bp fragment were amplified from C. auriculatum. We propose these three InDel markers as a valuable, simple, and efficient tool for identifying these medicinal herbs and will thus reduce adulteration of these herbal materials in commercial markets.
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Affiliation(s)
- Yonguk Kim
- Jeonnam Institute of Natural Resources Research, Jangheung-gun, Jeollanam-do 59338, Korea.
| | - Hakjoon Choi
- Jeonnam Institute of Natural Resources Research, Jangheung-gun, Jeollanam-do 59338, Korea.
| | - Jawon Shin
- Jeonnam Institute of Natural Resources Research, Jangheung-gun, Jeollanam-do 59338, Korea.
| | - Ara Jo
- Jeonnam Institute of Natural Resources Research, Jangheung-gun, Jeollanam-do 59338, Korea.
| | - Kyung-Eun Lee
- Jeonnam Institute of Natural Resources Research, Jangheung-gun, Jeollanam-do 59338, Korea.
| | - Seung-Sik Cho
- Department of Pharmacy, College of Pharmacy, Mokpo National University, Muan-gun, Jeollanam-do 58554, Korea.
| | - Yong-Pil Hwang
- Department of Pharmaceutical Engineering, International University of Korea, Jinju-si, Gyeongsangnam-do 52833, Korea.
| | - Chulyung Choi
- Jeonnam Institute of Natural Resources Research, Jangheung-gun, Jeollanam-do 59338, Korea.
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Kang SH, Oh JH, Kim HJ, Kim CK. The multipartite mitochondrial genome of Cynanchum wilfordii (Gentianales: Apocynaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:720-721. [PMID: 33473959 PMCID: PMC7799619 DOI: 10.1080/23802359.2017.1390405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cynanchum wilfordii is a traditional herbal medicine and belongs to the family Apocynaceae. The C. wilfordii mitochondrial genome consists of three circular chromosomes (named chromosomes I-III), the lengths of which are 379,060, 352,767 and 111,332 nucleotides. The mitochondrial genome encodes 58 genes, including 38 protein-coding genes, 17 transfer RNA genes and three ribosomal RNA genes. Of these 58 genes, 37 are located in chromosome I, 35 in chromosome II and 15 in chromosome III. Phylogenetic analysis suggests that among the 14 reported species of Asterids, C. wilfordii is most closely related to Asclepias syriaca.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Korea
| | - Jae-Hyeon Oh
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Korea
| | - Hyo-Jin Kim
- Jeollabukdo ARES Medicinal Resource Research Institute, Jinan, Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Korea
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Jo S, Kim HW, Kim YK, Cheon SH, Kim KJ. The complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:26-28. [PMID: 33473704 PMCID: PMC7800814 DOI: 10.1080/23802359.2016.1233468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this study, we determined the complete plastome sequence of Carissa macrocarpa (Eckl.) A. DC. (Apocynaceae) (NCBI acc. no. KX364402). The gene order and structure of the C. macrocarpa plastome are similar to those of a typical angiosperm. The complete plastome is 155,297 bp in length, and consists of a large single-copy region of 85,586 bp and a small single-copy region of 18,131 bp, which are separated by two inverted repeats of 25,792 bp. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes and 4 are rRNA genes. Sixteen genes contained one intron and two genes have two introns. The average A–T content of the plastome is 62.0%. A total of 31 simple sequence repeat loci were identified within the genome. Phylogenetic analysis revealed that C. macrocarpa is a member of the paraphyletic subfamily Rauvolfioideae of Apocynaceae. The sister group relationship of C. macrocarpa to the Apocynoideae–Asclepiadoideae clade is supported by 100% bootstrap values.
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Affiliation(s)
- Sangjin Jo
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Hoe-Won Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul, Korea
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Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
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