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Ahmed SS, Rahman MO. Deciphering the complete chloroplast genome sequence of Meconopsis torquata Prain: Insights into genome structure, comparative analysis and phylogenetic relationship. Heliyon 2024; 10:e36204. [PMID: 39224270 PMCID: PMC11367419 DOI: 10.1016/j.heliyon.2024.e36204] [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: 04/20/2024] [Revised: 06/22/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
In the present study, we have characterized the complete chloroplast (Cp) genome of Meconopsis torquata Prain (family Papaveraceae), revealing the plastome size of 153,290 bp, and a GC content of 38.72 %. The cp genome features the typical circular quadripartite structure found in flowering plants, including a pair of inverted repeat regions (25,816 bp), isolated by a small single-copy region (17,740 bp) and a large single-copy (83,918 bp). Genome annotation revealed 132 genes: 87 protein-coding genes, 37 tRNAs and eight rRNAs. This comparative study demonstrated that the genome structure, gene number and GC ratio are consistent with several other cp genomes of Meconopsis and Papaver genera. A total of 120 SSRs were detected in the plastome, the majority (111) of which were mononucleotide repeats. Among the longer repeats, palindromic sequences were most common, followed by forward, reverse, and complement repeats. The whole genome alignment revealed the conserved nature of the inverted repeat region over single-copy zones. Nucleotide diversity unveiled hypervariable sites (ycf1, rps16, accD, atpB and psbD) in both the small and large single-copy regions, which could be useful for designing molecular markers for taxonomic identification. Phylogenetic analysis revealed a close alliance of M. torquata with other Meconopsis species, such as M. pinnatifolia and M. paniculata, with strong bootstrap support. Molecular dating suggests that M. torquata originated during the Tortonian age of the Miocene epoch of the Cenozoic era. These findings provide valuable insights for biological research, especially in understanding the genetic and evolutionary divergence within the Papaveraceae family.
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Affiliation(s)
- Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
| | - M. Oliur Rahman
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
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Zhan Q, Huang Y, Xue X, Chen Y. Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae). BMC Genom Data 2024; 25:49. [PMID: 38816818 PMCID: PMC11141030 DOI: 10.1186/s12863-024-01236-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024] Open
Abstract
Oreomecon nudicaulis, commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis, which was previously classified under the genus Papaver, was reclassified within the genus Oreomecon. Nevertheless, the phylogenetic status and chloroplast genome within the genus Oreomecon have not yet been reported. This study elucidates the chloroplast genome sequence and structural features of O. nudicaulis and explores its evolutionary relationships within Papaveraceae. Using Illumina sequencing technology, the chloroplast genome of O. nudicaulis was sequenced, assembled, and annotated. The results indicate that the chloroplast genome of O. nudicaulis exhibits a typical circular quadripartite structure. The chloroplast genome is 153,903 bp in length, with a GC content of 38.87%, containing 84 protein-coding genes, 8 rRNA genes, 38 tRNA genes, and 2 pseudogenes. The genome encodes 25,815 codons, with leucine (Leu) being the most abundant codon, and the most frequently used codon is AUU. Additionally, 129 microsatellite markers were identified, with mononucleotide repeats being the most abundant (53.49%). Our phylogenetic analysis revealed that O. nudicaulis has a relatively close relationship with the genus Meconopsis within the Papaveraceae family. The phylogenetic analysis supported the taxonomic status of O. nudicaulis, as it did not form a clade with other Papaver species, consistent with the revised taxonomy of Papaveraceae. This is the first report of a phylogenomic study of the complete chloroplast genome in the genus Oreomecon, which is a significant genus worldwide. This analysis of the O. nudicaulis chloroplast genome provides a theoretical basis for research on genetic diversity, molecular marker development, and species identification, enriching genetic information and supporting the evolutionary relationships among Papaveraceae.
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Affiliation(s)
- Qingbin Zhan
- College of Criminal Science and Technology, Nanjing Police University, Nanjing, China
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, China
| | - Yalin Huang
- College of Criminal Science and Technology, Nanjing Police University, Nanjing, China
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, China
| | - Xiaoming Xue
- College of Criminal Science and Technology, Nanjing Police University, Nanjing, China
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, China
| | - Yunxia Chen
- College of Criminal Science and Technology, Nanjing Police University, Nanjing, China.
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, China.
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Ragupathy S, Thirugnanasambandam A, Vinayagam V, Newmaster SG. Nuclear Magnetic Resonance Fingerprints and Mini DNA Markers for the Authentication of Cinnamon Species Ingredients Used in Food and Natural Health Products. PLANTS (BASEL, SWITZERLAND) 2024; 13:841. [PMID: 38592863 PMCID: PMC10975438 DOI: 10.3390/plants13060841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Cinnamomum verum (syn C. zeylanicum) is considered 'true' cinnamon. However, it is reported that less expensive sources of cinnamon from C. cassia (syn C. aromaticum), C. loureiroi, and C. burmannii (toxic coumarin) may be used in the place of C. verum. We lack the quality assurance tools that are required to differentiate C. verum from other cinnamon species when verifying that the correct species is sourced from ingredient suppliers. The current research on cinnamon species authentication using DNA tools is limited to a few species and the use of high-quality DNA extracted from raw leaf materials. The cinnamon bark traded in the supply chain contains much less DNA and poorer-quality DNA than leaves. Our research advances DNA methods to authenticate cinnamon, as we utilized full-length chloroplast genomes via a genome skimming approach for C. burmannii and C. cassia to facilitate the design of optimal mini DNA markers. Furthermore, we developed and validated the use of NMR fingerprints for several commercial cinnamon species, including the quantification of 16 molecules. NMR fingerprints provided additional data that were useful for quality assessment in cinnamon extract powders and product consistency. Both the new mini DNA markers and NMR fingerprints were tested on commercial cinnamon products.
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Affiliation(s)
- Subramanyam Ragupathy
- Natural Health Products (NHP) Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.V.); (S.G.N.)
| | - Arunachalam Thirugnanasambandam
- Natural Health Products (NHP) Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.V.); (S.G.N.)
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Graham K, Houston R. Evaluation of chloroplast DNA barcoding markers to individualize Papaver somniferum for forensic intelligence purposes. Int J Legal Med 2024; 138:267-275. [PMID: 35788906 DOI: 10.1007/s00414-022-02862-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
Abstract
The opium poppy, Papaver somniferum L., is a forensically important plant due to the medicinal and illegal uses for the milky latex stored in the pods. This latex contains the alkaloids morphine, codeine, and thebaine that are used for their analgesic properties and/or for synthesizing other opioids. However, these compounds are highly addictive and have caused a national opioid epidemic. Two other Papaver species, P. setigerum DC. and P. bracteatum Lindl., are also of forensic interest because they pose both forensic and legal issues. They are largely uncontrolled under the Controlled Substances Act, making these species a common defense strategy. Current morphological and chemical identification methods have been moderately successful but have drawbacks. There is also a lack of sequencing data available. Therefore, exploiting the genome using chloroplast DNA barcoding markers could help to accurately identify these species of interest when plant material is taken. This study screened and assessed the genetic variation both between species and within populations of P. somniferum in nine cpDNA barcode regions (ndhF-rpl32, petA-psbJ, rpl32-trnL, rps16-trnQ, trnE-trnT, trnH-psbA, trnL-trnF, rpl16 intron, and psbE-petL). Published reference genomes from the NCBI GenBank database were aligned and compared for an initial in silico screening. Additionally, ten P. somniferum seed samples from various vendors were sequenced and compared across samples and to published reference data at the various barcode regions of interest. This study showed that the regions trnH-psbA and petA-psbJ have promise for utility in individualization for both inter- and intra-species individualization of P. somniferum.
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Affiliation(s)
- Kari Graham
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA.
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Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2023:elad050. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
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Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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Affiliation(s)
- David Love
- United States Drug Enforcement Administration, Special Testing and Research Laboratory, USA
| | - Nicole S. Jones
- RTI International, Applied Justice Research Division, Center for Forensic Sciences, 3040 E. Cornwallis Road, Research Triangle Park, NC, 22709-2194, USA
- 70113 Street, N.W., Suite 750, Washington, DC, 20005-3967, USA
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Ren W, Jiang Z, Zhang M, Kong L, Zhang H, Liu Y, Fu Q, Ma W. The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements. FRONTIERS IN PLANT SCIENCE 2022; 13:987443. [PMID: 36092427 PMCID: PMC9459086 DOI: 10.3389/fpls.2022.987443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Salix floderusii is a rare alpine tree species in the Salix genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of S. floderusii for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The S. floderusii cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of S. floderusii and Salix caprea were shorter than those of Salix cinerea, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the rpl22 coding region, psbM/trnD-GUC non-coding region, petA/psbJ non-coding region, and ycf1 coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future Salix species. In addition, phylogenetic analysis indicated that the cp genome of S. floderusii is sister to Salix cupularis and belongs to the Subgenus Vetrix. Genes (Sf-trnI, Sf-PpsbA, aadA, Sf-TpsbA, Sf-trnA) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene aadA. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the aadA gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent S. floderusii cp transformation systems and developing strategies for the genetic improvement of S. floderusii.
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Affiliation(s)
- Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhehui Jiang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Meiqi Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Lingyang Kong
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Houliang Zhang
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Yunwei Liu
- Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Qifeng Fu
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
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Chang M, Kim JY, Lee H, Lee EJ, Lee WH, Moon S, Choe S, Choung CM. Development of diagnostic SNP markers and a novel SNP genotyping assay for distinguishing opium poppies. Forensic Sci Int 2022; 339:111416. [DOI: 10.1016/j.forsciint.2022.111416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 11/04/2022]
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Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis. Sci Rep 2022; 12:111. [PMID: 34997061 PMCID: PMC8741915 DOI: 10.1038/s41598-021-04056-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
Opium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.
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Chang M, Lee EJ, Kim JY, Lee H, Choe S, Moon S. A new minisatellite VNTR marker, Pscp1, discovered for the identification of opium poppy. Forensic Sci Int Genet 2021; 55:102581. [PMID: 34517229 DOI: 10.1016/j.fsigen.2021.102581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Opium poppy, a member of the Papaveraceae family, is an ancient herbaceous plant and well-known medical resource in the pharmaceutical industry. However, opium poppies are grown worldwide for producing illicit drugs, significantly increasing the incidence of narcotic drug abuse. Since the narcotic poppy has not yet been genetically investigated, we characterized a novel variable number tandem repeat (VNTR) marker of forensically important poppy species based on the genetic analysis of 164 samples collected from two locations spanning the Jeolla province and Jeju island of South Korea. Comparing analysis of the chloroplast (cp) genome sequences for four representative species of Papaver (Papaver somniferum, Papaver somniferum subs. setigerum, Papaver orientale, and Papaver rhoeas) revealed a unique region with 1-3 repeats for 16 nucleotide motifs in the genome inverted repeat A (IRA, positions 128,651 to 128,698) region. For 16 nucleotide motifs, 3 repeats were found in P. somniferum, and 2 repeats were found in P. somniferum subs. setigerum. Therefore, 10 known and the 133 unknown, seized Papaver species were compared to determine whether the species could be identified via variations in the repeat units. The sizes of a novel VNTR ranged from 181 to 252 bp between the species. Phylogenetic analysis confirmed that a novel VNTR, which we named Pscp1, could clearly distinguish between the narcotic and non-narcotic types of Papaver species based on the patterns of sequence variation. Interestingly, we found that Pscp1 could also distinguish between P. somniferum and P. somniferum subs. setigerum. The regions of eight non-narcotic species displayed similar patterns and also differences were found due to the nucleotide substitution and deletion events. The structural differences of Pscp1 were observed within the two narcotic species or between the narcotic and non-narcotic species, suggesting that these variations may act as a genetic marker. We, therefore, developed a new Pscp1 PCR-capillary electrophoresis (CE) method that can reliably identify the narcotic type of Papaver species. Taken together, our findings suggest that the newly developed Pscp1 can be used as an identification marker of opium poppy, and establish that the Pscp1 genotyping method by PCR-CE is an effective primary screening tool that can also contribute to species discrimination in the field of forensic diagnosis and applications.
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Affiliation(s)
- Miwha Chang
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Eun-Jung Lee
- Crime-scene DNA Section, Gwangju Institute, National Forensic Service, Gwangju 57231, Republic of Korea
| | - Joo-Young Kim
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Haeyong Lee
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea
| | - Sanggil Choe
- Forensic Toxicology and Chemistry Division, Seoul Institute, National Forensic Service, Seoul 08036, Republic of Korea
| | - Seohyun Moon
- Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
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