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Successful identification of the species of the semipetrified amber medicinal resin benzoin using molecular diagnostic technology. Sci Rep 2023; 13:2943. [PMID: 36808137 PMCID: PMC9941088 DOI: 10.1038/s41598-023-30034-y] [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: 08/13/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Benzoin is an incomplete lithified resin secreted from the trunk of the Styrax Linn. that is known as "semipetrified amber" and has been widely used in medicine due to its blood circulation-promoting and pain-relieving properties. However, the lack of an effective species identification method due to the numerous sources of benzoin resin and the difficulty of DNA extraction has led to the uncertainty of species of benzoin in the trade process. Here, we report the successful extraction of DNA from benzoin resin containing bark-like residues and the evaluation of commercially available benzoin species using molecular diagnostic techniques. By performing a BLAST alignment of ITS2 primary sequences and homology prediction analysis of ITS2 secondary structures, we found that commercially available benzoin species were derived from Styrax tonkinensis (Pierre) Craib ex Hart. and Styrax japonicus Sieb. et Zucc. of the genus Styrax Linn. In addition, some of the benzoin samples were mixed with plant tissues from other genera, accounting for 29.6%. Therefore, this study provides a new method to solve the problem of species identification of semipetrified amber benzoin using information from bark residues.
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Li KP, Wu YX, Zhao H, Wang Y, Lü XM, Wang JM, Xu Y, Li ZY, Han YH. Cytogenetic relationships among Citrullus species in comparison with some genera of the tribe Benincaseae (Cucurbitaceae) as inferred from rDNA distribution patterns. BMC Evol Biol 2016; 16:85. [PMID: 27090090 PMCID: PMC4835933 DOI: 10.1186/s12862-016-0656-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/12/2016] [Indexed: 12/27/2022] Open
Abstract
Background Comparative mapping of 5S and 45S rDNA by fluorescent in situ hybridization (FISH) technique is an excellent tool to determine cytogenetic relationships among closely related species. Results In this study, the number and position of 5S and 45S rDNA loci in all Citrullus species and subspecies were determined. The cultivated watermelon (C. lanatus subsp. vulgaris), C. lanatus subsp. mucosospermus, C. colocynthis and C. naudinianus (or Acanthosicyos naudinianus) had two 45S rDNA loci and one 5S rDNA locus which was located syntenic to one of the 45S rDNA loci. C. ecirrhosus and C. lanatus subsp. lanatus had one 45S rDNA locus and two 5S rDNA loci, each located on a different chromosome. C. rehmii had one 5S and one 45S rDNA locus positioned on different chromosomes. The distribution of 5S and 45S rDNA in several species belonging to other genera in Benincaseae tribe was also investigated. The distribution pattern of rDNAs showed a great difference among these species. Conclusions The present study confirmed evolutionary closeness among cultivated watermelon (C. lanatus subsp. vulgaris), C. lanatus subsp. mucosospermus and C. colocynthis. Our result also supported that C. lanatus subsp. lanatus was not a wild form of the cultivated watermelon instead was a separate crop species. In addition, present cytogenetic analysis suggested that A. naudinianus was more closely related to Cucumis than to Citrullus or Acanthosicyos, but with a unique position and may be a link bridge between the Citrullus and the Cucumis.
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Affiliation(s)
- Kun-Peng Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yun-Xiang Wu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Hong Zhao
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, 100097, China
| | - Yan Wang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Xing-Ming Lü
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Ji-Ming Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, 100097, China
| | - Zong-Yun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
| | - Yong-Hua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
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Bang SW, Chung SM. One size does not fit all: the risk of using amplicon size of chloroplast SSR marker for genetic relationship studies. PLANT CELL REPORTS 2015; 34:1681-1683. [PMID: 26252979 DOI: 10.1007/s00299-015-1849-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 06/04/2023]
Abstract
Even within closely related taxa, total length variation of PCR amplicons from chloroplast SSR must be confirmed by sequencing to avoid misinterpreting genetic relationships.
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Affiliation(s)
- Sun Woong Bang
- Department of Life Science, Dongguk University-Seoul, Seoul, 100-715, South Korea
| | - Sang-Min Chung
- Department of Life Science, Dongguk University-Seoul, Seoul, 100-715, South Korea.
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Eurlings MC, Heuveling van Beek H, Gravendeel B. Polymorphic microsatellites for forensic identification of agarwood (Aquilaria crassna). Forensic Sci Int 2010; 197:30-4. [DOI: 10.1016/j.forsciint.2009.12.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 11/09/2009] [Accepted: 12/08/2009] [Indexed: 11/15/2022]
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Angioi SA, Desiderio F, Rau D, Bitocchi E, Attene G, Papa R. Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes. PLANT BIOLOGY (STUTTGART, GERMANY) 2009; 11:598-612. [PMID: 19538398 DOI: 10.1111/j.1438-8677.2008.00143.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Chloroplast microsatellites (cpSSRs) provide a powerful tool to study the genetic variation and evolution of plants. We have investigated the usefulness of 39 primer pairs tagging cpSSR loci on a set of eight different genera of Leguminosae (Papilionoideae subfamily) and five species belonging to the genus Phaseolus. Thirty-six 'universal' primer pairs were retrieved from the literature, one was re-designed and a further two were designed de novo. The cpSSR loci analysed were highly polymorphic across the individuals examined. Twenty-seven primer pairs were polymorphic in the overall sample, 18 within Phaseolus, and 16 in both P. vulgaris and P. coccineus. Analysis of the plastome sequences of four Leguminosae species (obtained from GenBank) showed that in the loci targeted by universal primer pairs: (i) the originally tagged cpSSRs can be lost; (ii) other cpSSRs can be present; and (iii) polymorphism arises not only from differences in the numbers of cpSSR repeats, but often from other insertion/deletion events. Multilocus linkage disequilibrium analysis suggests that homoplasy is not a major problem in our dataset, and principal component analysis indicates intelligible relationships among the species considered. Our study demonstrates that this set of chloroplast markers provides a useful tool to study the diversity and the evolution of several legumes, and particularly P. vulgaris and P. coccineus.
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Affiliation(s)
- S A Angioi
- Dipartimento di Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari, Sassari, Italy
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Strong Genetic Differentiation of Primula sikkimensis in the East Himalaya–Hengduan Mountains. Biochem Genet 2007; 46:75-87. [PMID: 18157690 DOI: 10.1007/s10528-007-9131-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Accepted: 09/12/2007] [Indexed: 10/22/2022]
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Chung SM, Gordon VS, Staub JE. Sequencing cucumber (Cucumis sativus L.) chloroplast genomes identifies differences between chilling-tolerant and -susceptible cucumber lines. Genome 2007; 50:215-25. [PMID: 17546086 DOI: 10.1139/g07-003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chilling injury in cucumber (Cucumis sativus L.) is conditioned by maternal factors, and the sequencing of its chloroplast genome could lead to the identification of economically important candidate genes. Complete sequencing of cucumber chloroplast (cp)DNA was facilitated by the development of 414 consensus chloroplast sequencing primers (CCSPs) from conserved cpDNA sequences of Arabidopsis (Arabidopsis thaliana L.), spinach (Spinacia oleracea L.), and tobacco (Nicotiana tabacum L.) cpDNAs, using degenerative primer technologies. Genomic sequence analysis led to the construction of 301 CCSPs and 72 cucumber chloroplast-specific sequencing primers (CSSPs), which were used for the complete sequencing of cpDNA of Gy14 (155 525 bp) and 'Chipper' (155 524 bp) cucumber lines, which are, respectively, susceptible and tolerant to chilling injury (4 degrees C for 5.5 h) in the first leaf stage. Comparative cpDNA sequence analyses revealed that 1 sequence span (located between genes trnK and rps16) and 2 nucleotides (located in genes atpB and ycf1) differed between chilling-susceptible and -tolerant lines. These sequence differences correspond to previously reported maternally inherited differences in chilling response between reciprocal F1 progeny derived from these lines. Sequence differences at these 3 cpDNA sites were also detected in a genetically diverse array of cucumber germplasm with different chilling responses. These and previously reported results suggest that 1 or several of these sequences could be responsible for the observed response to chilling injury in cucumber. The comprehensive sequencing of cpDNA of cucumber by CCSPs and CSSPs indicates that these primers have immediate applications in the analysis of cpDNAs from other dicotyledonous species and the investigation of evolutionary relationships.
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Affiliation(s)
- Sang-Min Chung
- USDA/ARS, Vegetable Crops Research Unit, Department of Horticulture, 1575 Linden Dr., University of Wisconsin, Madison, WI 53706, USA.
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Kocyan A, Zhang LB, Schaefer H, Renner SS. A multi-locus chloroplast phylogeny for the Cucurbitaceae and its implications for character evolution and classification. Mol Phylogenet Evol 2007; 44:553-77. [PMID: 17321763 DOI: 10.1016/j.ympev.2006.12.022] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 12/01/2006] [Accepted: 12/28/2006] [Indexed: 11/21/2022]
Abstract
Cucurbitaceae contain c. 800 species in 130 genera and are among the economically most important families of plants. We inferred their phylogeny based on chloroplast DNA sequences from two genes, one intron, and two spacers (rbcL, matK, trnL, trnL-trnF, rpl20-rps12) obtained for 171 species in 123 genera. Molecular data weakly support the traditional subfamilies Cucurbitoideae (111 genera) and Nhandiroboideae (19 genera, 60 species), and recover most of the eleven tribes, but almost none of the subtribes. Indofevillea khasiana is sister to all other Cucurbitoideae, and the genera of Joliffieae plus a few Trichosantheae form a grade near the base of Cucurbitoideae. A newly discovered large clade consists of the ancestrally Asian genera Nothoalsomitra, Luffa, Gymnopetalum, Hodgsonia, Trichosanthes, and the New World tribe Sicyeae. Genera that are poly- or paraphyletic include Ampelosicyos, Cucumis, Ibervillea, Neoachmandra, Psiguria, Trichosanthes, and Xerosicyos. Flower characters, especially number of free styles, fusion of filaments and/or anthers, tendril type, and pollen size, exine, and aperture number correlate well with the chloroplast phylogeny, while petal and fruit characters as well as karyotype exhibit much evolutionary flexibility.
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MESH Headings
- Base Sequence
- Biological Evolution
- Cucurbitaceae/chemistry
- Cucurbitaceae/classification
- Cucurbitaceae/genetics
- DNA, Chloroplast/genetics
- Databases, Nucleic Acid
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Promoter Regions, Genetic/genetics
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/genetics
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
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Affiliation(s)
- Alexander Kocyan
- Department of Biology, Ludwig Maximilians University, D-80638 Munich, Germany
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Lebeda A, Widrlechner M, Staub J, Ezura H, Zalapa J, Kristkova E. Cucurbits (Cucurbitaceae; Cucumis spp., Cucurbita spp., Citrullus spp.). GENETIC RESOURCES, CHROMOSOME ENGINEERING, AND CROP IMPROVEMENT 2006. [DOI: 10.1201/9781420009569.ch8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chung SM, Staub JE, Chen JF. Molecular phylogeny of Cucumis species as revealed by consensus chloroplast SSR marker length and sequence variation. Genome 2006; 49:219-29. [PMID: 16604104 DOI: 10.1139/g05-101] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate phylogenetic relationships in the genus Cucumis, 9 consensus chloroplast simple sequence repeat (ccSSR) primer pairs (ccSSR3, 9, 11, 13, 14, 17, 20, 21, and 23) were employed for DNA fragment length variation and 5 amplified fragments, ccSSR4, 12, 13, 19, and 20, were sequenced using total DNA from 13 accessions representing 7 African Cucumis species (x = 12), 3 Cucumis melo L. (x = 12) accessions, 2 Cucumis sativus L. (x = 7) accessions, and 1 Cucumis hystrix Chakr. (x = 12) accession. A Citrullus lanatus (Thunb.) Matsum. & Nakai (x = 11) accession was used as an outgroup. While fragment length analysis revealed the existence of 3 major species clusters (i.e., a group of African Cucumis species, a group composed of C. melo accessions, and a group containing C. sativus and C. hystrix species), sequence variation analysis identified 2 major species clusters (i.e., a group of African Cucumis species and a group composed of C. melo, C. sativus, and C. hystrix species). Comparative analysis using nuclear DNA (previous studies) and cpDNA sequence substitution data resulted in the placement of C. melo and C. sativus in different cluster groupings. Thus, both nuclear and cytoplasmic DNA should be employed and compared when a putative progenitor or specimens of an ancestral Cucumis species lineage is investigated. In addition, C. ficifolius (2x) and C. aculeatus (4x) of the African Cucumis species clustered together in this study. This result does not agree with reported isozyme analyses, but does agree with previously characterized chromosome homologies between these 2 species. Although African Cucumis species and C. hystrix do not share a close relationship, genetic affinities between C. sativus and C. hystrix are considerable. Combined evidence from previously published studies and data presented herein lend support to the hypothesis that C. hystrix is either a progenitor species of C. sativus or that they at least share a common ancestral lineage.
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Affiliation(s)
- S-M Chung
- Vegetable Crops Research Unit, Department of Horticulture, US Department of Agriculture-ARS, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA.
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Dane F, Lang P, Bakhtiyarova R. Comparative analysis of chloroplast DNA variability in wild and cultivated Citrullus species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:958-966. [PMID: 14634729 DOI: 10.1007/s00122-003-1512-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2003] [Accepted: 09/25/2003] [Indexed: 05/24/2023]
Abstract
PCR amplification and restriction site analysis of chloroplast (cp) DNA regions was used to detect inter- and intraspecific differences in the genus Citrullus. More than 55 C. lanatus and 15 C. colocynthis accessions collected from diverse geographical areas, C. ecirrhosus and C. rehmii were used. Most of the cpDNA variation within Citrullus was the result of large indels and transitions and transversions. Indels at the ndhA, trnS- trnfM and trnC- trnD regions and several substitutions at restriction enzyme sites can be used to separate C. colocynthis from the other Citrullus species. A nucleotide substitution at a restriction enzyme site at the 3' flanking region of ndhF provided a diagnostic haplotype for C. lanatus var. lanatus, the cultivated watermelon. Similarly, a nucleotide substitution at an intergenic spacer region of the trnC- trnD region resulted in a diagnostic haplotype for citron, C. lanatus var. citroides. Several C. lanatus var. citroides accessions showed the var. lanatus haplotype. C. rehmii showed almost the same haplotype as C. lanatus var. citroides with the exception of a unique insertion at a cpSSR site. Since C. ecirrhosus lacks the derived diagnostic nucleotide substitutions of C. lanatus, it is probably the progenitor of the cultivated watermelon. Intraspecific haplotypes detected within C. colocynthis were associated with geographic origin.
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Affiliation(s)
- F Dane
- Department of Horticulture, Auburn University, Auburn, AL, USA.
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