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Islam MF, Yamatani H, Takami T, Kusaba M, Sakamoto W. Characterization of organelle DNA degradation mediated by DPD1 exonuclease in the rice genome-edited line. PLANT MOLECULAR BIOLOGY 2024; 114:71. [PMID: 38856917 PMCID: PMC11164812 DOI: 10.1007/s11103-024-01452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/05/2024] [Indexed: 06/11/2024]
Abstract
Mitochondria and plastids, originated as ancestral endosymbiotic bacteria, contain their own DNA sequences. These organelle DNAs (orgDNAs) are, despite the limited genetic information they contain, an indispensable part of the genetic systems but exist as multiple copies, making up a substantial amount of total cellular DNA. Given this abundance, orgDNA is known to undergo tissue-specific degradation in plants. Previous studies have shown that the exonuclease DPD1, conserved among seed plants, degrades orgDNAs during pollen maturation and leaf senescence in Arabidopsis. However, tissue-specific orgDNA degradation was shown to differ among species. To extend our knowledge, we characterized DPD1 in rice in this study. We created a genome-edited (GE) mutant in which OsDPD1 and OsDPD1-like were inactivated. Characterization of this GE plant demonstrated that DPD1 was involved in pollen orgDNA degradation, whereas it had no significant effect on orgDNA degradation during leaf senescence. Comparison of transcriptomes from wild-type and GE plants with different phosphate supply levels indicated that orgDNA had little impact on the phosphate starvation response, but instead had a global impact in plant growth. In fact, the GE plant showed lower fitness with reduced grain filling rate and grain weight in natural light conditions. Taken together, the presented data reinforce the important physiological roles of orgDNA degradation mediated by DPD1.
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Affiliation(s)
- Md Faridul Islam
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Hiroshi Yamatani
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233, Watanuki, Takasaki, Gunma, 370-1292, Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Makoto Kusaba
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-3 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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2
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Nair A, Harshith CY, Narjala A, Shivaprasad PV. Begomoviral βC1 orchestrates organellar genomic instability to augment viral infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:934-950. [PMID: 36919198 DOI: 10.1111/tpj.16186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 05/27/2023]
Abstract
Chloroplast is the site for transforming light energy to chemical energy. It also acts as a production unit for a variety of defense-related molecules. These defense moieties are necessary to mount a successful counter defense against pathogens, including viruses. Previous studies indicated disruption of chloroplast homeostasis as a basic strategy of Begomovirus for its successful infection leading to the production of vein-clearing, mosaic, and chlorotic symptoms in infected plants. Although begomoviral pathogenicity determinant protein Beta C1 (βC1) was implicated for pathogenicity, the underlying mechanism was unclear. Here we show that, begomoviral βC1 directly interferes with the host plastid homeostasis. βC1 induced DPD1, an organelle-specific nuclease, implicated in nutrient salvage and senescence, as well as modulated the function of a major plastid genome maintainer protein RecA1, to subvert plastid genome. We show that βC1 was able to physically interact with bacterial RecA and its plant homolog RecA1, resulting in its altered activity. We observed that knocking-down DPD1 during virus infection significantly reduced virus-induced necrosis. These results indicate the presence of a strategy in which a viral protein alters host defense by targeting modulators of chloroplast DNA. We predict that the mechanism identified here might have similarities in other plant-pathogen interactions.
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Affiliation(s)
- Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Chitthavalli Y Harshith
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India
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3
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Pandey A, Chaudhary S, Bhat B. The Potential Role of Plastome Copy Number as a Quality Biomarker for Plant Products using Real-time Quantitative Polymerase Chain Reaction. Curr Genomics 2022; 23:289-298. [PMID: 36777877 PMCID: PMC9875542 DOI: 10.2174/1389202923666220513111643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/28/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Plastids are plant-specific semi-autonomous self-replicating organelles, containing circular DNA molecules called plastomes. Plastids perform crucial functions, including photosynthesis, stress perception and response, synthesis of metabolites, and storage. The plastome and plastid numbers have been shown to be modulated by developmental stage and environmental stimuli and have been used as a biomarker (identification of plant species) and biosensor (an indicator of abiotic and biotic stresses). However, the determination of plastome sequence and plastid number is a laborious process requiring sophisticated equipment. Methods: This study proposes using plastome copy number (PCN), which can be determined rapidly by real-time quantitative polymerase chain reaction (RT-qPCR) as a plant product quality biomarker. This study shows that the PCN log10 and range PCN log10 values calculated from RT-qPCR data, which was obtained for two years from leaves and lint samples of cotton and seed samples of cotton, rice, soybean, maize, and sesame can be used for assessing the quality of the samples. Results: Observation of lower range PCN log10 values for CS (0.31) and CR (0.58) indicated that the PCN showed little variance from the mean PCN log10 values for CS (3.81) and CR (3.85), suggesting that these samples might have encountered ambient environmental conditions during growth and/ or post-harvest storage and processing. This conclusion was further supported by observation of higher range PCN log10 values for RS (3.09) versus RP (0.05), where rice seeds in the RP group had protective hull covering compared to broken hull-less seeds in the RS group. To further support that PCN is affected by external factors, rice seeds treated with high temperatures and pathogens exhibited lower PCN values when compared to untreated seeds. Furthermore, the range PCN log10 values were found to be high for cotton leaf (CL) and lint (Clt) sample groups, 4.11 and 3.63, respectively, where leaf and lint samples were of different sizes, indicating that leaf samples might be of different developmental stage and lint samples might have been processed differently, supporting that the PCN is affected by both internal and external factors, respectively. Moreover, PCN log10 values were found to be plant specific, with oil containing seeds such as SeS (6.49) and MS (5.05) exhibiting high PCN log10 values compared to non-oil seeds such as SS (1.96). Conclusion: In conclusion, it was observed that PCN log10 values calculated from RT-qPCR assays were specific to plant species and the range of PCN log10 values can be directly correlated to the internal and external factors and, therefore might be used as a potential biomarker for assessing the quality of plant products.
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Affiliation(s)
- Amita Pandey
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
| | - Shifa Chaudhary
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
| | - Binu Bhat
- 19 University Road, Shriram Institute for Industrial Research, Analytical Science Division - Biology, Molecular Biology Laboratory, New Delhi, India
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Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, Jansen RK, Ruhlman TA. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:861-875. [PMID: 34021942 DOI: 10.1111/tpj.15351] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study three non-papilioniods were included among 34 newly sequenced legume plastomes, along with 33 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, approximately 20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the IR has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in the progression of plastome change is discussed.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - In-Su Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal de Bahia (UFBA), Rua Barão de Jeremoabo, s.n., Ondina, Salvador, Bahia, 40170-115, Brazil
| | - Haroldo C de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, Rio de Janeiro, 915 22460-030, Brazil
| | - Luciano P de Queiroz
- Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana, Bahia, 44036-900, Brazil
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Center of Excellence for Bionanoscience Research, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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5
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Abstract
The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Robert K Jansen
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Raime K, Krjutškov K, Remm M. Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin. FRONTIERS IN PLANT SCIENCE 2020; 11:646. [PMID: 32528502 PMCID: PMC7253697 DOI: 10.3389/fpls.2020.00646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Fast and reliable analytical methods for the identification of plants from metagenomic samples play an important role in identifying the components of complex mixtures of processed biological materials, including food, herbal products, gut contents or environmental samples. Different PCR-based methods that are commonly used for plant identification from metagenomic samples are often inapplicable due to DNA degradation, a low level of successful amplification or a lack of detection power. We introduce a method that combines metagenomic sequencing and an alignment-free k-mer based approach for the identification of plant DNA in processed metagenomic samples. Our method identifies plant DNA directly from metagenomic sequencing reads and does not require mapping or assembly of the reads. We identified more than 31,000 Lupinus-specific 32-mers from assembled chloroplast genome sequences. We demonstrate that lupin DNA can be detected from controlled mixtures of sequences from target species (different Lupinus species) and closely related non-target species (Arachis hypogaea, Glycine max, Pisum sativum, Vicia faba, Phaseolus vulgaris, Lens culinaris, and Cicer arietinum). Moreover, these 32-mers are detectable in the following processed samples: lupin flour, conserved seeds and baked cookies containing different amounts of lupin flour. Under controlled conditions, lupin-specific components are detectable in baked cookies containing a minimum of 0.05% of lupin flour in wheat flour.
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Affiliation(s)
- Kairi Raime
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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7
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Greiner S, Golczyk H, Malinova I, Pellizzer T, Bock R, Börner T, Herrmann RG. Chloroplast nucleoids are highly dynamic in ploidy, number, and structure during angiosperm leaf development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:730-746. [PMID: 31856320 DOI: 10.1111/tpj.14658] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/20/2019] [Accepted: 12/10/2019] [Indexed: 05/19/2023]
Abstract
Chloroplast nucleoids are large, compact nucleoprotein structures containing multiple copies of the plastid genome. Studies on structural and quantitative changes of plastid DNA (ptDNA) during leaf development are scarce and have produced controversial data. We have systematically investigated nucleoid dynamics and ptDNA quantities in the mesophyll of Arabidopsis, tobacco, sugar beet, and maize from the early post-meristematic stage until necrosis. DNA of individual nucleoids was quantified by DAPI-based supersensitive epifluorescence microscopy. Nucleoids occurred in scattered, stacked, or ring-shaped arrangements and in recurring patterns during leaf development that was remarkably similar between the species studied. Nucleoids per organelle varied from a few in meristematic plastids to >30 in mature chloroplasts (corresponding to about 20-750 nucleoids per cell). Nucleoid ploidies ranged from haploid to >20-fold even within individual organelles, with average values between 2.6-fold and 6.7-fold and little changes during leaf development. DNA quantities per organelle increased gradually from about a dozen plastome copies in tiny plastids of apex cells to 70-130 copies in chloroplasts of about 7 μm diameter in mature mesophyll tissue, and from about 80 plastome copies in meristematic cells to 2600-3300 copies in mature diploid mesophyll cells without conspicuous decline during leaf development. Pulsed-field electrophoresis, restriction of high-molecular-weight DNA from chloroplasts and gerontoplasts, and CsCl equilibrium centrifugation of single-stranded and double-stranded ptDNA revealed no noticeable fragmentation of the organelle DNA during leaf development, implying that plastid genomes in mesophyll tissues are remarkably stable until senescence.
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Affiliation(s)
- Stephan Greiner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Hieronim Golczyk
- Department of Molecular Biology, Institute of Biotechnology, John Paul II Catholic University of Lublin, Konstantynów 1i, 20-708, Lublin, Poland
| | - Irina Malinova
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Tommaso Pellizzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Thomas Börner
- Institut für Biologie/Molekulare Genetik, Humboldt-Universität zu Berlin, Rhoda Erdmann Haus, Philippstr. 13, D-10115, Berlin, Germany
| | - Reinhold G Herrmann
- Department für Biologie I, Ludwig-Maximilians-Universität München, Bereich Botanik, Menzinger Str. 67, D-80638, Munich, Germany
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8
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Ma Q, Song Y, Sun W, Cao J, Yuan H, Wang X, Sun Y, Shum HC. Cell-Inspired All-Aqueous Microfluidics: From Intracellular Liquid-Liquid Phase Separation toward Advanced Biomaterials. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903359. [PMID: 32274317 PMCID: PMC7141073 DOI: 10.1002/advs.201903359] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 01/06/2020] [Indexed: 05/24/2023]
Abstract
Living cells have evolved over billions of years to develop structural and functional complexity with numerous intracellular compartments that are formed due to liquid-liquid phase separation (LLPS). Discovery of the amazing and vital roles of cells in life has sparked tremendous efforts to investigate and replicate the intracellular LLPS. Among them, all-aqueous emulsions are a minimalistic liquid model that recapitulates the structural and functional features of membraneless organelles and protocells. Here, an emerging all-aqueous microfluidic technology derived from micrometer-scaled manipulation of LLPS is presented; the technology enables the state-of-art design of advanced biomaterials with exquisite structural proficiency and diversified biological functions. Moreover, a variety of emerging biomedical applications, including encapsulation and delivery of bioactive gradients, fabrication of artificial membraneless organelles, as well as printing and assembly of predesigned cell patterns and living tissues, are inspired by their cellular counterparts. Finally, the challenges and perspectives for further advancing the cell-inspired all-aqueous microfluidics toward a more powerful and versatile platform are discussed, particularly regarding new opportunities in multidisciplinary fundamental research and biomedical applications.
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Affiliation(s)
- Qingming Ma
- Department of PharmaceuticsSchool of PharmacyQingdao UniversityQingdao266021China
| | - Yang Song
- Wallace H Coulter Department of Biomedical EngineeringGeorgia Institute of Technology & Emory School of MedicineAtlantaGA30332USA
| | - Wentao Sun
- Center for Basic Medical ResearchTEDA International Cardiovascular HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjin300457China
| | - Jie Cao
- Department of PharmaceuticsSchool of PharmacyQingdao UniversityQingdao266021China
| | - Hao Yuan
- Institute of Applied MechanicsNational Taiwan UniversityTaipei10617Taiwan
| | - Xinyu Wang
- Institute of Thermal Science and TechnologyShandong UniversityJinan250061China
| | - Yong Sun
- Department of PharmaceuticsSchool of PharmacyQingdao UniversityQingdao266021China
| | - Ho Cheung Shum
- Department of Mechanical EngineeringUniversity of Hong KongPokfulam RoadHong Kong
- HKU‐Shenzhen Institute of Research and Innovation (HKU‐SIRI)Shenzhen518000China
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9
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High-throughput sequencing analysis of Eugenia uniflora: insights into repetitive DNA, gene content and potential biotechnological applications. 3 Biotech 2019; 9:200. [PMID: 31065500 DOI: 10.1007/s13205-019-1729-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/24/2019] [Indexed: 10/26/2022] Open
Abstract
In this study, the Ion Torrent PGM platform was employed to conduct a whole-genome sequencing analysis of Eugenia uniflora L., aiming to generate new genomic information for this non-model species. The whole-genome set of assembled sequences (WGSAS) generated 2601 contigs, with a cumulative length of 3.15 Mbp. About 2.60% of the WGSAS was characterized by repetitive sequences, while 71.66% of the WGSAS was represented by predicted genes. A total of 147 metabolic pathways related to enzymes characterized in the E. uniflora WGSAS were detected. Proteins related to antifungal activity and to bacterium and fungi defense response as well as transcriptions factors related to abiotic stress responses were also identified. This sequencing provides important genomic resources for future breeding and selection regarding plants with higher production of such metabolites, as well as source of genes for genetic engineering of cultivated species, supporting a wide application of marker-assisted and genomic selection, towards the establishment of commercial orchards with improved cultivars of E. uniflora.
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10
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Takami T, Ohnishi N, Kurita Y, Iwamura S, Ohnishi M, Kusaba M, Mimura T, Sakamoto W. Organelle DNA degradation contributes to the efficient use of phosphate in seed plants. NATURE PLANTS 2018; 4:1044-1055. [PMID: 30420711 DOI: 10.1038/s41477-018-0291-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/27/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and chloroplasts (plastids) both harbour extranuclear DNA that originates from the ancestral endosymbiotic bacteria. These organelle DNAs (orgDNAs) encode limited genetic information but are highly abundant, with multiple copies in vegetative tissues, such as mature leaves. Abundant orgDNA constitutes a substantial pool of organic phosphate along with RNA in chloroplasts, which could potentially contribute to phosphate recycling when it is degraded and relocated. However, whether orgDNA is degraded nucleolytically in leaves remains unclear. In this study, we revealed the prevailing mechanism in which organelle exonuclease DPD1 degrades abundant orgDNA during leaf senescence. The DPD1 degradation system is conserved in seed plants and, more remarkably, we found that it was correlated with the efficient use of phosphate when plants were exposed to nutrient-deficient conditions. The loss of DPD1 compromised both the relocation of phosphorus to upper tissues and the response to phosphate starvation, resulting in reduced plant fitness. Our findings highlighted that DNA is also an internal phosphate-rich reservoir retained in organelles since their endosymbiotic origin.
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Affiliation(s)
- Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yuko Kurita
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Shoko Iwamura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Miwa Ohnishi
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
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11
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Vasselon V, Bouchez A, Rimet F, Jacquet S, Trobajo R, Corniquel M, Tapolczai K, Domaizon I. Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12960] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valentin Vasselon
- CARRTELFrench National Institute for Agricultural Research (INRA)University of Savoie Mont Blanc Thonon‐les‐Bains France
| | - Agnès Bouchez
- CARRTELFrench National Institute for Agricultural Research (INRA)University of Savoie Mont Blanc Thonon‐les‐Bains France
| | - Frédéric Rimet
- CARRTELFrench National Institute for Agricultural Research (INRA)University of Savoie Mont Blanc Thonon‐les‐Bains France
| | - Stéphan Jacquet
- CARRTELFrench National Institute for Agricultural Research (INRA)University of Savoie Mont Blanc Thonon‐les‐Bains France
| | - Rosa Trobajo
- Aquatic EcosystemsInstitute for Food and Agricultural Research and Technology (IRTA) Catalunya Spain
| | - Méline Corniquel
- CARRTELFrench National Institute for Agricultural Research (INRA)University of Savoie Mont Blanc Thonon‐les‐Bains France
| | - Kálmán Tapolczai
- CARRTELFrench National Institute for Agricultural Research (INRA)University of Savoie Mont Blanc Thonon‐les‐Bains France
| | - Isabelle Domaizon
- CARRTELFrench National Institute for Agricultural Research (INRA)University of Savoie Mont Blanc Thonon‐les‐Bains France
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12
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Massouh A, Schubert J, Yaneva-Roder L, Ulbricht-Jones ES, Zupok A, Johnson MTJ, Wright SI, Pellizzer T, Sobanski J, Bock R, Greiner S. Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera. THE PLANT CELL 2016; 28:911-29. [PMID: 27053421 PMCID: PMC4863383 DOI: 10.1105/tpc.15.00879] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 03/23/2016] [Accepted: 03/31/2016] [Indexed: 05/08/2023]
Abstract
Spontaneous plastome mutants have been used as a research tool since the beginning of genetics. However, technical restrictions have severely limited their contributions to research in physiology and molecular biology. Here, we used full plastome sequencing to systematically characterize a collection of 51 spontaneous chloroplast mutants in Oenothera (evening primrose). Most mutants carry only a single mutation. Unexpectedly, the vast majority of mutations do not represent single nucleotide polymorphisms but are insertions/deletions originating from DNA replication slippage events. Only very few mutations appear to be caused by imprecise double-strand break repair, nucleotide misincorporation during replication, or incorrect nucleotide excision repair following oxidative damage. U-turn inversions were not detected. Replication slippage is induced at repetitive sequences that can be very small and tend to have high A/T content. Interestingly, the mutations are not distributed randomly in the genome. The underrepresentation of mutations caused by faulty double-strand break repair might explain the high structural conservation of seed plant plastomes throughout evolution. In addition to providing a fully characterized mutant collection for future research on plastid genetics, gene expression, and photosynthesis, our work identified the spectrum of spontaneous mutations in plastids and reveals that this spectrum is very different from that in the nucleus.
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Affiliation(s)
- Amid Massouh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Julia Schubert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Liliya Yaneva-Roder
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | | | - Arkadiusz Zupok
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Marc T J Johnson
- Department of Biology, University of Toronto-Mississauga, Mississauga, Ontario L5L 1C6, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Tommaso Pellizzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Johanna Sobanski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
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13
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Dodsworth S. Genome skimming for next-generation biodiversity analysis. TRENDS IN PLANT SCIENCE 2015; 20:525-527. [PMID: 26205170 DOI: 10.1016/j.tplants.2015.06.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/26/2015] [Accepted: 06/30/2015] [Indexed: 05/18/2023]
Affiliation(s)
- Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK; Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK.
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14
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Fan G, Wang L, Deng M, Niu S, Zhao Z, Xu E, Cao X, Zhang X. Transcriptome analysis of the variations between autotetraploid Paulownia tomentosa and its diploid using high-throughput sequencing. Mol Genet Genomics 2015; 290:1627-38. [PMID: 25773315 DOI: 10.1007/s00438-015-1023-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/01/2015] [Indexed: 11/30/2022]
Abstract
Timber properties of autotetraploid Paulownia tomentosa are heritable with whole genome duplication, but the molecular mechanisms for the predominant characteristics remain unclear. To illuminate the genetic basis, high-throughput sequencing technology was used to identify the related unigenes. 2677 unigenes were found to be significantly differentially expressed in autotetraploid P. tomentosa. In total, 30 photosynthesis-related, 21 transcription factor-related, and 22 lignin-related differentially expressed unigenes were detected, and the roles of the peroxidase in lignin biosynthesis, MYB DNA-binding proteins, and WRKY proteins associated with the regulation of relevant hormones are extensively discussed. The results provide transcriptome data that may bring a new perspective to explain the polyploidy mechanism in the long growth cycle of plants and offer some help to the future Paulownia breeding.
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Affiliation(s)
- Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan, China,
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15
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Martín M, Noarbe DM, Serrot PH, Sabater B. The rise of the photosynthetic rate when light intensity increases is delayed in ndh gene-defective tobacco at high but not at low CO2 concentrations. FRONTIERS IN PLANT SCIENCE 2015; 6:34. [PMID: 25709611 PMCID: PMC4321573 DOI: 10.3389/fpls.2015.00034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 01/13/2015] [Indexed: 05/02/2023]
Abstract
The 11 plastid ndh genes have hovered frequently on the edge of dispensability, being absent in the plastid DNA of many algae and certain higher plants. We have compared the photosynthetic activity of tobacco (Nicotiana tabacum, cv. Petit Havana) with five transgenic lines (ΔndhF, pr-ΔndhF, T181D, T181A, and ndhF FC) and found that photosynthetic performance is impaired in transgenic ndhF-defective tobacco plants at rapidly fluctuating light intensities and higher than ambient CO2 concentrations. In contrast to wild type and ndhF FC, which reach the maximum photosynthetic rate in less than 1 min when light intensity suddenly increases, ndh defective plants (ΔndhF and T181A) show up to a 5 min delay in reaching the maximum photosynthetic rate at CO2 concentrations higher than the ambient 360 ppm. Net photosynthesis was determined at different CO2 concentrations when sequences of 130, 870, 61, 870, and 130 μmol m(-2) s(-1) PAR sudden light changes were applied to leaves and photosynthetic efficiency and entropy production (Sg) were determined as indicators of photosynthesis performance. The two ndh-defective plants, ΔndhF and T181A, had lower photosynthetic efficiency and higher Sg than wt, ndhF FC and T181D tobacco plants, containing full functional ndh genes, at CO2 concentrations above 400 ppm. We propose that the Ndh complex improves cyclic electron transport by adjusting the redox level of transporters during the low light intensity stage. In ndhF-defective strains, the supply of electrons through the Ndh complex fails, transporters remain over-oxidized (specially at high CO2 concentrations) and the rate of cyclic electron transport is low, impairing the ATP level required to rapidly reach high CO2 fixation rates in the following high light phase. Hence, ndh genes could be dispensable at low but not at high atmospheric concentrations of CO2.
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Affiliation(s)
- Mercedes Martín
- Department of Life Sciences, University of Alcalá, Alcalá de HenaresSpain
| | - Dolores M. Noarbe
- Department of Physical Chemistry, University of Alcalá, Alcalá de HenaresSpain
| | - Patricia H. Serrot
- Department of Life Sciences, University of Alcalá, Alcalá de HenaresSpain
| | - Bartolomé Sabater
- Department of Life Sciences, University of Alcalá, Alcalá de HenaresSpain
- *Correspondence: Bartolomé Sabater, Department of Life Sciences, University of Alcalá, Alcalá de Henares, 28805 Madrid, Spain e-mail:
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16
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Mariac C, Scarcelli N, Pouzadou J, Barnaud A, Billot C, Faye A, Kougbeadjo A, Maillol V, Martin G, Sabot F, Santoni S, Vigouroux Y, Couvreur TLP. Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mol Ecol Resour 2014; 14:1103-13. [DOI: 10.1111/1755-0998.12258] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Cédric Mariac
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Nora Scarcelli
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Juliette Pouzadou
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Adeline Barnaud
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Laboratoire National de Recherche sur les Productions Végétales; Institut Sénégalais de Recherches Agricoles; Centre de Recherche de Bel Air; Dakar Senegal
- Laboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress Environnementaux; Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop; Centre de Recherche de Bel Air; Dakar Senegal
| | | | - Adama Faye
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Université de Yaoundé I; Ecole Normale Supérieure; Département des Sciences Biologiques; Laboratoire de Botanique; Systématique et d'Ecologie; B.P.047 Yaoundé Cameroon
| | - Ayite Kougbeadjo
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Vincent Maillol
- UMR AGAP; Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; INRA; 2 Place Viala 34060 Montpellier France
| | | | - François Sabot
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Sylvain Santoni
- UMR AGAP; Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes; INRA; 2 Place Viala 34060 Montpellier France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
| | - Thomas L. P. Couvreur
- Institut de Recherche pour le Développement; UMR DIADE; BP 64501 34394 Montpellier France
- Université de Yaoundé I; Ecole Normale Supérieure; Département des Sciences Biologiques; Laboratoire de Botanique; Systématique et d'Ecologie; B.P.047 Yaoundé Cameroon
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17
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Golczyk H, Greiner S, Wanner G, Weihe A, Bock R, Börner T, Herrmann RG. Chloroplast DNA in mature and senescing leaves: a reappraisal. THE PLANT CELL 2014; 26:847-54. [PMID: 24668747 PMCID: PMC4001396 DOI: 10.1105/tpc.113.117465] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/07/2013] [Accepted: 03/11/2014] [Indexed: 05/04/2023]
Abstract
The fate of plastid DNA (ptDNA) during leaf development has become a matter of contention. Reports on little change in ptDNA copy number per cell contrast with claims of complete or nearly complete DNA loss already in mature leaves. We employed high-resolution fluorescence microscopy, transmission electron microscopy, semithin sectioning of leaf tissue, and real-time quantitative PCR to study structural and quantitative aspects of ptDNA during leaf development in four higher plant species (Arabidopsis thaliana, sugar beet [Beta vulgaris], tobacco [Nicotiana tabacum], and maize [Zea mays]) for which controversial findings have been reported. Our data demonstrate the retention of substantial amounts of ptDNA in mesophyll cells until leaf necrosis. In ageing and senescent leaves of Arabidopsis, tobacco, and maize, ptDNA amounts remain largely unchanged and nucleoids visible, in spite of marked structural changes during chloroplast-to-gerontoplast transition. This excludes the possibility that ptDNA degradation triggers senescence. In senescent sugar beet leaves, reduction of ptDNA per cell to ∼30% was observed reflecting primarily a decrease in plastid number per cell rather than a decline in DNA per organelle, as reported previously. Our findings are at variance with reports claiming loss of ptDNA at or after leaf maturation.
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Affiliation(s)
- Hieronim Golczyk
- Department of Molecular Biology, Institute of
Biotechnology, John Paul II Catholic University of Lublin, 20-708 Lublin,
Poland
| | - Stephan Greiner
- Max-Planck-Institut für Molekulare
Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Gerhard Wanner
- Department für Biologie I, Bereich Botanik,
Biozentrum der Ludwig-Maximilians–Universität München, D-82152
Planegg-Martinsried, Germany
| | - Andreas Weihe
- Institut für Biologie/Genetik,
Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare
Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Thomas Börner
- Institut für Biologie/Genetik,
Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
| | - Reinhold G. Herrmann
- Department für Biologie I, Bereich Botanik,
Biozentrum der Ludwig-Maximilians–Universität München, D-82152
Planegg-Martinsried, Germany
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18
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Abstract
The plastid genome (plastome) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations are allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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19
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Powikrowska M, Oetke S, Jensen PE, Krupinska K. Dynamic composition, shaping and organization of plastid nucleoids. FRONTIERS IN PLANT SCIENCE 2014; 5:424. [PMID: 25237313 PMCID: PMC4154389 DOI: 10.3389/fpls.2014.00424] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/08/2014] [Indexed: 05/18/2023]
Abstract
In this article recent progress on the elucidation of the dynamic composition and structure of plastid nucleoids is reviewed from a structural perspective. Plastid nucleoids are compact structures of multiple copies of different forms of ptDNA, RNA, enzymes for replication and gene expression as well as DNA binding proteins. Although early electron microscopy suggested that plastid DNA is almost free of proteins, it is now well established that the DNA in nucleoids similarly as in the nuclear chromatin is associated with basic proteins playing key roles in organization of the DNA architecture and in regulation of DNA associated enzymatic activities involved in transcription, replication, and recombination. This group of DNA binding proteins has been named plastid nucleoid associated proteins (ptNAPs). Plastid nucleoids are unique with respect to their variable number, genome copy content and dynamic distribution within different types of plastids. The mechanisms underlying the shaping and reorganization of plastid nucleoids during chloroplast development and in response to environmental conditions involve posttranslational modifications of ptNAPs, similarly to those changes known for histones in the eukaryotic chromatin, as well as changes in the repertoire of ptNAPs, as known for nucleoids of bacteria. Attachment of plastid nucleoids to membranes is proposed to be important not only for regulation of DNA availability for replication and transcription, but also for the coordination of photosynthesis and plastid gene expression.
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Affiliation(s)
- Marta Powikrowska
- Department of Plant and Environmental Sciences, VILLUM Research Centre for Plant Plasticity and Copenhagen Plant Science Centre, University of CopenhagenCopenhagen, Denmark
| | - Svenja Oetke
- Plant Cell Biology, Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
| | - Poul E. Jensen
- Department of Plant and Environmental Sciences, VILLUM Research Centre for Plant Plasticity and Copenhagen Plant Science Centre, University of CopenhagenCopenhagen, Denmark
| | - Karin Krupinska
- Plant Cell Biology, Institute of Botany, Christian-Albrechts-University of KielKiel, Germany
- *Correspondence: Karin Krupinska, Plant Cell Biology, Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany e-mail:
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20
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Parducci L, Matetovici I, Fontana SL, Bennett KD, Suyama Y, Haile J, Kjaer KH, Larsen NK, Drouzas AD, Willerslev E. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Mol Ecol 2013; 22:3511-24. [PMID: 23587049 DOI: 10.1111/mec.12298] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/18/2013] [Accepted: 01/29/2013] [Indexed: 11/26/2022]
Abstract
Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
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21
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Abstract
Large cell size is not restricted to a particular bacterial lifestyle, dispersal method, or cell envelope type. What is conserved among the very large bacteria are the quantity and arrangement of their genomic resources. All large bacteria described to date appear to be highly polyploid. This review focuses on Epulopiscium sp. type B, which maintains tens of thousands of genome copies throughout its life cycle. Only a tiny proportion of mother cell DNA is inherited by intracellular offspring, but surprisingly DNA replication takes place in the terminally differentiated mother cell as offspring grow. Massive polyploidy supports the acquisition of unstable genetic elements normally not seen in essential genes. Further studies of how large bacteria manage their genomic resources will provide insight into how simple cellular modifications can support unusual lifestyles and exceptional cell forms.
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Affiliation(s)
- Esther R Angert
- Department of Microbiology, Cornell University, Ithaca, New York 14853, USA.
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22
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Development-Dependent Changes in the Amount and Structural Organization of Plastid DNA. PLASTID DEVELOPMENT IN LEAVES DURING GROWTH AND SENESCENCE 2013. [DOI: 10.1007/978-94-007-5724-0_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Tang LY, Matsushima R, Sakamoto W. Mutations defective in ribonucleotide reductase activity interfere with pollen plastid DNA degradation mediated by DPD1 exonuclease. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:637-49. [PMID: 22239102 DOI: 10.1111/j.1365-313x.2012.04904.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Organellar DNAs in mitochondria and plastids are present in multiple copies and make up a substantial proportion of total cellular DNA despite their limited genetic capacity. We recently demonstrated that organellar DNA degradation occurs during pollen maturation, mediated by the Mg(2+) -dependent organelle exonuclease DPD1. To further understand organellar DNA degradation, we characterized a distinct mutant (dpd2). In contrast to the dpd1 mutant, which retains both plastid and mitochondrial DNAs, dpd2 showed specific accumulation of plastid DNAs. Multiple abnormalities in vegetative and reproductive tissues of dpd2 were also detected. DPD2 encodes the large subunit of ribonucleotide reductase, an enzyme that functions at the rate-limiting step of de novo nucleotide biosynthesis. We demonstrated that the defects in ribonucleotide reductase indirectly compromise the activity of DPD1 nuclease in plastids, thus supporting a different regulation of organellar DNA degradation in pollen. Several lines of evidence provided here reinforce our previous conclusion that the DPD1 exonuclease plays a central role in organellar DNA degradation, functioning in DNA salvage rather than maternal inheritance during pollen development.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Exoribonucleases/genetics
- Exoribonucleases/metabolism
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genetic Complementation Test
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Microscopy, Electron, Scanning
- Microscopy, Fluorescence
- Mutation
- Phenotype
- Plants, Genetically Modified
- Plastids/genetics
- Pollen/genetics
- Pollen/ultrastructure
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleotide Reductases/genetics
- Ribonucleotide Reductases/metabolism
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Affiliation(s)
- Lay Yin Tang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
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24
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Parducci L, Jorgensen T, Tollefsrud MM, Elverland E, Alm T, Fontana SL, Bennett KD, Haile J, Matetovici I, Suyama Y, Edwards ME, Andersen K, Rasmussen M, Boessenkool S, Coissac E, Brochmann C, Taberlet P, Houmark-Nielsen M, Larsen NK, Orlando L, Gilbert MTP, Kjaer KH, Alsos IG, Willerslev E. Glacial Survival of Boreal Trees in Northern Scandinavia. Science 2012; 335:1083-6. [DOI: 10.1126/science.1216043] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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25
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Straub SCK, Parks M, Weitemier K, Fishbein M, Cronn RC, Liston A. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. AMERICAN JOURNAL OF BOTANY 2012; 99:349-64. [PMID: 22174336 DOI: 10.3732/ajb.1100335] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. METHODS Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). KEY RESULTS Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40× and 30×, respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. CONCLUSIONS Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.
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Affiliation(s)
- Shannon C K Straub
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, Oregon 97331, USA.
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26
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27
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Butorina AK, Kornienko AV. Molecular genetic investigation of sugar beet (Beta vulgaris L.). RUSS J GENET+ 2011. [DOI: 10.1134/s102279541110005x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Lutz KA, Wang W, Zdepski A, Michael TP. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. BMC Biotechnol 2011; 11:54. [PMID: 21599914 PMCID: PMC3131251 DOI: 10.1186/1472-6750-11-54] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Accepted: 05/20/2011] [Indexed: 12/22/2022] Open
Abstract
Background High throughput sequencing (HTS) technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR). We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.
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Affiliation(s)
- Kerry A Lutz
- Rutgers, The State University of New Jersey, Department of Plant Biology and Pathology, The Waksman Institute of Microbiology, Piscataway, NJ 08854, USA.
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29
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Matsushima R, Tang LY, Zhang L, Yamada H, Twell D, Sakamoto W. A conserved, Mg²+-dependent exonuclease degrades organelle DNA during Arabidopsis pollen development. THE PLANT CELL 2011; 23:1608-24. [PMID: 21521697 PMCID: PMC3101548 DOI: 10.1105/tpc.111.084012] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/01/2011] [Accepted: 04/11/2011] [Indexed: 05/18/2023]
Abstract
In plant cells, mitochondria and plastids contain their own genomes derived from the ancestral bacteria endosymbiont. Despite their limited genetic capacity, these multicopy organelle genomes account for a substantial fraction of total cellular DNA, raising the question of whether organelle DNA quantity is controlled spatially or temporally. In this study, we genetically dissected the organelle DNA decrease in pollen, a phenomenon that appears to be common in most angiosperm species. By staining mature pollen grains with fluorescent DNA dye, we screened Arabidopsis thaliana for mutants in which extrachromosomal DNAs had accumulated. Such a recessive mutant, termed defective in pollen organelle DNA degradation1 (dpd1), showing elevated levels of DNAs in both plastids and mitochondria, was isolated and characterized. DPD1 encodes a protein belonging to the exonuclease family, whose homologs appear to be found in angiosperms. Indeed, DPD1 has Mg²⁺-dependent exonuclease activity when expressed as a fusion protein and when assayed in vitro and is highly active in developing pollen. Consistent with the dpd phenotype, DPD1 is dual-targeted to plastids and mitochondria. Therefore, we provide evidence of active organelle DNA degradation in the angiosperm male gametophyte, primarily independent of maternal inheritance; the biological function of organellar DNA degradation in pollen is currently unclear.
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Affiliation(s)
- Ryo Matsushima
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Lay Yin Tang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Lingang Zhang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Hiroshi Yamada
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - David Twell
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
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GREINER STEPHAN, RAUWOLF UWE, MEURER JÖRG, HERRMANN REINHOLDG. The role of plastids in plant speciation. Mol Ecol 2011; 20:671-91. [DOI: 10.1111/j.1365-294x.2010.04984.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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