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Schnittler M, Inoue M, Shchepin ON, Fuchs J, Chang H, Lamkowski P, Knapp R, Horn K, Bennert HW, Bog M. Hybridization and reticulate evolution in Diphasiastrum (flat-branched clubmosses, Lycopodiaceae) - New data from the island of Taiwan and Vietnam. Mol Phylogenet Evol 2024; 196:108067. [PMID: 38561082 DOI: 10.1016/j.ympev.2024.108067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
In the species groups related to Diphasiastrum multispicatum and D. veitchii, hybridization was investigated in samples from northern and southern Vietnam and the island of Taiwan, including available herbarium specimens from southeast Asia. The accessions were analyzed using flow cytometry (living material only), Sanger sequencing and multiplexed inter-simple sequence repeat genotyping by sequencing. We detected two cases of ancient hybridization involving different combinations of parental species; both led via subsequent duplication to tetraploid taxa. A cross D. multispicatum × D. veitchii from Malaysia represents D. wightianum, a tetraploid taxon according to reported DNA content measurements of dried material (genome formulas MM, VV and MMVV, respectively). The second case involves D. veitchii and an unknown diploid parent (genome formula XX). Three hybridogenous taxa (genome formulas VVX, VVXX, VVVX) were discernable by a combination of flow cytometry and molecular data. Taxon I (VVX, three clones found on Taiwan island) is apparently triploid. Taxon II represents another genetically diverse and sexual tetraploid species (VVXX) and can be assigned to D. yueshanense, described from Taiwan island but occurring as well in mainland China and Vietnam. Taxon III is as well most likely tetraploid (VVVX) and represented by at least one, more likely two, clones from Taiwan island. Taxa I and III are presumably asexual and new to science. Two independently inherited nuclear markers recombine only within, not between these hybrids, pointing towards reproductive isolation. We present an evolutionary scheme which explains the origin of the hybrids and the evolution of new and fully sexual species by hybridization and subsequent allopolyploidization in flat-branched clubmosses.
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Affiliation(s)
- M Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany
| | - M Inoue
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany
| | - O N Shchepin
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany
| | - J Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Stadt Seeland, D-06466 OT Gatersleben, Germany
| | - H Chang
- Division of Botany, Endemic Species Research Institute, 1, Ming Seng E. Road, Jiji, Nantou 552, Taiwan, ROC
| | - P Lamkowski
- Nature Conservation and Land Use Planning, University of Applied Sciences Neubrandenburg, Brodaer Straße 2, D-17033 Neubrandenburg, Germany
| | - R Knapp
- Steigestraße 78, D-69412 Eberbach, Germany
| | - K Horn
- Büro für angewandte Geobotanik und Landschaftsökologie (BaGL), Frankenstraße 2, D-91077 Dormitz, Germany
| | - H W Bennert
- Evolution and Biodiversity of Plants, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - M Bog
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Soldmannstraße 15, D-17487 Greifswald, Germany.
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Ji HY, Ye C, Chen YQ, Li JW, Hidayat A, Miao JL, Li JH, Wu JY, Zhai JW, Lan SR, Jin XH. Phylogenomics and biogeographical diversification of Collabieae (Orchidaceae) and its implication in the reconstruction of the dynamic history of Asian evergreen broadleaved forests. Mol Phylogenet Evol 2024; 196:108084. [PMID: 38688440 DOI: 10.1016/j.ympev.2024.108084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/16/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
The tribe Collabieae (Epidendroideae, Orchidaceae) comprises approximately 500 species. Generic delimitation within Collabieae are confusing and phylogenetic interrelationships within the Collabieae have not been well resolved. Plastid genomes and nuclear internal transcribed spacer (ITS) sequences were used to estimate the phylogenetic relationships, ancestral ranges, and diversification rates of Collabieae. The results showed that Collabieae was subdivided into nine clades with high support. We proposed to combine Ancistrochilus and Pachystoma into Spathoglottis, merge Collabium and Chrysoglossum into Diglyphosa, and separate Pilophyllum and Hancockia as distinctive genera. The diversification of the nine clades of Collabieae might be associated with the uplift of the Himalayas during the Late Oligocene/Early Miocene. The enhanced East Asian summer monsoon in the Late Miocene may have promoted the rapid diversification of Collabieae at a sustained high diversification rate. The increased size of terrestrial pseudobulbs may be one of the drivers of Collabieae diversification. Our results suggest that the establishment and development of evergreen broadleaved forests facilitated the diversification of Collabieae.
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Affiliation(s)
- Hong-Yu Ji
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Ye
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yan-Qiong Chen
- College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Jian-Wu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Arief Hidayat
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, Indonesia
| | - Jiang-Lin Miao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Jian-Yong Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment (MEE), China
| | - Jun-Wen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Xiao-Hua Jin
- State Key Laboratory of Plant Diversity and Speciality Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China; China National Botanical Garden, Beijing, China.
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Yan Y, da Fonseca RR, Rahbek C, Borregaard MK, Davis CC. A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia. Mol Phylogenet Evol 2024; 196:108089. [PMID: 38679302 DOI: 10.1016/j.ympev.2024.108089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 03/08/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.
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Affiliation(s)
- Yujing Yan
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA.
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Life Sciences, Imperial College London, Silkwood Park campus, Ascot SL5 7PY, UK; Danish Institute for Advanced Study, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michael K Borregaard
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA
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Villa C, Costa J, Mafra I. First nanoplate digital PCR method to trace allergenic foods: Improved sensitivity for the detection of sesame. Food Chem 2024; 444:138650. [PMID: 38330611 DOI: 10.1016/j.foodchem.2024.138650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Sesame (Sesamum indicum L.) is an important allergenic food whose presence can be the cause of severe allergic reactions in sensitised individuals. In this work, nanoplate digital PCR (ndPCR) was used to develop two methods to detect trace amounts of sesame in processed foods and compared with previously proposed real-time PCR assays. Two independent ndPCR approaches were successfully advanced, achieving sensitivities of 5 and 0.1 mg/kg of sesame in dough/biscuits, targeting the CO6b-1 and ITS regions, respectively. The sensitivity using both targets was improved by one order of magnitude comparing with real-time PCR and was not affected by food processing. CO6b-1 system was not influenced by food matrix, exhibiting similar performance regardless the use of complex matrix extracts or serial diluted DNA. Herein, ndPCR was proposed for the first time for the detection of allergenic foods with the advantage of providing better performance than real-time PCR regarding sensitivity and robustness.
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Affiliation(s)
- Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal.
| | - Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal
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Minami M, Tanaka R, Mori T, Fujii T, Tsuchida T. Identification of Angelica acutiloba, A. sinensis, and other Chinese medicinal Apiaceae plants by DNA barcoding. J Nat Med 2024; 78:792-798. [PMID: 38427209 DOI: 10.1007/s11418-024-01796-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Crude drug Angelicae acutilobae radix is one of the most important crude drugs in Japanese traditional medicine and is used mainly for the treatment of gynecological disorders. In the listing in the Japanese Pharmacopoeia XVIII, Angelicae acutilobae radix is defined as the root of Angelica acutiloba (Apiaceae), which has long been produced on an industrial scale in Japan. With the aging of farmers and depopulation of production areas, the domestic supply has recently declined and the majority of the supply is now imported from China. Due to having only slightly different morphological and chemical characteristics for the Apiaceae roots used to produce dried roots for Chinese medicines, the plant species originating the crude drug Apiaceae roots may be incorrectly identified. In particular, Angelicae sinensis radix, which is widely used in China, and Angelicae acutilobae radix are difficult to accurately identify by morphology and chemical profiles. Thus, in order to differentiate among Angelicae acutilobae radix and other radixes originated from Chinese medicinal Apiaceae plants, we established DNA markers. Using DNA sequences for the chloroplast psbA-trnH intergenic spacer and nuclear internal transcribed spacer regions, Angelicae acutilobae radix and other Chinese Apiaceae roots, including Angelicae sinensis radix, can be definitively identified.
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Affiliation(s)
- Motoyasu Minami
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan.
| | - Ryusaku Tanaka
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Takako Mori
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Taichi Fujii
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Takashi Tsuchida
- Central R&D Laboratory, Kobayashi Pharmaceutical Co., Ltd, 1-30-3 Toyokawa, Ibaraki, Osaka, 567-0057, Japan
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Rodrigues V, Honrado M, Santos J, Pinto MA, Amaral JS. Development of a loop-mediated isothermal amplification assay for the rapid detection of Styphnolobium japonicum (L.) Schott as an adulterant of Ginkgo biloba (L.). Phytomedicine 2024; 128:155322. [PMID: 38569291 DOI: 10.1016/j.phymed.2023.155322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 04/05/2024]
Abstract
BACKGROUND Species adulteration is a concern in herbal products, especially when plant substitutes of lower economic value replace valuable botanicals. Styphnolobium japonicum is well known as a potential adulterant of Ginkgo biloba, which is one of the most demanded medicinal plants due to its wide use in pharmaceuticals, food supplements, and traditional medicine. Despite bearing some resemblance to ginkgo's flavonol composition, S. japonicum lacks many of G. biloba's desired therapeutic properties. To prevent adulteration practices, it is crucial to implement rigorous quality control measures, including fast and simple diagnostic tools that can be used on-field. PURPOSE This study aims to develop for the first time a species-specific loop-mediated isothermal amplification (LAMP) method for the fast identification of S. japonicum in ginkgo-containing products. METHODS A set of four specific primers (SjF3, SjB3, SjFIP, and SjBIP) and loop primers (SjLF and SjLB) were designed for a LAMP based assay using the 5.8S partial sequence and the internal transcribed spacer 2 of nuclear ribosomal DNA of S. japonicum. RESULTS The successful amplification of the LAMP assay was inspected through visual detection, with the highest intensity recorded at the optimal conditions set at 68 °C for 40 min. The primers showed high specificity and were able to accurately discriminate S. japonicum from G. biloba and 49 other species of medicinal plants. Furthermore, the proposed LAMP assay proved to be fast, selective, and highly sensitive, as demonstrated by the absolute and relative limits of detection, which were reached at 0.5 pg for S. japonicum DNA and 0.01 % S. japonicum in G. biloba, respectively. CONCLUSIONS This novel approach allows easy identification and discrimination of S. japonicum as a potential adulterant of G. biloba, thus being a useful tool for quality control. Compared to chromatographic or PCR-based methods, the assay proved to be fast, sensitive and did not require expensive equipment, thus offering the possibly usage in field analysis.
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Affiliation(s)
- Vânia Rodrigues
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Mónica Honrado
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal; LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Joana Santos
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Joana S Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal; Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal.
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Peñafiel-Ayala A, Peralta-Castro A, Mora-Garduño J, García-Medel P, Zambrano-Pereira AG, Díaz-Quezada C, Abraham-Juárez MJ, Benítez-Cardoza CG, Sloan DB, Brieba LG. Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease. Plant Cell Physiol 2024; 65:560-575. [PMID: 37756637 DOI: 10.1093/pcp/pcad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
MutS HOMOLOG 1 (MSH1) is an organellar-targeted protein that obstructs ectopic recombination and the accumulation of mutations in plant organellar genomes. MSH1 also modulates the epigenetic status of nuclear DNA, and its absence induces a variety of phenotypic responses. MSH1 is a member of the MutS family of DNA mismatch repair proteins but harbors an additional GIY-YIG nuclease domain that distinguishes it from the rest of this family. How MSH1 hampers recombination and promotes fidelity in organellar DNA inheritance is unknown. Here, we elucidate its enzymatic activities by recombinantly expressing and purifying full-length MSH1 from Arabidopsis thaliana (AtMSH1). AtMSH1 is a metalloenzyme that shows a strong binding affinity for displacement loops (D-loops). The DNA-binding abilities of AtMSH1 reside in its MutS domain and not in its GIY-YIG domain, which is the ancillary nickase of AtMSH1. In the presence of divalent metal ions, AtMSH1 selectively executes multiple incisions at D-loops, but not other DNA structures including Holliday junctions or dsDNA, regardless of the presence or absence of mismatches. The selectivity of AtMSH1 to dismantle D-loops supports the role of this enzyme in preventing recombination between short repeats. Our results suggest that plant organelles have evolved novel DNA repair routes centered around the anti-recombinogenic activity of MSH1.
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Affiliation(s)
- Alejandro Peñafiel-Ayala
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Antolin Peralta-Castro
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Josue Mora-Garduño
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Paola García-Medel
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Angie G Zambrano-Pereira
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Corina Díaz-Quezada
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - María Jazmín Abraham-Juárez
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Guillermo Massieu Helguera No. 239, La Escalera Ticoman 07320 DF, México
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Luis G Brieba
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, Irapuato, Guanajuato 36821, México
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8
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Sakamoto W, Takami T. Plastid Inheritance Revisited: Emerging Role of Organelle DNA Degradation in Angiosperms. Plant Cell Physiol 2024; 65:484-492. [PMID: 37702423 DOI: 10.1093/pcp/pcad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/15/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
Plastids are essential organelles in angiosperms and show non-Mendelian inheritance due to their evolution as endosymbionts. In approximately 80% of angiosperms, plastids are thought to be inherited from the maternal parent, whereas other species transmit plastids biparentally. Maternal inheritance can be generally explained by the stochastic segregation of maternal plastids after fertilization because the zygote is overwhelmed by the maternal cytoplasm. In contrast, biparental inheritance shows the transmission of organelles from both parents. In some species, maternal inheritance is not absolute and paternal leakage occurs at a very low frequency (∼10-5). A key process controlling the inheritance mode lies in the behavior of plastids during male gametophyte (pollen) development, with accumulating evidence indicating that the plastids themselves or their DNAs are eliminated during pollen maturation or at fertilization. Cytological observations in numerous angiosperm species have revealed several critical steps that mutually influence the degree of plastid transmission quantitatively among different species. This review revisits plastid inheritance from a mechanistic viewpoint. Particularly, we focus on a recent finding demonstrating that both low temperature and plastid DNA degradation mediated by the organelle exonuclease DEFECTIVE IN POLLEN ORGANELLE DNA DEGRADATION1 (DPD1) influence the degree of paternal leakage significantly in tobacco. Given these findings, we also highlight the emerging role of DPD1 in organelle DNA degradation.
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Affiliation(s)
- Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-2 Chuo, Kurashiki, Okayama, 710-0046 Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-2 Chuo, Kurashiki, Okayama, 710-0046 Japan
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Correia JP. Multifractal analysis of maize and soybean DNA. Sci Rep 2024; 14:10687. [PMID: 38724570 PMCID: PMC11082218 DOI: 10.1038/s41598-024-60722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
This paper investigates the complexity of DNA sequences in maize and soybean using the multifractal detrended fluctuation analysis (MF-DFA) method, chaos game representation (CGR), and the complexity-entropy plane approach. The study aims to understand the patterns and structures of these DNA sequences, which can provide insights into their genetic makeup and improve crop yield and quality. The results show that maize and soybean DNA sequences exhibit fractal properties, indicating a complex and self-organizing structure. We observe the persistence trend between sequences of base pairs, which indicates long-range correlations between base pairs. We also identified the stochastic nature of the DNA sequences of both species.
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Affiliation(s)
- J P Correia
- Departamento de Física, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brasil.
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10
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Gupta A, Yu J, Challita EJ, Standeven J, Bhamla MS. OpenCell: A low-cost, open-source, 3-in-1 device for DNA extraction. PLoS One 2024; 19:e0298857. [PMID: 38696375 PMCID: PMC11065270 DOI: 10.1371/journal.pone.0298857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/01/2024] [Indexed: 05/04/2024] Open
Abstract
High-cost DNA extraction procedures pose significant challenges for budget-constrained laboratories. To address this, we introduce OpenCell, an economical, open-source, 3-in-1 laboratory device that combines the functionalities of a bead homogenizer, a microcentrifuge, and a vortex mixer. OpenCell utilizes modular attachments that magnetically connect to a central rotating brushless motor. This motor couples to an epicyclic gearing mechanism, enabling efficient bead homogenization, vortex mixing, and centrifugation within one compact unit. OpenCell's design incorporates multiple redundant safety features, ensuring both the device's and operator's safety. Additional features such as RPM measurement, programmable timers, battery operation, and optional speed control make OpenCell a reliable and reproducible laboratory instrument. In our study, OpenCell successfully isolated DNA from Spinacia oleracea (spinach), with an average yield of 2.3 μg and an A260/A280 ratio of 1.77, demonstrating its effectiveness for downstream applications such as Polymerase Chain Reaction (PCR) amplification. With its compact size (20 cm x 28 cm x 6.7 cm) and lightweight design (0.8 kg), comparable to the size and weight of a laptop, OpenCell is portable, making it an attractive component of a 'lab-in-a-backpack' for resource-constrained environments in low-and-middle-income countries and synthetic biology in remote field stations. Leveraging the accessibility of 3D printing and off-the-shelf components, OpenCell can be manufactured and assembled at a low unit cost of less than $50, providing an affordable alternative to expensive laboratory equipment costing over $4000. OpenCell aims to overcome the barriers to entry in synthetic biology research and contribute to the growing collection of frugal and open hardware.
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Affiliation(s)
- Aryan Gupta
- School of Electrical & Computer Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Justin Yu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Elio J Challita
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Janet Standeven
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
- Lambert High School, Suwanee, Georgia, United States of America
| | - M Saad Bhamla
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
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11
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Ekram MAE, Campbell M, Kose SH, Plet C, Hamilton R, Bijaksana S, Grice K, Russell J, Stevenson J, Vogel H, Coolen MJL. A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia). Geobiology 2024; 22:e12599. [PMID: 38745401 DOI: 10.1111/gbi.12599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/24/2023] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.
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Affiliation(s)
- Md Akhtar-E Ekram
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Matthew Campbell
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Sureyya H Kose
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Chloe Plet
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - Rebecca Hamilton
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Satria Bijaksana
- Faculty of Mining and Petroleum Engineering, Institut Teknologi Bandung, Bandung, Indonesia
| | - Kliti Grice
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
| | - James Russell
- Department of Earth, Environmental, and Planetary Sciences (DEEPS), Brown University, Providence, Rhode Island, USA
| | - Janelle Stevenson
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Archaeology and Natural History, School of Culture, History, and Language, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Marco J L Coolen
- The Institute for Geoscience Research (TIGeR), Western Australia Organic and Isotope Geochemistry Centre (WAOIGC), School of Earth and Planetary Sciences (EPS), Curtin University, Bentley, Western Australia, Australia
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12
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Dokane K. Analysis of markers for forensic plant species identification. Forensic Sci Int 2024; 358:112007. [PMID: 38579526 DOI: 10.1016/j.forsciint.2024.112007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/08/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024]
Abstract
While plant species identification in forensics can be useful in cases involving poisonous, psychoactive, or endangered plant species, it can also become quite challenging, especially, when dealing with processed, decaying, colonized or infected material of plant origin. The Animal Plant and Soil Traces expert working group of the European Network of Forensic Science Institutes in their best practice manual has recommended several markers for plant species identification. Current study is a part of implementation of method in a forensic laboratory and its aim is to evaluate four of the recommended markers (ITS, matK, rbcL, and trnH-psbA) for species identification of forensically important plant species including medicinal, poisonous, psychoactive, and other plants. Such parameters as PCR and sequencing success, sequence length, species resolution rate and species cover in GenBank were analysed. Blind testing was performed to evaluate use of the markers for identification of forensically more complicated samples. According to results, a combination of ITS, matK and trnH-psbA is the best choice for plant species identification. The best results with fresh plant material can be achieved with ITS, trnH-psbA, and matK, while ITS and matK are the best choice when working with low quality plant material. rbcL due to its low species discrimination rate can be used only as an indicative marker.
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Affiliation(s)
- Kristine Dokane
- Biological and Chemical Investigations, State Forensic Science Bureau, 1 Invalidu street, Riga LV-1013, Latvia.
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13
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Rocha VDD, Dal'Sasso TCDS, Williams CCV, Simon MF, Bueno ML, Oliveira LOD. From forest to savanna and back to forest: Evolutionary history of the genus Dimorphandra (Fabaceae). J Plant Res 2024; 137:377-393. [PMID: 38369599 DOI: 10.1007/s10265-024-01523-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
The tree genus Dimorphandra (Fabaceae), which contains 26 species divided into three subgenera, was studied using DNA sequence data from six chloroplast genome regions (cpDNA) and the nuclear internal transcribed spacer (ITS). The analyses, which included Bayesian phylogenies and haplotype networks, ancestral area reconstructions, and ecological niche modeling, allowed for exploring the evolutionary history of Dimorphandra. Within the subgenus Phaneropsia, the cpDNA sequence data were more closely-related to species from the genus Mora, while the ITS sequence data displayed a closer phylogenetic relationship with the subgenus Pocillum. This incongruence may be due to incomplete lineage sorting associated with ancient polymorphisms. The Amazonian Dimophandra lineages were highly polymorphic and divergent, while those from the Cerrado and the Atlantic Forest had low levels of polymorphisms. The Amazon likely gave rise to the Dimophandra lineage that produced the Cerrado species, while a Cerrado lineage likely gave rise to the Atlantic Forest species. Habitat shifts were identified as a key factor in shaping the late evolutionary history of Dimorphandra.
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Affiliation(s)
- Vinicius Delgado da Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs s/n, Vicosa, Minas Gerais, 36570-000, Brazil
| | - Thaís Carolina da Silva Dal'Sasso
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs s/n, Vicosa, Minas Gerais, 36570-000, Brazil
- Environmental Genomics Group, Christian-Albrechts University of Kiel, and the Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | | | - Marcelo Leandro Bueno
- Laboratório de Macroecologia e Evolução (LAMEV), Universidade Estadual de Mato Grosso do Sul, Mundo Novo, Brazil
| | - Luiz Orlando de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs s/n, Vicosa, Minas Gerais, 36570-000, Brazil.
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14
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Lee Y, Kato S, Kim JY, Shimono Y, Shiga T. Two lineages of Lemna aequinoctialis (Araceae, Lemnoideae) based on physiology, morphology, and phylogeny. J Plant Res 2024; 137:359-376. [PMID: 38349478 DOI: 10.1007/s10265-023-01509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 11/08/2023] [Indexed: 05/12/2024]
Abstract
Lemna aequinoctialis Welw. is a widely spread species that has diverse physiological and molecular properties. Flower characteristics are important factors in deducing taxonomical status; however, owing to the rarity of flowering observations in Lemna, studying them has been a prolonged challenge. In this study, physiological and morphological analyses were conducted by inducing flowering, and molecular analysis was done based on the two chloroplast DNA loci (matK, atpF-atpH intergeneric spacer) of L. aequinoctialis sensu Landolt (1986) from 70 strains found in 70 localities in Japan, Korea, Thailand, and the US. In total, 752 flowering fronds from 13 strains were observed based on axenic conditions. Two different trends in flower organ development-protogyny and adichogamy-were detected in these strains. Their physiological traits were divided into two groups, showing different morphological features based on frond thickness, root cap, and anther sizes. Molecular analysis showed two lineages corresponding to two physiological groups. These were identified as L. aequinoctialis sensu Beppu et al. (1985) and L. aoukikusa Beppu et Murata based on the description of the nomenclature of L. aoukikusa. These were concluded as independent taxa and can be treated as different species. Furthermore, the distribution of L. aoukikusa is not only limited to Japan.
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Affiliation(s)
- Yuri Lee
- Graduate School of Science and Technology, Niigata University, Ikarashi Ninocho, Nishi-ku, Niigata, 950-2181, Japan
- Faculty of Education, Niigata University, Ikarashi Ninocho, Nishi-ku, Niigata, 950-2181, Japan
| | - Syou Kato
- Faculty of Education, Niigata University, Ikarashi Ninocho, Nishi-ku, Niigata, 950-2181, Japan
| | - Jae Young Kim
- Division of Horticulture and Medicinal Plant, Andong National University, Andong, 36729, Republic of Korea
| | - Yoshiko Shimono
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Shiga
- Graduate School of Science and Technology, Niigata University, Ikarashi Ninocho, Nishi-ku, Niigata, 950-2181, Japan.
- Faculty of Education, Niigata University, Ikarashi Ninocho, Nishi-ku, Niigata, 950-2181, Japan.
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15
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Lingwan M. Damage and repair: How Poaceae plants fix DNA damaged by UV-B radiation. Plant Physiol 2024; 195:265-267. [PMID: 38378163 PMCID: PMC11060675 DOI: 10.1093/plphys/kiae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 02/22/2024]
Affiliation(s)
- Maneesh Lingwan
- Plant Physiology, American Society of Plant Biologists
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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16
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Yalinkiliç NA, Başbağ S, Altaf MT, Ali A, Nadeem MA, Baloch FS. Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm. Mol Biol Rep 2024; 51:584. [PMID: 38683231 DOI: 10.1007/s11033-024-09526-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/05/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. METHODS AND RESULTS During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. CONCLUSION The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.
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Affiliation(s)
- Nazlı Aybar Yalinkiliç
- Faculty of Applied Sciences, Department of Plant Production and Technologies, Mus Alparslan University, Muş, Türkiye, Turkey
| | - Sema Başbağ
- Department of field crops, Faculty of agriculture, Dicle University, Diyarbakir, Türkiye, Turkey
| | - Muhammad Tanveer Altaf
- Department of Plant Production and Technologies, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Türkiye, Turkey
| | - Amjad Ali
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Türkiye, Turkey
| | - Muhammad Azhar Nadeem
- Department of Plant Production and Technologies, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Türkiye, Turkey
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, Yenişehir, Mersin, Türkiye, 33343, Turkey.
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17
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Rios-Willars E, Chirinos-Arias MC. Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm. Planta 2024; 259:134. [PMID: 38671234 DOI: 10.1007/s00425-024-04420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024]
Abstract
MAIN CONCLUSION Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.
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Affiliation(s)
- Ernesto Rios-Willars
- Faculty of Systems, Autonomous University of Coahuila (UAdeC), 25350, Saltillo, Coahuila, México.
| | - Michelle C Chirinos-Arias
- Molecular Biology and Bioinformatics Area, Instituto de Genetica Barbara McClintock (IGBM), Lima, 15022, Peru
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18
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Han J, Wang H, Song J, Jia H, Zhang X, Li S, Xu C, Li Z, Yang W. [Genetic background of lily germplasm resources based on SSR markers]. Sheng Wu Gong Cheng Xue Bao 2024; 40:1211-1224. [PMID: 38658158 DOI: 10.13345/j.cjb.230862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
To study the genetic background of lily (Lilium spp.) germplasm resources, and accurately evaluate and select excellent germplasm for genetic improvement of lily, we analyzed the genetic background of 62 lily germplasm accessions from 11 provinces of China by using simple sequence repeat (SSR) molecular markers. The results showed that 15 out of 83 pairs of lily SSR primers were polymorphic. A total of 157 allelic loci were amplified, with the number of alleles per locus ranging from 5 to 19 and the average number of effective alleles per locus being 4.162 8. The average observed heterozygosity and expected heterozygosity were 0.228 2 and 0.694 1, respectively. The average polymorphic information content was 0.678 8. The average Nei's diversity index and Shannon's information index were 0.694 1 and 1.594 9, respectively, indicating that the tested lily germplasm had high genetic diversity. The 62 germplasm accessions were classified into 5 groups by the unweighted pair group method with arithmetic mean (UPGMA) and into 3 groups by the principal component analysis. The two analyses revealed a geographic correlation among different groups. The majority of lily germplasm accessions from the same source tended to cluster together. The population structure analysis classified the lily accessions into 4 populations and 1 mixed population. The above results provide a theoretical basis and genetic resources for the precise identification and breeding of lily germplasm resources.
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Affiliation(s)
- Jiaqi Han
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixia Jia
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Chu Xu
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijie Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenlong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Merkulov P, Serganova M, Petrov G, Mityukov V, Kirov I. Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions. BMC Genomics 2024; 25:404. [PMID: 38658857 PMCID: PMC11044480 DOI: 10.1186/s12864-024-10314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Interspecific hybridization, a widely employed technique in tomato breeding, results in the creation of novel combinations of TEs from distinct species. The implications of this process for TE transposition activity have not been studied in modern cultivars. In this study, we used nanopore sequencing of extrachromosomal circular DNA (eccDNA) and identified two highly active Ty1/Copia LTR retrotransposon families of tomato (Solanum lycopersicum), called Salsa and Ketchup. Elements of these families produce thousands of eccDNAs under controlled conditions and epigenetic stress. EccDNA sequence analysis revealed that the major parts of eccDNA produced by Ketchup and Salsa exhibited low similarity to the S. lycopersicum genomic sequence. To trace the origin of these TEs, whole-genome nanopore sequencing and de novo genome assembly were performed. We found that these TEs occurred in a tomato breeding line via interspecific introgression from S. peruvianum. Our findings collectively show that interspecific introgressions can contribute to both genetic and phenotypic diversity not only by introducing novel genetic variants, but also by importing active transposable elements from other species.
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Affiliation(s)
- Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Melania Serganova
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Georgy Petrov
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Vladislav Mityukov
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051, Moscow, Russia
| | - Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia.
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia.
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20
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Dong Q, Zhang Y, Zhong S, Zhang Q, Yang H, Yang H, Yi X, Tan F, Chen C, Luo P. Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China. BMC Ecol Evol 2024; 24:52. [PMID: 38654171 DOI: 10.1186/s12862-024-02243-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions. RESULTS Sixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution. CONCLUSIONS Our results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.
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Affiliation(s)
- Qing Dong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongle Zhang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiuyi Zhang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaoxiao Yi
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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21
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Healey AL, Garsmeur O, Lovell JT, Shengquiang S, Sreedasyam A, Jenkins J, Plott CB, Piperidis N, Pompidor N, Llaca V, Metcalfe CJ, Doležel J, Cápal P, Carlson JW, Hoarau JY, Hervouet C, Zini C, Dievart A, Lipzen A, Williams M, Boston LB, Webber J, Keymanesh K, Tejomurthula S, Rajasekar S, Suchecki R, Furtado A, May G, Parakkal P, Simmons BA, Barry K, Henry RJ, Grimwood J, Aitken KS, Schmutz J, D'Hont A. The complex polyploid genome architecture of sugarcane. Nature 2024; 628:804-810. [PMID: 38538783 PMCID: PMC11041754 DOI: 10.1038/s41586-024-07231-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
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Affiliation(s)
- A L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - O Garsmeur
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - J T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Shengquiang
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - C B Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - N Piperidis
- Sugar Research Australia, Te Kowai, Queensland, Australia
| | - N Pompidor
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - V Llaca
- Corteva Agriscience, Johnston, IA, USA
| | - C J Metcalfe
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - P Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - J W Carlson
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Y Hoarau
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- ERCANE, Sainte-Clotilde, La Réunion, France
| | - C Hervouet
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Zini
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Dievart
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - L B Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Tejomurthula
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Rajasekar
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
| | - R Suchecki
- CSIRO Agriculture and Food, Urrbrae, South Australia, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - G May
- Corteva Agriscience, Johnston, IA, USA
| | | | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - K Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, Queensland, Australia
| | - J Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K S Aitken
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - A D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, France.
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
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22
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Liu J, Zhong X. Population epigenetics: DNA methylation in the plant omics era. Plant Physiol 2024; 194:2039-2048. [PMID: 38366882 PMCID: PMC10980424 DOI: 10.1093/plphys/kiae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
DNA methylation plays an important role in many biological processes. The mechanisms underlying the establishment and maintenance of DNA methylation are well understood thanks to decades of research using DNA methylation mutants, primarily in Arabidopsis (Arabidopsis thaliana) accession Col-0. Recent genome-wide association studies (GWASs) using the methylomes of natural accessions have uncovered a complex and distinct genetic basis of variation in DNA methylation at the population level. Sequencing following bisulfite treatment has served as an excellent method for quantifying DNA methylation. Unlike studies focusing on specific accessions with reference genomes, population-scale methylome research often requires an additional round of sequencing beyond obtaining genome assemblies or genetic variations from whole-genome sequencing data, which can be cost prohibitive. Here, we provide an overview of recently developed bisulfite-free methods for quantifying methylation and cost-effective approaches for the simultaneous detection of genetic and epigenetic information. We also discuss the plasticity of DNA methylation in a specific Arabidopsis accession, the contribution of DNA methylation to plant adaptation, and the genetic determinants of variation in DNA methylation in natural populations. The recently developed technology and knowledge will greatly benefit future studies in population epigenomes.
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Affiliation(s)
- Jie Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xuehua Zhong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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23
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Silva GS, Souza MM, Pamponét VDCC, Micheli F, de Melo CAF, de Oliveira SG, Costa EA. Cytogenomic Characterization of Transposable Elements and Satellite DNA in Passiflora L. Species. Genes (Basel) 2024; 15:418. [PMID: 38674353 PMCID: PMC11049143 DOI: 10.3390/genes15040418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The species Passiflora alata, P. cincinnata, and P. edulis have great economic value due to the use of their fruits for human consumption. In this study, we compared the repetitive genome fractions of these three species. The compositions of the repetitive DNA of these three species' genomes were analyzed using clustering and identification of the repetitive sequences with RepeatExplorer. It was found that repetitive DNA content represents 74.70%, 66.86%, and 62.24% of the genome of P. alata, P. edulis, and P. cincinnata, respectively. LTR Ty3/Gypsy retrotransposons represent the highest genome proportions in P. alata and P. edulis, while Ty1/Copia comprises the largest proportion of P. cincinnata genome. Chromosomal mapping by Fluorescent In Situ Hybridization (FISH) showed that LTR retrotransposons have a dispersed distribution along chromosomes. The subtelomeric region of chromosomes is where 145 bp satellite DNA is located, suggesting that these elements may play important roles in genome structure and organization in these species. In this work, we obtained the first global characterization of the composition of repetitive DNA in Passiflora, showing that an increase in genome size is related to an increase in repetitive DNA, which represents an important evolutionary route for these species.
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Affiliation(s)
- Gonçalo Santos Silva
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Margarete Magalhães Souza
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Vanessa de Carvalho Cayres Pamponét
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Fabienne Micheli
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Cláusio Antônio Ferreira de Melo
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Sárah Gomes de Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 01049-010, SP, Brazil;
| | - Eduardo Almeida Costa
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
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24
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Zwonitzer KD, Tressel LG, Wu Z, Kan S, Broz AK, Mower JP, Ruhlman TA, Jansen RK, Sloan DB, Havird JC. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proc Natl Acad Sci U S A 2024; 121:e2317240121. [PMID: 38427600 DOI: 10.1073/pnas.2317240121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024] Open
Abstract
Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, in some exceptional angiosperm clades, mtDNA substitution rates have increased up to 5,000-fold compared with closely related lineages. The mechanisms responsible for this acceleration are generally unknown. Because plants rely on homologous recombination to repair mtDNA damage, we hypothesized that mtDNA copy numbers may predict evolutionary rates, as lower copy numbers may provide fewer templates for such repair mechanisms. In support of this hypothesis, we found that copy number explains 47% of the variation in synonymous substitution rates of mtDNA across 60 diverse seed plant species representing ~300 million years of evolution. Copy number was also negatively correlated with mitogenome size, which may be a cause or consequence of mutation rate variation. Both relationships were unique to mtDNA and not observed in plastid DNA. These results suggest that homologous recombinational repair plays a role in driving mtDNA substitution rates in plants and may explain variation in mtDNA evolution more broadly across eukaryotes. Our findings also contribute to broader questions about the relationships between mutation rates, genome size, selection efficiency, and the drift-barrier hypothesis.
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Affiliation(s)
- Kendra D Zwonitzer
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Lydia G Tressel
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Marine College, Shandong University, Weihai 264209, China
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Tracey A Ruhlman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
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25
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Wahyuni DK, Indriati DT, Ilham M, Murtadlo AAA, Purnobasuki H, Junairiah, Purnama PR, Ikram NKK, Samian MZ, Subramaniam S. Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L. BRAZ J BIOL 2024; 84:e278393. [PMID: 38422290 DOI: 10.1590/1519-6984.278393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/06/2024] [Indexed: 03/02/2024] Open
Abstract
Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.
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Affiliation(s)
- D K Wahyuni
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - D T Indriati
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - M Ilham
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - A A A Murtadlo
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - H Purnobasuki
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - Junairiah
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - P R Purnama
- Chulalongkorn University, Faculty of Science, Graduate Program in Bioinformatics and Computational Biology, Bangkok, Thailand
| | - N K K Ikram
- Universiti Malaya, Faculty of Science, Institute of Biological Sciences, Kuala Lumpur, Malaysia
- Universiti Malaya, Centre for Research in Biotechnology for Agriculture - CEBAR, Kuala Lumpur, Malaysia
| | - M Z Samian
- Universiti Malaya, Faculty of Science, Institute of Biological Sciences, Kuala Lumpur, Malaysia
- Universiti Malaya, Centre for Research in Biotechnology for Agriculture - CEBAR, Kuala Lumpur, Malaysia
| | - S Subramaniam
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
- Universiti Sains Malaysia, School of Biological Science, Georgetown, Malaysia
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26
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Liang M, Huai B, Lin J, Liang X, He H, Bai M, Wu H. Ca2+- and Zn2+-dependent nucleases co-participate in nuclear DNA degradation during programmed cell death in secretory cavity development in Citrus fruits. Tree Physiol 2024; 44:tpad122. [PMID: 37738622 DOI: 10.1093/treephys/tpad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Calcium (Ca2+)- and zinc Zn2+-dependent nucleases play pivotal roles in plant nuclear DNA degradation in programmed cell death (PCD). However, the mechanisms by which these two nucleases co-participate in PCD-associated nuclear DNA degradation remain unclear. Here, the spatiotemporal expression patterns of two nucleases (CrCAN and CrENDO1) were analyzed qualitatively and quantitatively during PCD in secretory cavity formation in Citrus reticulata 'Chachi' fruits. Results show that the middle and late initial cell stages and lumen-forming stages are key stages for nuclear degradation during the secretory cavity development. CAN and ENDO1 exhibited potent in vitro DNA degradation activity at pH 8.0 and pH 5.5, respectively. Quantitative real-time reverse-transcription polymerase chain reaction, in situ hybridization assays, the subcellular localization of Ca2+ and Zn2+, and immunocytochemical localization showed that CrCAN was activated at the middle and late initial cell stages, while CrENDO1 was activated at the late initial cell and lumen-forming stages. Furthermore, we used immunocytochemical double-labelling to simultaneously locate CrCAN and CrENDO1. The DNA degradation activity of the two nucleases was verified by simulating the change of intracellular pH in vitro. Our results also showed that CrCAN and CrENDO1 worked respectively and co-participated in nuclear DNA degradation during PCD of secretory cavity cells. In conclusion, we propose the model for the synergistic effect of Ca2+- and Zn2+-dependent nucleases (CrCAN and CrENDO1) in co-participating in nuclear DNA degradation during secretory cavity cell PCD in Citrus fruits. Our findings provide direct experimental evidence for exploring different ion-dependent nucleases involved in nuclear degradation during plant PCD.
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Affiliation(s)
- Minjian Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Wushan Road, Guangzhou 510642, China
- College of Biology and Food Engineering, Guangdong University of Education, Guangzhou 510303, China
| | - Bin Huai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Wushan Road, Guangzhou 510642, China
| | - Junjun Lin
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Wushan Road, Guangzhou 510642, China
| | - Xiangxiu Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Wushan Road, Guangzhou 510642, China
| | - Hanjun He
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Wushan Road, Guangzhou 510642, China
- Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Natural Medicine, South China Agricultural University, Wushan Road, Guangzhou 510642, China
| | - Mei Bai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Wushan Road, Guangzhou 510642, China
- Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Natural Medicine, South China Agricultural University, Wushan Road, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Wushan Road, Guangzhou 510642, China
| | - Hong Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Wushan Road, Guangzhou 510642, China
- Guangdong Technology Research Center for Traditional Chinese Veterinary Medicine and Natural Medicine, South China Agricultural University, Wushan Road, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Wushan Road, Guangzhou 510642, China
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27
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Liu ZW, Zhou J. DNA barcoding of Notopterygii Rhizoma et Radix (Qiang-huo) and identification of adulteration in its medicinal services. Sci Rep 2024; 14:2879. [PMID: 38311607 PMCID: PMC10838912 DOI: 10.1038/s41598-024-53008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/25/2024] [Indexed: 02/06/2024] Open
Abstract
Safety concerns, stemming from the presence of complex and unpredictable adulterants, permeate the entire industrial chain of traditional Chinese medicines (TCMs). The Notopterygii Rhizoma et Radix (NReR) from the Apiaceae family, commonly known as "Qiang-huo", is a widely used herbal medicine. The recent surge in its demand has given rise to a proliferation of counterfeit and substituted products in the market. Traditional identification presents inherent limitations, while DNA mini-barcoding, reliant on sequencing a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In this study, we constructed a comprehensive Internal Transcribed Spacer 2 (ITS2) matrix encompassing genuine NReR and their commonly found adulterants for the first time. Leveraging this matrix, we conducted a thorough assessment of the genetic profiles and sources of NReR available in the Chinese herbal medicine market. Following established DNA barcoding protocols, the intra-specific genetic divergences within NReR species were found to be lower than the inter-specific genetic divergences from other species. Among the 120 samples that were successfully amplified, ITS2 exhibits an outstanding species-level identification efficiency of 100% when evaluated using both the BLASTN and neighbor-joining (NJ) tree methods. We concluded that ITS2 is a mini-barcode that has shown its potential and may become a universal mini-barcode for the quality control of "Qiang-huo", thereby ensuring the safety of clinical medication.
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Affiliation(s)
- Zhen-Wen Liu
- Yunnan Key Laboratory of Biodiversity of Gaoligong Mountain, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
- Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province, Kunming, 650201, China
| | - Jing Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China.
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Paschalidis K, Fanourakis D, Tsaniklidis G, Tsichlas I, Tzanakakis VA, Bilias F, Samara E, Ipsilantis I, Grigoriadou K, Samartza I, Matsi T, Tsoktouridis G, Krigas N. DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value. Int J Mol Sci 2024; 25:1891. [PMID: 38339166 PMCID: PMC10856587 DOI: 10.3390/ijms25031891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.
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Affiliation(s)
- Konstantinos Paschalidis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Dimitrios Fanourakis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Georgios Tsaniklidis
- Hellenic Agricultural Organization (ELGO-DIMITRA), Institute of Olive Tree, Subtropical Crops and Viticulture, 73134 Chania, Greece;
| | - Ioannis Tsichlas
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Vasileios A. Tzanakakis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Fotis Bilias
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Eftihia Samara
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Ioannis Ipsilantis
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Katerina Grigoriadou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
| | - Ioulietta Samartza
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Georgios Tsoktouridis
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
- Theofrastos Fertilizers, Industrial Area of Korinthos, Irinis & Filias, Ikismos Arion, Examilia, 20100 Korinthos, Greece
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
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Weber S, Stothut M, Mahla L, Kripp A, Hirschler L, Lenz N, Junker A, Künzel S, Krehenwinkel H. Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant-arthropod interactions. Mol Ecol Resour 2024; 24:e13900. [PMID: 38010630 DOI: 10.1111/1755-0998.13900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant-derived eDNA analysis for large-scale biodiversity assessments that include information about community-level interactions.
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Affiliation(s)
- Sven Weber
- Department of Biogeography, Trier University, Trier, Germany
| | - Manuel Stothut
- Department of Biogeography, Trier University, Trier, Germany
| | - Lisa Mahla
- Department of Biogeography, Trier University, Trier, Germany
| | - Alanah Kripp
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau in der Pfalz, Germany
| | - Lena Hirschler
- Department of Biogeography, Trier University, Trier, Germany
| | - Nina Lenz
- Department of Biogeography, Trier University, Trier, Germany
| | - Anneke Junker
- Department of Biogeography, Trier University, Trier, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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Quaresma A, Ankenbrand MJ, Garcia CAY, Rufino J, Honrado M, Amaral J, Brodschneider R, Brusbardis V, Gratzer K, Hatjina F, Kilpinen O, Pietropaoli M, Roessink I, van der Steen J, Vejsnæs F, Pinto MA, Keller A. Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. Sci Data 2024; 11:129. [PMID: 38272945 PMCID: PMC10810873 DOI: 10.1038/s41597-024-02962-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.
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Affiliation(s)
- Andreia Quaresma
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, S/N, Edifício FC4, 4169-007, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Vila do Conde, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Vila do Conde, Portugal
| | - Markus J Ankenbrand
- Center for Computational and Theoretical Biology, Faculty of Biology, Julius-Maximilians-Universität Würzburg, Klara-Oppenheimer-Weg 32, 97074, Würzburg, Germany
| | - Carlos Ariel Yadró Garcia
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - José Rufino
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Research Centre in Digitalization and Intelligent Robotics (CeDRI), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Mónica Honrado
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Joana Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Robert Brodschneider
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Valters Brusbardis
- Latvian Beekeepers' Association (LBA), Rigas iela 22, LV-3004, Jelgava, Latvia
| | - Kristina Gratzer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Fani Hatjina
- Ellinikos Georgikos Organismos DIMITRA (ELGO- DIMITRA), Kourtidou 56-58, GR-11145, Athina, Greece
| | - Ole Kilpinen
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - Marco Pietropaoli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri" (IZSLT), Via Appia Nuova 1411, IT-00178, Roma, Italy
| | - Ivo Roessink
- Wageningen Environmental Research, WageningenUniversity&Research, Droevendaalsesteeg 3, 6700 AA, Wageningen, Netherlands
| | | | - Flemming Vejsnæs
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Alexander Keller
- Cellular and Organismic Interactions, Biocenter, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany.
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Marczuk-Rojas JP, Álamo-Sierra AM, Salmerón A, Alcayde A, Isanbaev V, Carretero-Paulet L. Spatial and temporal characterization of the rich fraction of plastid DNA present in the nuclear genome of Moringa oleifera reveals unanticipated complexity in NUPTs´ formation. BMC Genomics 2024; 25:60. [PMID: 38225585 PMCID: PMC10789010 DOI: 10.1186/s12864-024-09979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/06/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA. RESULTS Here, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms. CONCLUSIONS Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.
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Affiliation(s)
- Juan Pablo Marczuk-Rojas
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Angélica María Álamo-Sierra
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Antonio Salmerón
- Department of Mathematics, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Alfredo Alcayde
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Viktor Isanbaev
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Lorenzo Carretero-Paulet
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain.
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain.
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Whitley BS, Li Z, Jones L, de Vere N. Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants. Methods Mol Biol 2024; 2744:445-473. [PMID: 38683335 DOI: 10.1007/978-1-0716-3581-0_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.
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Affiliation(s)
- Brandon S Whitley
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Zhao Li
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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Krishnan S, Sasi S, Kodakkattumannil P, Al Senaani S, Lekshmi G, Kottackal M, Amiri KMA. Cationic and anionic detergent buffers in sequence yield high-quality genomic DNA from diverse plant species. Anal Biochem 2024; 684:115372. [PMID: 37940013 DOI: 10.1016/j.ab.2023.115372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Because of the heterogeneity among seedlings of outbreeding species, the use of seedling tissues as a source of DNA is unsuitable for the genomic characterization of elite germplasms. High-quality DNA, free of RNA, proteins, polysaccharides, secondary metabolites, and shearing, is mandatory for downstream molecular biology applications, especially for next-generation genome sequencing and pangenome analysis aiming to capture the complete genetic diversity within a species. The study aimed to accomplish an efficient protocol for the extraction of high-quality DNA suitable for diverse plant species/tissues. We describe a reliable, and consistent protocol suitable for the extraction of DNA from 42 difficult-to-extract plant species belonging to 33 angiosperm (monocot and dicot) families, including tissues such as seeds, roots, endosperm, and flower/fruit tissues. The protocol was first optimized for the outbreeding recalcitrant trees viz., Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera, which are rich in proteins, polysaccharides, and secondary metabolites, and the quality of the extracted DNA was confirmed by downstream applications. Nine procedures were attempted to extract high-quality, impurities-free DNA from these three plant species. Extraction of the ethanol-precipitated DNA from cetyltrimethylammonium bromide (CTAB) protocol using sodium dodecyl sulfate (SDS) buffer, i.e., the extraction using a cationic (CTAB) detergent followed by an anionic (SDS) detergent was the key for high yield and high purity (1.75-1.85 against A260/280 and an A260/230 ratio of >2) DNA. A vice versa extraction procedure, i.e., SDS buffer followed by CTAB buffer, and also CTAB buffer followed by CTAB, did not yield good-quality DNA. PCR (using different primers) and restriction endonuclease digestion of the DNA extracted from these three plants validated the protocol. The accomplishment of the genome of P. cineraria using the DNA extracted using the modified protocol confirmed its applicability to genomic studies. The optimized protocol successful in extracting high-quality DNA from diverse plant species/tissues extends its applicability and is useful for accomplishing genome sequences of elite germplasm of recalcitrant plant species with quality reads.
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Affiliation(s)
- Saranya Krishnan
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Preshobha Kodakkattumannil
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Salima Al Senaani
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Geetha Lekshmi
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates.
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, Affiliated with United Arab Emirates University, The Presidential Court, United Arab Emirates; Department of Biology, College of Science, United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates.
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Egi T, Takabatake R, Kishine M, Soga K, Yoshiba S, Shibata N, Kondo K, Takashima Y. [Comparison of DNA Extraction Methods for Processed Foods Containing Soybean or Maize]. Shokuhin Eiseigaku Zasshi 2024; 65:25-30. [PMID: 38658344 DOI: 10.3358/shokueishi.65.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Processed foods containing soybean or maize are subject to labeling regulations pertinent to genetically modified (GM) foods in Japan. To confirm the reliability of the labeling procedure of GM foods, the Japanese standard analytical methods (standard methods) using real-time PCR technique have been established. Although certain DNA extraction protocols are stipulated as standard in these methods, the use of other protocols confirmed to be equivalent to the existing ones was permitted. In this study, the equivalence testing of the techniques employed for DNA extraction from processed foods containing soybean or corn was conducted. In this study, the equivalence testing of the techniques employed for DNA extraction from processed foods containing soybean or maize was conducted. The silica membrane-based DNA extraction kits, GM quicker 4 and DNeasy Plant Maxi Kit (Maxi Kit), as an existing method were compared. GM quicker 4 was considered to be equivalent to or better than Maxi Kit.
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Affiliation(s)
- Tomohiro Egi
- Food and Agricultural Materials Inspection Center
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35
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Pepenella S, Hackett J, Fernandez-Marco C, Petracca J, Marizzi C, Nash B, Micklos DA. A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding. Methods Mol Biol 2024; 2744:517-523. [PMID: 38683339 DOI: 10.1007/978-1-0716-3581-0_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
This rapid, equipment-free DNA isolation procedure using chromatography paper is a simple method that can be performed in less than 30 min and requires no wet lab experience. With minimal expense, it offers an affordable alternative for anyone wanting to explore biodiversity. It also provides an excellent option for use in classrooms or other activities that are time limited. The method works best for plants or lichens, producing stable DNA on Whatman® chromatography paper at room temperature, which can be eluted as needed.
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Affiliation(s)
- Sharon Pepenella
- Cold Spring Harbor Laboratory DNA Learning Center, Cold Spring Harbor, NY, USA
| | - Jennifer Hackett
- Cold Spring Harbor Laboratory DNA Learning Center, Cold Spring Harbor, NY, USA
| | | | - Jeffry Petracca
- Cold Spring Harbor Laboratory DNA Learning Center, Cold Spring Harbor, NY, USA
| | | | - Bruce Nash
- Cold Spring Harbor Laboratory DNA Learning Center, Cold Spring Harbor, NY, USA.
| | - David A Micklos
- Cold Spring Harbor Laboratory DNA Learning Center, Cold Spring Harbor, NY, USA
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Salava H, Deák T, Czepe C, Maghuly F. Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine. Methods Mol Biol 2024; 2787:183-197. [PMID: 38656490 DOI: 10.1007/978-1-0716-3778-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
PacBio long-read sequencing is a third-generation technology that generates long reads up to 20 kilobases (kb), unlike short-read sequencing instruments that produce up to 600 bases. Long-read sequencing is particularly advantageous in higher organisms, such as humans and plants, where repetitive regions in the genome are more abundant. The PacBio long-read sequencing uses a single molecule, real-time approach where the SMRT cells contain several zero-mode waveguides (ZMWs). Each ZMW contains a single DNA molecule bound by a DNA polymerase. All ZMWs are flushed with deoxy nucleotides with a fluorophore specific to each nucleotide. As the sequencing proceeds, the detector detects the wavelength of the fluorescence and the nucleotides are read in real-time. This chapter describes the sample and library preparation for PacBio long-read sequencing for grapevine.
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Affiliation(s)
- Hymavathi Salava
- Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Tamás Deák
- Institute of Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences (MATE), Budapest, Hungary
| | - Carmen Czepe
- Next Generation Sequencing Unit, Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Fatemeh Maghuly
- Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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Masoomi-Aladizgeh F, Jabbari L, Khayam Nekouei R, Aalami A, Atwell BJ, Haynes PA. A universal protocol for high-quality DNA and RNA isolation from diverse plant species. PLoS One 2023; 18:e0295852. [PMID: 38096235 PMCID: PMC10721051 DOI: 10.1371/journal.pone.0295852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Next-generation sequencing demands high-quality nucleic acid, yet isolating DNA and RNA is often challenging, particularly from plant tissues. Despite advances in developing various kits and reagents, these products are tailored to isolation of nucleic acid from model plant tissues. Here we introduce a universal lysis buffer to separate nucleic acid from various plant species, including recalcitrant plants, to facilitate molecular analyses, such as quantitative PCR (qPCR), transcriptomics, and whole-genome sequencing (WGS). The protocol is a modification of the original CTAB methods, which leads to nucleic acid isolation from many plant species, including monocots and eudicots. The lysis buffer consists of hexadecyltrimethylammonium bromide (CTAB), sodium chloride (NaCl), Tris base, ethylenediaminetetraacetic acid (EDTA) and β-mercaptoethanol (βME). The modified CTAB method enables the isolation of nucleic acid from small amounts of plant tissues (e.g., 15-100 mg) in a timely manner, which is well-suited for a large number of samples and also when adequate sample collection is a limiting factor. The protocol isolates not only DNA from various plant species but also RNA. This makes it highly effective for molecular analyses compared to previously described CTAB methods optimised for DNA isolation. The appropriate concentration of the components enables high-quality DNA and RNA isolation from plant tissues simultaneously. Additionally, this protocol is compatible with commercially available columns. For DNA and RNA to be qualified for next-generation sequencing platforms, the protocol is supplemented with columns to purify either DNA or RNA from the same tissue to meet high standards for sequencing analyses. This protocol provides an ideal approach to overcome potential obstacles in isolating high-quality DNA or RNA from a wide range of plant species for downstream molecular analysis.
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Affiliation(s)
| | - Leila Jabbari
- Department of Tissue Culture and Gene Transformation, Agricultural Biotechnology Research Institute of Iran (ABRII), AREEO, Karaj, Iran
| | - Reza Khayam Nekouei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Ali Aalami
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Brian J. Atwell
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Paul A. Haynes
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
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Karakas E, Ferrante P, Schafleitner R, Giuliano G, Fernie AR, Alseekh S. Plant Sample Collection and Shipment for Multi-omic Analyses and Phytosanitary Evaluation. Curr Protoc 2023; 3:e952. [PMID: 38131272 DOI: 10.1002/cpz1.952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Plant sample preparation for analyses is a fundamental step in high-throughput omics strategies. Especially for plant metabolomics, quenching of hydrolytic enzymes able to affect metabolite concentrations is crucial for the accuracy of results. Given that DNA is usually less labile than metabolites, most sampling and shipment procedures able to preserve the metabolome are also suitable for preventing the degradation of plant DNA or of DNA of pathogens in the plant tissue. In this article, we describe all the steps of sample collection, shipment (including the phytosanitary issues of moving plant samples), and processing for combined genomics and metabolomics from a single sample, as well as the protocols used in our laboratories for downstream approaches for crop plants, allowing collection of multi-omic datasets in large experimental setups. The protocols have been adjusted to apply to both freeze-dried and fresh-frozen material to allow the processing of crop plant samples that will require long-distance transport. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of freeze-dried leaf disks for multiplexed PCR or DArT-Seq genotyping Basic Protocol 2: Medium-throughput preparation of pathogen-free nucleic acids for most genotyping-resequencing applications or pathogen detection Alternate Protocol: Low-throughput extraction of high-quality DNA for resequencing using commercial kits Support Protocol: DNA quality control Basic Protocol 3: Preparation of freeze-dried plant material for metabolomics Basic Protocol 4: Preparation of fresh-frozen plant material for metabolomics Basic Protocol 5: Preparation and shipment of metabolite extracts for metabolomic analyses Basic Protocol 6: Sample shipping and long-term storage.
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Affiliation(s)
- Esra Karakas
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Paola Ferrante
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, Rome, Italy
| | | | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, Rome, Italy
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Institute of Plants Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Institute of Plants Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Schweikle S, Häser A, Wetters S, Raisin M, Greiner M, Rigbers K, Fischer U, Pietsch K, Suntz M, Nick P. DNA barcoding as new diagnostic tool to lethal plant poisoning in herbivorous mammals. PLoS One 2023; 18:e0292275. [PMID: 37967132 PMCID: PMC10650979 DOI: 10.1371/journal.pone.0292275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/17/2023] [Indexed: 11/17/2023] Open
Abstract
Reliable identification of plant species in the digestive tract of a deceased animal often represents the major key to diagnose a lethal intoxication with poisonous plants in veterinary pathology. In many cases, identification of the species is challenging or even impossible because the diagnostic morphological features have been degraded, and because the interpretation of such features requires a considerable expertise in plant anatomy and biodiversity. The use of DNA barcoding markers can support or even replace classical morphological assessment. While these markers have been widely used for plant taxonomy, their forensic application to clarify causes of animal poisoning is novel. In addition, we use specific single-nucleotide polymorphisms as fingerprints. This allows for a clear decision even in cases, where the conventionally used statistical e-values remain ambiguous. In the current work, we explore the feasibility of this strategy in a couple of exemplary cases, either in concert with anatomical diagnostics, or in cases where visual species identification is not possible, or where chemical toxin detection methods are not well established, complex, time consuming and expensive.
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Affiliation(s)
- Sandra Schweikle
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
- State Institute for Chemical and Veterinary Analysis Karlsruhe, Karlsruhe, Germany
| | - Annette Häser
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sascha Wetters
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Moses Raisin
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Maica Greiner
- State Institute for Chemical and Veterinary Analysis Freiburg, Freiburg im Breisgau, Germany
| | - Kerstin Rigbers
- State Institute for Chemical and Veterinary Analysis Karlsruhe, Karlsruhe, Germany
| | - Ulrike Fischer
- State Institute for Chemical and Veterinary Analysis Freiburg, Freiburg im Breisgau, Germany
| | - Klaus Pietsch
- State Institute for Chemical and Veterinary Analysis Freiburg, Freiburg im Breisgau, Germany
| | - Michael Suntz
- State Institute for Chemical and Veterinary Analysis Freiburg, Freiburg im Breisgau, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Wang W, Chen B, Ma R, Qiao M, Fu Y. The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain. BMC Plant Biol 2023; 23:546. [PMID: 37936056 PMCID: PMC10629101 DOI: 10.1186/s12870-023-04513-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method. RESULTS Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades. CONCLUSIONS The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis.
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Affiliation(s)
- Weijie Wang
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Baixu Chen
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Ruoke Ma
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Mengji Qiao
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China.
| | - Yunlin Fu
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China.
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Ferraz ME, Ribeiro T, Sader M, Nascimento T, Pedrosa-Harand A. Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans. Chromosome Res 2023; 31:30. [PMID: 37812264 DOI: 10.1007/s10577-023-09739-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species present relatively stable karyotypes with 2n = 22 chromosomes, the karyotypes of species of the Leptostachyus group show high rates of structural rearrangements, including a nested chromosome fusion that led to the dysploid chromosome number of the group (2n = 20). We examined the roles of repetitive landscapes in the rearrangements of species of the Leptostachyus group using genome-skimming data to characterize the repeatome in a range of Phaseolus species and compared them to species of that group (P. leptostachyus and P. macvaughii). LTR retrotransposons, especially the Ty3/gypsy lineage Chromovirus, were the most abundant elements in the genomes. Differences in the abundance of Tekay, Retand, and SIRE elements between P. macvaughii and P. leptostachyus were reflected in their total amounts of Ty3/gypsy and Ty1/copia. The satellite DNA fraction was the most divergent among the species, varying both in abundance and distribution, even between P. leptostachyus and P. macvaughii. The rapid turnover of repeats in the Leptostachyus group may be associated with the several rearrangements observed.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Tiago Ribeiro
- Integrative Plant Research Lab, Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Mariela Sader
- Multidisciplinary Institute of Plant Biology, National Council for Scientific and Technical Research, National University of Córdoba, Córdoba, Argentina
| | - Thiago Nascimento
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil.
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Islam MS, Chekhovskiy K, Saha MC. Dig up tall fescue plastid genomes for the identification of morphotype-specific DNA variants. BMC Genomics 2023; 24:586. [PMID: 37789301 PMCID: PMC10546690 DOI: 10.1186/s12864-023-09631-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species. Hexaploid tall fescue has three distinct morphotypes used either as forage or turf purposes. Its chloroplast genome is conserved due to it being maternally inherited to the next generation progenies. To identify morphotype-specific DNA markers and the genetic variations, plastid genomes of all three tall fescue morphotypes, i.e., Continental cv. Texoma MaxQ II, Rhizomatous cv. Torpedo, and Mediterranean cv. Resolute, have been sequenced using Illumina MiSeq sequencing platform. RESULTS The plastid genomes of Continental-, Rhizomatous-, and Mediterranean tall fescue were assembled into circular master molecules of 135,283 bp, 135,336 bp, and 135,324 bp, respectively. The tall fescue plastid genome of all morphotypes contained 77 protein-coding, 20 tRNAs, four rRNAs, two pseudo protein-coding, and three hypothetical protein-coding genes. We identified 630 SNPs and 124 InDels between Continental and Mediterranean, 62 SNPs and 20 InDels between Continental and Rhizomatous, and 635 SNPs and 123 InDels between Rhizomatous and Mediterranean tall fescue. Only four InDels in four genes (ccsA, rps18, accD, and ndhH-p) were identified, which discriminated Continental and Rhizomatous plastid genomes from the Mediterranean plastid genome. Here, we identified and reported eight InDel markers (NRITCHL18, NRITCHL35, NRITCHL43, NRITCHL65, NRITCHL72, NRITCHL101, NRITCHL104, and NRITCHL110) from the intergenic regions that can successfully discriminate tall fescue morphotypes. Divergence time estimation revealed that Mediterranean tall fescue evolved approximately 7.09 Mya, whereas the divergence between Continental- and Rhizomatous tall fescue occurred about 0.6 Mya. CONCLUSIONS To our knowledge, this is the first report of the assembled plastid genomes of Rhizomatous and Mediterranean tall fescue. Our results will help to identify tall fescue morphotypes at the time of pre-breeding and will contribute to the development of lawn and forage types of commercial varieties.
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Affiliation(s)
- Md Shofiqul Islam
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
- Genetics Laboratory, Indiana Crop Improvement Association, 7700 Stockwell Road, Lafayette, IN, 47909, USA.
- Department of Agronomy, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47906, USA.
| | - Konstantin Chekhovskiy
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Malay C Saha
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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Neelakandan AK, Kabahuma M, Yang Q, Lopez M, Wisser RJ, Balint-Kurti P, Lauter N. Characterization of integration sites and transfer DNA structures in Agrobacterium-mediated transgenic events of maize inbred B104. G3 (Bethesda) 2023; 13:jkad166. [PMID: 37523773 PMCID: PMC10542558 DOI: 10.1093/g3journal/jkad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error-prone repair pathways of nonhomologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize with respect to insertion site features, the genomic distribution of T-DNA incorporation, and the mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique, which can be adapted to any species of interest.
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Affiliation(s)
| | - Mercy Kabahuma
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdisciplinary Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Qin Yang
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Miriam Lopez
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Randall J Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L’Institut Agro, Montpellier 34000, France
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Plant Science Research Unit, USDA-ARS, Raleigh, NC 27695, USA
| | - Nick Lauter
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdisciplinary Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
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Grin IR, Petrova DV, Endutkin AV, Ma C, Yu B, Li H, Zharkov DO. Base Excision DNA Repair in Plants: Arabidopsis and Beyond. Int J Mol Sci 2023; 24:14746. [PMID: 37834194 PMCID: PMC10573277 DOI: 10.3390/ijms241914746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.
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Affiliation(s)
- Inga R. Grin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Daria V. Petrova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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Ito Y, Tanaka N. Phylogeny of Alisma (Alismataceae) revisited: implications for polyploid evolution and species delimitation. J Plant Res 2023; 136:613-629. [PMID: 37402089 DOI: 10.1007/s10265-023-01477-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
Alisma L. is a genus of aquatic and wetland plants belonging to family Alismataceae. At present, it is thought to contain ten species. Variation in ploidy level is known in the genus, with diploids, tetraploids and hexaploids recorded. Previous molecular phylogenetic studies of Alisma have generated a robust backbone that reveals important aspects of the evolutionary history of this cosmopolitan genus, yet questions remain unresolved about the formation of the polyploid taxa and the taxonomy of one particularly challenging, widely distributed species complex. Here we directly sequenced, or cloned and sequenced, nuclear DNA (nrITS and phyA) and chloroplast DNA (matK, ndhF, psbA-trnH and rbcL) of multiple samples of six putative species and two varieties, and conducted molecular phylogenetic analyses. Alisma canaliculatum and its two varieties known in East Asia and A. rariflorum endemic to Japan possess closely related but heterogeneous genomes, strongly indicating that the two species were generated from two diploid progenitors, and are possibly siblings of one another. This evolutionary event may have occurred in Japan. Alisma canaliculatum var. canaliculatum is segregated into two types, each of which are geographically slightly differentiated in Japan. We reconstructed a single phylogeny based on the multi-locus data using Homologizer and then applied species delimitation analysis (STACEY). This allowed us to discern A. orientale as apparently endemic to the Southeast Asian Massif and distinct from the widespread A. plantago-aquatica. The former species was most likely formed through parapatric speciation at the southern edge of the distribution of the latter.
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Affiliation(s)
- Yu Ito
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-Cho, Hirakata, Osaka, 573-0101, Japan.
| | - Norio Tanaka
- Department of Botany, National Museum of Nature and Science, Tsukuba, 305-0005, Japan
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Chen Q, Liu M, Xu C, Bai J, Feng H, Chen C, Zhao L, Liu Y, Zhou S, Zhao D. Potential of plant DNA information in determining the provenance and identify of unknown victims. Forensic Sci Int 2023; 350:111786. [PMID: 37481907 DOI: 10.1016/j.forsciint.2023.111786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 07/15/2023] [Indexed: 07/25/2023]
Abstract
Determination of the personal identity of victims is particularly important for the settlement of criminal cases. Unfortunately, useful information for identification is not always available. We here propose that the particles (pollens) of some plants with specific geographical distributions extracted from human lung tissues contribute to further determining the provenance or long-term residence of unknown victims, thereby considerably narrowing the search scope of the victims. We collected lung tissues from 155 victims with diverse causes of death, extracted DNA from lung tissues, sequenced the DNA fragments of plants on the Illumina Hiseq platform, and barcoded the plant species using phylogenetic methods. Finally, 108 unique plant sequences were detected in 55 samples and identified to belong to 36 species in 32 genera of 29 families. These plants were predominantly insect-pollinated crops and ornamental plants. No significant difference was observed between male and female samples, between urban and rural samples, or among samples of different ages and different sample sizes. There were 16 samples with 21 wild plant species. The original sources of 15 samples were overlapped with the distribution regions of detected plants; 2 samples narrowed the original sources to 2 provinces, which were quite coincident with their source places; 1 sample had no overlapping with its victim source region. Although plant information was only found in one-third of the samples, we further demonstrated the great potential of plant eDNA in identifying the source of unnamed corpses in a real-world case. We used plant eDNA from lung tissues to explore the provenance of an unknown female corpse found in Beijing. The source place of this victim was narrowed to Guangdong and Guangxi provinces, and finally, we confirmed her true identity in the list of missing persons in Guangxi Province. In the presence of a well-covered local reference library, the plant species detected in the lungs can be accurately identified. In difficult criminal cases where physical evidence is relatively weak, plant DNA information may provide new clues. In conclusion, the plant particles trapped in the lungs are promising to help forensic experts narrow the search scope for the identity of unknown victims.
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Affiliation(s)
- Qing Chen
- China University of Political Science and Law, Beijing 100091, China; Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Mengyan Liu
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jie Bai
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Hua Feng
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Changcan Chen
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Liang Zhao
- ShanXi Medical University, Jinzhong 030001, China
| | - Yanlei Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Dong Zhao
- Key Laboratory of Evidence Science, CUPL, Ministry of Education, Beijing 100088, China.
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Petrone BL, Aqeel A, Jiang S, Durand HK, Dallow EP, McCann JR, Dressman HK, Hu Z, Tenekjian CB, Yancy WS, Lin PH, Scialla JJ, Seed PC, Rawls JF, Armstrong SC, Stevens J, David LA. Diversity of plant DNA in stool is linked to dietary quality, age, and household income. Proc Natl Acad Sci U S A 2023; 120:e2304441120. [PMID: 37368926 PMCID: PMC10319039 DOI: 10.1073/pnas.2304441120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/10/2023] [Indexed: 06/29/2023] Open
Abstract
Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number of plant taxa per sample (plant metabarcoding richness or pMR) correlated with recorded intakes in interventional diets and with indices calculated from a food frequency questionnaire in typical diets (ρ = 0.40 to 0.63). In adolescents unable to collect validated dietary survey data, trnL metabarcoding detected 111 plant taxa, with 86 consumed by more than one individual and four (wheat, chocolate, corn, and potato family) consumed by >70% of individuals. Adolescent pMR was associated with age and household income, replicating prior epidemiologic findings. Overall, trnL metabarcoding promises an objective and accurate measure of the number and types of plants consumed that is applicable to diverse human populations.
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Affiliation(s)
- Brianna L. Petrone
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC27710
| | - Ammara Aqeel
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Heather K. Durand
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Eric P. Dallow
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
| | - Holly K. Dressman
- Duke Microbiome Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC27710
| | - Zhengzheng Hu
- Duke Microbiome Core Facility, Center for Genomic and Computational Biology, Duke University, Durham, NC27710
| | | | - William S. Yancy
- Duke Lifestyle and Weight Management Center, Durham, NC27710
- Department of Medicine, Duke University School of Medicine, Durham, NC27710
| | - Pao-Hwa Lin
- Department of Medicine, Nephrology Division, Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC27705
| | - Julia J. Scialla
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA22903
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA22903
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL60611
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC27710
| | - Sarah C. Armstrong
- Department of Pediatrics, Duke University School of Medicine, Durham, NC27710
| | - June Stevens
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Lawrence A. David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC27710
- Duke Microbiome Center, Duke University School of Medicine, Durham, NC27710
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Safhi FA, Alshamrani SM, Bogmaza AFM, El-Moneim DA. DNA Barcoding of Wild Plants with Potential Medicinal Properties from Faifa Mountains in Saudi Arabia. Genes (Basel) 2023; 14:469. [PMID: 36833396 PMCID: PMC9957057 DOI: 10.3390/genes14020469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/21/2022] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Wild medicinal plants are the main source of active ingredients and provide a continuous natural source for many folk medicinal products, a role that is important for society's health with an impressive record of utilization. Thus, surveying, conserving, and precisely identifying wild medicinal plants is required. The current study aimed to precisely identify fourteen wild-sourced medicinal plants from southwest Saudi Arabia, within the Fifa mountains area located in Jazan province, using the DNA barcoding technique. Two DNA regions (nuclear ITS and chloroplast rbcL) were sequenced and analyzed for the collected species using BLAST-based and phylogeny-based identification methods. Based on our analysis, ten of the fourteen species were successfully identified by DNA barcoding, five were identified as morphologically inspected, and three were morphologically indifferent. The study was able to distinguish some key medicinal species and highlight the importance of combining morphological observation with DNA barcoding to ensure the precise identification of wild plants, especially if they are medicinally relevant and associated with public health and safety usage.
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Affiliation(s)
- Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | | | | | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
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Rodríguez-González R, Gutiérrez ML, Fuentes I, Gálvez-Prada F, Sochorová J, Kovařík A, Garcia S. Release 4.0 of the Plant rDNA Database: A Database on Plant Ribosomal DNA Loci Number, Their Position, and Organization: An Information Source for Comparative Cytogenetics. Methods Mol Biol 2023; 2703:237-245. [PMID: 37646950 DOI: 10.1007/978-1-0716-3389-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
This paper presents the latest update to the Plant rDNA database (Release 4.0), a valuable resource for researchers in the field of plant cytogenetics. The database provides information on the number, position, and arrangement of ribosomal DNA loci in plants, including angiosperms, gymnosperms, bryophytes, and pteridophytes. The new release includes new data for 820 species coming from additional 173 papers. In the updated version of the Plant rDNA database, 4948 entries comprising 2760 organisms can be found. A brief guide on how to navigate the database and obtain the desired information is also provided. The regular updating of the database is important for ensuring the information it contains is accurate, up-to-date, and useful for the research community. The Plant rDNA database continues to be beneficial for phylogenetic and cytogenetic studies in a wide range of taxa including angiosperms, gymnosperms, and early diverging groups, such as bryophytes and lycophytes.
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Affiliation(s)
- Roi Rodríguez-González
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - María Luisa Gutiérrez
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Inés Fuentes
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
- Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Catalonia, Spain
| | | | - Jana Sochorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
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50
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Wang Y, Yao X, Liu R, Liu C. DDQR (dynamic DNA QR coding): An efficient algorithm to represent DNA barcode sequences. PLoS One 2023; 18:e0279994. [PMID: 36649276 PMCID: PMC9844917 DOI: 10.1371/journal.pone.0279994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 12/19/2022] [Indexed: 01/18/2023] Open
Abstract
A DNA barcode is a short piece of standard DNA sequence used for species determination and discrimination. Representation of DNA barcodes is essential for DNA barcodes' applications in the transportation and recognition of biological materials. Previously, we have compared different strategies for representing the DNA barcodes. In the present study, we have developed a compression algorithm based on binary coding or Huffman coding scheme, followed by converting the binary digits into Base64 digits. The combination of this compression algorithm and the QR representation leads to the dynamic DNA QR coding algorithm (DDQR). We tested the DDQR algorithm on simulated data and real DNA barcode sequences from the commonly used plant and animal DNA barcode markers: rbcL, matK, trnH-psbA, ITS2, and COI. We compared the compression efficiency of DDQR and another state-of-the-art DNA compression algorithm GeCo3 for sequences with various base compositions and lengths. We found that DDQR had a higher compression rate than GeCo3 for DNA sequences shorter than 800 bp, which is the typical size range for DNA barcodes. We also upgraded a web server (http://www.1kmpg.cn/ddqr) that provides three functions: retrieval of DNA barcode sequences, encoding DNA barcode sequences to DDQR codes, and decoding DDQR codes to DNA barcode sequences. The DDQR algorithm and the webserver will be invaluable to applying DNA barcode technology in the food and traditional medicine industries.
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Affiliation(s)
- Yujun Wang
- School of Information Management, Central China Normal University, Wuhan, Hubei, P.R. China
| | - Xinjing Yao
- School of Information Management, Central China Normal University, Wuhan, Hubei, P.R. China
| | - Rui Liu
- School of Information Management, Central China Normal University, Wuhan, Hubei, P.R. China
- * E-mail: (RL); (CL)
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Beijing, P.R. China
- * E-mail: (RL); (CL)
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