1
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Smith KE, Zhou M, Flis P, Jones DH, Bishopp A, Yant L. The evolution of the duckweed ionome mirrors losses in structural complexity. ANNALS OF BOTANY 2024; 133:997-1006. [PMID: 38307008 PMCID: PMC11089258 DOI: 10.1093/aob/mcae012] [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: 12/14/2023] [Accepted: 02/03/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND AND AIMS The duckweeds (Lemnaceae) consist of 36 species exhibiting impressive phenotypic variation, including the progressive evolutionary loss of a fundamental plant organ, the root. Loss of roots and reduction of vascular tissues in recently derived taxa occur in concert with genome expansions of ≤14-fold. Given the paired loss of roots and reduction in structural complexity in derived taxa, we focus on the evolution of the ionome (whole-plant elemental contents) in the context of these fundamental changes in body plan. We expect that progressive vestigiality and eventual loss of roots might have both adaptive and maladaptive consequences that are hitherto unknown. METHODS We quantified the ionomes of 34 accessions in 21 species across all duckweed genera, spanning 70 Myr in this rapidly cycling plant (doubling times are as rapid as ~24 h). We related both micro- and macroevolutionary ionome contrasts to body plan remodelling and showed nimble microevolutionary shifts in elemental accumulation and exclusion in novel accessions. KEY RESULTS We observed a robust directional trend in calcium and magnesium levels, decreasing from the ancestral representative Spirodela genus towards the derived rootless Wolffia, with the latter also accumulating cadmium. We also identified abundant within-species variation and hyperaccumulators of specific elements, with this extensive variation at the fine (as opposed to broad) scale. CONCLUSIONS These data underscore the impact of root loss and reveal the very fine scale of microevolutionary variation in hyperaccumulation and exclusion of a wide range of elements. Broadly, they might point to trade-offs not well recognized in ionomes.
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Affiliation(s)
- Kellie E Smith
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Min Zhou
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Paulina Flis
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Dylan H Jones
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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2
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Smith KE, Cowan L, Taylor B, McAusland L, Heatley M, Yant L, Murchie EH. Physiological adaptation to irradiance in duckweeds is species and accession specific and depends on light habitat niche. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2046-2063. [PMID: 38217537 DOI: 10.1093/jxb/erad499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Duckweeds span 36 species of free-floating aquatic organisms with body sizes ranging from 2 mm to 10 mm, where each plant body plan is reduced to a largely leaf-like structure. As an emerging crop, their fast growth rates offer potential for cultivation in closed systems. We describe a novel UK collection derived from low light (dLL) or high light (dHL) habitats, profiled for growth, photosynthesis, and photoprotection (non-photochemical quenching, NPQ) responses. Twenty-three accessions of three Lemna species and one Spirodela polyrhiza were grown under relatively low light (LL: 100 μmol m-2 s-1) and high light (HL: 350 μmol m-2 s-1) intensities. We observed broad within- and between-species level variation in photosynthesis acclimation. Duckweeds grown under HL exhibited a lower growth rate, biomass, chlorophyll, and quantum yield of photosynthesis. In HL compared with LL, carotenoid de-epoxidation state and NPQ were higher, whilst PSII efficiency (φPSII) and Chl a:b ratios were unchanged. The dLL plants showed relatively stronger acclimation to HL compared with dHL plants, especially Lemna japonica accessions. These achieved faster growth in HL with concurrent higher carotenoid levels and NPQ, and less degradation of chlorophyll. We conclude that these data support local adaptation to the light environment in duckweed affecting acclimation in controlled conditions.
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Affiliation(s)
- Kellie E Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Beth Taylor
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Lorna McAusland
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Matthew Heatley
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Erik H Murchie
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
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3
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Yang J, Zhao X, Wang X, Xia M, Ba S, Lim BL, Hou H. Biomonitoring of heavy metals and their phytoremediation by duckweeds: Advances and prospects. ENVIRONMENTAL RESEARCH 2024; 245:118015. [PMID: 38141920 DOI: 10.1016/j.envres.2023.118015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 12/25/2023]
Abstract
Heavy metals (HMs) contamination of water bodies severely threatens human and ecosystem health. There is growing interest in the use of duckweeds for HMs biomonitoring and phytoremediation due to their fast growth, low cultivation costs, and excellent HM uptake efficiency. In this review, we summarize the current state of knowledge on duckweeds and their suitability for HM biomonitoring and phytoremediation. Duckweeds have been used for phytotoxicity assays since the 1930s. Some toxicity tests based on duckweeds have been listed in international guidelines. Duckweeds have also been recognized for their ability to facilitate HM phytoremediation in aquatic environments. Large-scale screening of duckweed germplasm optimized for HM biomonitoring and phytoremediation is still essential. We further discuss the morphological, physiological, and molecular effects of HMs on duckweeds. However, the existing data are clearly insufficient, especially in regard to dissection of the transcriptome, metabolome, proteome responses and molecular mechanisms of duckweeds under HM stresses. We also evaluate the influence of environmental factors, exogenous substances, duckweed community composition, and HM interactions on their HM sensitivity and HM accumulation, which need to be considered in practical application scenarios. Finally, we identify challenges and propose approaches for improving the effectiveness of duckweeds for bioremediation from the aspects of selection of duckweed strain, cultivation optimization, engineered duckweeds. We foresee great promise for duckweeds as phytoremediation agents, providing environmentally safe and economically efficient means for HM removal. However, the primary limiting issue is that so few researchers have recognized the outstanding advantages of duckweeds. We hope that this review can pique the interest and attention of more researchers.
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Affiliation(s)
- Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Xiaoyu Wang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Sang Ba
- Center for Carbon Neutrality in the Third Pole of the Earth, Tibet University, Lhasa, 850000, China; Laboratory of Tibetan Plateau Wetland and Watershed Ecosystem, College of Science, Tibet University, Lhasa, 850000, China.
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China; HKU Shenzhen Institute of Research and Innovation, Shenzhen, China; State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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4
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Subbaraman B, de Lange O, Ferguson S, Peek N. The Duckbot: A system for automated imaging and manipulation of duckweed. PLoS One 2024; 19:e0296717. [PMID: 38261570 PMCID: PMC10805289 DOI: 10.1371/journal.pone.0296717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/17/2023] [Indexed: 01/25/2024] Open
Abstract
Laboratory automation can boost precision and reproducibility of science workflows. However, current laboratory automation systems are difficult to modify for custom applications. Automating new experiment workflows therefore requires development of one-off research platforms, a process which requires significant time, resources, and experience. In this work, we investigate systems to lower the threshold to automation for plant biologists. Our approach establishes a direct connection with a generic motion platform to support experiment development and execution from a computational notebook environment. Specifically, we investigate the use of the open-source tool-changing motion platform Jubilee controlled using Jupyter notebooks. We present the Duckbot, a machine customized for automating laboratory research workflows with duckweed, a common multicellular plant. The Duckbot comprises (1) a set of end-effectors relevant for plant biology, (2) software modules which provide flexible control of these tools, and (3) computational notebooks which make use of these tools to automate duckweed experiments. We demonstrate the Duckbot's functionality by automating a particular laboratory research workflow, namely, duckweed growth assays. The Duckbot supports setting up sample plates with duckweed and growth media, gathering image data, and conducting relevant data analysis. We discuss the opportunities and limitations for developing custom laboratory automation with this platform and provide instructions on usage and customization.
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Affiliation(s)
- Blair Subbaraman
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Orlando de Lange
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
- Biology Department, Shoreline Community College, Shoreline, Washington, United States of America
| | - Sam Ferguson
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Nadya Peek
- Department of Human Centered Design & Engineering, University of Washington, Seattle, Washington, United States of America
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5
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Romano LE, van Loon JJWA, Izzo LG, Iovane M, Aronne G. Effects of altered gravity on growth and morphology in Wolffia globosa implications for bioregenerative life support systems and space-based agriculture. Sci Rep 2024; 14:410. [PMID: 38172193 PMCID: PMC10764921 DOI: 10.1038/s41598-023-49680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Understanding the response of plants to varied gravitational conditions is vital for developing effective food production in space bioregenerative life support systems. This study examines the impact of altered gravity conditions on the growth and morphological responses of Wolffia globosa (commonly known as "water lentils" or "duckweed"), assessing its potential as a space crop. Although an experiment testing the effect of simulated microgravity on Wolffia globosa has been previously conducted, for the first time, we investigated the effect of multiple gravity levels on the growth and morphological traits of Wolffia globosa plants. The plant responses to simulated microgravity, simulated partial gravity (Moon), and hypergravity environments were evaluated using random positioning machines and the large-diameter centrifuge. As hypothesized, we observed a slight reaction to different gravitational levels in the growth and morphological traits of Wolffia globosa. The relative growth rates (RGR) of plants subjected to simulated microgravity and partial gravity were reduced when compared to those in other gravity levels. The morphological analysis revealed differences in plant dimensions and frond length-to-width ratios under diverse gravity conditions. Our findings showed that Wolffia globosa is responsive to gravitational changes, with its growth and morphological adaptations being slightly influenced by varying gravitational environments. As for other crop species, growth was reduced by the microgravity conditions; however, RGR remained substantial at 0.33 a day. In conclusion, this study underscores the potential of Wolffia globosa as a space crop and its adaptability to diverse gravitational conditions, contributing to the development of sustainable food production and bioregenerative life support systems for future space exploration missions.
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Affiliation(s)
- Leone Ermes Romano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
| | - Jack J W A van Loon
- Department Oral and Maxillofacial Surgery/Pathology, Amsterdam Movement Sciences and Amsterdam Bone Center (ABC), Amsterdam University Medical Center Location VUmc and Academic Center for Dentistry Amsterdam (ACTA), Amsterdam, The Netherlands
- TEC-MMG-LIS Lab, European Space Agency (ESA) Technology Center (ESTEC), Noordwijk, The Netherlands
| | - Luigi Gennaro Izzo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Maurizio Iovane
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Giovanna Aronne
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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6
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Clark JW. Genome evolution in plants and the origins of innovation. THE NEW PHYTOLOGIST 2023; 240:2204-2209. [PMID: 37658677 DOI: 10.1111/nph.19242] [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: 03/14/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.
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Affiliation(s)
- James W Clark
- School of Biological Sciences, University of Bristol, Tyndall Ave, Bristol, BS8 1TQ, UK
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7
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Islam T, Kalkar S, Tinker-Kulberg R, Ignatova T, Josephs EA. The "Duckweed Dip": Aquatic Spirodela polyrhiza Plants Can Efficiently Uptake Dissolved, DNA-Wrapped Carbon Nanotubes from Their Environment for Transient Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554121. [PMID: 37662322 PMCID: PMC10473656 DOI: 10.1101/2023.08.21.554121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Duckweeds (Lemnaceae) are aquatic non-grass monocots that are the smallest and fastest-growing flowering plants in the world. While having simplified morphologies, relatively small genomes, and many other ideal traits for emerging applications in plant biotechnology, duckweeds have been largely overlooked in this era of synthetic biology. Here, we report that Greater Duckweed (Spirodela polyrhiza), when simply incubated in a solution containing plasmid-wrapped carbon nanotubes (DNA-CNTs), can directly up-take the DNA-CNTs from their growth media with high efficiency and that transgenes encoded within the plasmids are expressed by the plants-without the usual need for large doses of nanomaterials or agrobacterium to be directly infiltrated into plant tissue. This process, called the "duckweed dip", represents a streamlined, 'hands-off' tool for transgene delivery to a higher plant that we expect will enhance the throughput of duckweed engineering and help to realize duckweed's potential as a powerhouse for plant synthetic biology. (148 words).
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Affiliation(s)
- Tasmia Islam
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, NC. 27401
| | - Swapna Kalkar
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, NC. 27401
| | - Rachel Tinker-Kulberg
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, NC. 27401
| | - Tetyana Ignatova
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, NC. 27401
| | - Eric A. Josephs
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, NC. 27401
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8
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Mayes R, Dauer J, Owens D. Convergence and transdisciplinary teaching in quantitative biology. QUANTITATIVE PLANT BIOLOGY 2023; 4:e8. [PMID: 37587988 PMCID: PMC10425763 DOI: 10.1017/qpb.2023.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 08/18/2023]
Abstract
The United States National Science and Technology Council has made a call for improving STEM (Science, Technology, Engineering, and Mathematics) education at the convergence of science, technology, engineering, and mathematics. The National Science Foundation (NSF) views convergence as the merging of ideas, approaches, and technologies from widely diverse fields of knowledge to stimulate innovation and discovery. Teaching convergency requires moving to the transdisciplinary level of integration where there is deep integration of skills, disciplines, and knowledge to solve a challenging real-world problem. Here we present a summary on convergence and transdisciplinary teaching. We then provide examples of convergence and transdisciplinary teaching in plant biology, and conclude by discussing limitations to contemporary conceptions of convergency and transdisciplinary STEM.
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Affiliation(s)
- Robert Mayes
- Georgia Southern University, Statesboro, GA, United States
| | - Joseph Dauer
- University of Nebraska—Lincoln, Lincoln, NE, USA
| | - David Owens
- Georgia Southern University, Statesboro, GA, United States
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9
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Pasricha Sarin L, Sree KS, Bóka K, Keresztes Á, Fuchs J, Tyagi AK, Khurana JP, Appenroth KJ. Characterisation of a Spontaneous Mutant of Lemna gibba G3 (Lemnaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:2525. [PMID: 37447086 DOI: 10.3390/plants12132525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/17/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
A spontaneous mutant of the duckweed Lemna gibba clone no. 7796 (known as strain G3, WT) was discovered. In this mutant clone, L. gibba clone no. 9602 (mt), the morphological parameters (frond length, frond width, root length, root diameter) indicated an enlarged size. A change in the frond shape was indicated by the decreased frond length/width ratio, which could have taxonomic consequences. Several different cell types in both the frond and the root were also enlarged. Flow cytometric measurements disclosed the genome size of the WT as 557 Mbp/1C and that of the mt strain as 1153 Mbp/1C. This represents the results of polyploidisation of a diploid clone to a tetraploid one. The mutant clone flowered under the influence of long day-treatment in half-strength Hutner's medium in striking contrast to the diploid WT. Low concentration of salicylic acid (<1 µM) induced flowering in the tetraploid mutant but not in the diploid plants. The transcript levels of nuclear-encoded genes of the photosynthetic apparatus (CAB, RBCS) showed higher abundance in light and less dramatic decline in darkness in the mt than in WT, while this was not the case with plastid-encoded genes (RBCL, PSAA, PSBA, PSBC).
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Affiliation(s)
- Lakshmi Pasricha Sarin
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Áron Keresztes
- Department of Plant Anatomy, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Jörg Fuchs
- The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Akhilesh K Tyagi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Jitendra Paul Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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10
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Sree KS, Appenroth KJ, Oelmüller R. Sustainable Stress Management: Aquatic Plants vs. Terrestrial Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112208. [PMID: 37299187 DOI: 10.3390/plants12112208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The Indo-German Science and Technology Centre (IGSTC) funded an Indo-German Workshop on Sustainable Stress Management: Aquatic plants vs. Terrestrial plants (IGW-SSMAT) which was jointly organized at the Friedrich Schiller University of Jena, Germany from 25 to 27 July 2022 by Prof. Dr. Ralf Oelmüller, Friedrich Schiller University of Jena, Germany as the German coordinator and Dr. K. Sowjanya Sree, Central University of Kerala, India as the Indian Coordinator. The workshop constituted researchers working in this field from both India and Germany and brought together these experts in the field of sustainable stress management for scientific discussions, brainstorming and networking.
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Affiliation(s)
- K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
| | - Klaus J Appenroth
- Matthias Schleiden Institute-Plant Physiology, Friedrich Schiller University of Jena, 07743 Jena, Germany
| | - Ralf Oelmüller
- Matthias Schleiden Institute-Plant Physiology, Friedrich Schiller University of Jena, 07743 Jena, Germany
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11
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Pasaribu B, Acosta K, Aylward A, Liang Y, Abramson BW, Colt K, Hartwick NT, Shanklin J, Michael TP, Lam E. Genomics of turions from the Greater Duckweed reveal its pathways for dormancy and re-emergence strategy. THE NEW PHYTOLOGIST 2023. [PMID: 37149888 DOI: 10.1111/nph.18941] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/24/2023] [Indexed: 05/09/2023]
Abstract
Over 15 families of aquatic plants are known to use a strategy of developmental switching upon environmental stress to produce dormant propagules called turions. However, few molecular details for turion biology have been elucidated due to the difficulties in isolating high-quality nucleic acids from this tissue. We successfully developed a new protocol to isolate high-quality transcripts and carried out RNA-seq analysis of mature turions from the Greater Duckweed Spirodela polyrhiza. Comparison of turion transcriptomes to that of fronds, the actively growing leaf-like tissue, were carried out. Bioinformatic analysis of high confidence, differentially expressed transcripts between frond and mature turion tissues revealed major pathways related to stress tolerance, starch and lipid metabolism, and dormancy that are mobilized to reprogram frond meristems for turion differentiation. We identified the key genes that are likely to drive starch and lipid accumulation during turion formation, as well as those in pathways for starch and lipid utilization upon turion germination. Comparison of genome-wide cytosine methylation levels also revealed evidence for epigenetic changes in the formation of turion tissues. Similarities between turions and seeds provide evidence that key regulators for seed maturation and germination were retooled for their function in turion biology.
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Affiliation(s)
- Buntora Pasaribu
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Marine Science Department, Faculty of Fishery and Marine Science, Universitas Padjadjaran, Bandung, 40600, Indonesia
| | - Kenneth Acosta
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Anthony Aylward
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Yuanxue Liang
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Bradley W Abramson
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Kelly Colt
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Nolan T Hartwick
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Eric Lam
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
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12
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Li F, Yang JJ, Sun ZY, Wang L, Qi LY, A S, Liu YQ, Zhang HM, Dang LF, Wang SJ, Luo CX, Nian WF, O’Conner S, Ju LZ, Quan WP, Li XK, Wang C, Wang DP, You HL, Cheng ZK, Yan J, Tang FC, Yang DC, Xia CW, Gao G, Wang Y, Zhang BC, Zhou YH, Guo X, Xiang SH, Liu H, Peng TB, Su XD, Chen Y, Ouyang Q, Wang DH, Zhang DM, Xu ZH, Hou HW, Bai SN, Li L. Plant-on-chip: Core morphogenesis processes in the tiny plant Wolffia australiana. PNAS NEXUS 2023; 2:pgad141. [PMID: 37181047 PMCID: PMC10169700 DOI: 10.1093/pnasnexus/pgad141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
A plant can be thought of as a colony comprising numerous growth buds, each developing to its own rhythm. Such lack of synchrony impedes efforts to describe core principles of plant morphogenesis, dissect the underlying mechanisms, and identify regulators. Here, we use the minimalist known angiosperm to overcome this challenge and provide a model system for plant morphogenesis. We present a detailed morphological description of the monocot Wolffia australiana, as well as high-quality genome information. Further, we developed the plant-on-chip culture system and demonstrate the application of advanced technologies such as single-nucleus RNA-sequencing, protein structure prediction, and gene editing. We provide proof-of-concept examples that illustrate how W. australiana can decipher the core regulatory mechanisms of plant morphogenesis.
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Affiliation(s)
- Feng Li
- The High School Affiliated to Renmin University of China, Beijing 100080, China
- Center of Quantitative Biology, Peking University, Beijing 100871, China
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Jing-Jing Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zong-Yi Sun
- GrandOmics Biosciences Ltd., Wuhan 430076, China
| | - Lei Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Le-Yao Qi
- The High School Affiliated to Renmin University of China, Beijing 100080, China
| | - Sina A
- The High School Affiliated to Renmin University of China, Beijing 100080, China
| | - Yi-Qun Liu
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Hong-Mei Zhang
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Lei-Fan Dang
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Shu-Jing Wang
- Center of Quantitative Biology, Peking University, Beijing 100871, China
| | - Chun-Xiong Luo
- Center of Quantitative Biology, Peking University, Beijing 100871, China
| | - Wei-Feng Nian
- The High School Affiliated to Renmin University of China, Beijing 100080, China
| | - Seth O’Conner
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Long-Zhen Ju
- GrandOmics Biosciences Ltd., Wuhan 430076, China
| | | | - Xiao-Kang Li
- GrandOmics Biosciences Ltd., Wuhan 430076, China
| | - Chao Wang
- GrandOmics Biosciences Ltd., Wuhan 430076, China
| | - De-Peng Wang
- GrandOmics Biosciences Ltd., Wuhan 430076, China
| | - Han-Li You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhu-Kuan Cheng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jia Yan
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Fu-Chou Tang
- College of Life Sciences, Peking University, Beijing 100871, China
| | - De-Chang Yang
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Beijing 100871, China
- Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Chu-Wei Xia
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Beijing 100871, China
- Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Ge Gao
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovative Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Beijing 100871, China
- Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Yan Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Bao-Cai Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yi-Hua Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Sun-Huan Xiang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Tian-Bo Peng
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiao-Dong Su
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Yong Chen
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, Paris 75005, France
| | - Qi Ouyang
- Center of Quantitative Biology, Peking University, Beijing 100871, China
- School of Physics, Peking University, Beijing 100871, China
| | - Dong-Hui Wang
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Da-Ming Zhang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhi-Hong Xu
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Hong-Wei Hou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shu-Nong Bai
- Center of Quantitative Biology, Peking University, Beijing 100871, China
- State Key Laboratory of Protein & Plant Gene Research, Peking University, Beijing 100871, China
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
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13
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. ANNALS OF BOTANY 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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14
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Mateo-Elizalde C, Lynn J, Ernst E, Martienssen R. Duckweeds. Curr Biol 2023; 33:R89-R91. [PMID: 36750028 DOI: 10.1016/j.cub.2022.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Mateo-Elizalde et al. introduce duckweeds, a family of freshwater plants.
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Affiliation(s)
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, NY 11724, USA
| | - Rob Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, NY 11724, USA
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15
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Liang Y, Yu X, Anaokar S, Shi H, Dahl WB, Cai Y, Luo G, Chai J, Cai Y, Mollá‐Morales A, Altpeter F, Ernst E, Schwender J, Martienssen RA, Shanklin J. Engineering triacylglycerol accumulation in duckweed (Lemna japonica). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:317-330. [PMID: 36209479 PMCID: PMC9884027 DOI: 10.1111/pbi.13943] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 05/13/2023]
Abstract
Duckweeds are amongst the fastest growing of higher plants, making them attractive high-biomass targets for biofuel feedstock production. Their fronds have high rates of fatty acid synthesis to meet the demand for new membranes, but triacylglycerols (TAG) only accumulate to very low levels. Here we report on the engineering of Lemna japonica for the synthesis and accumulation of TAG in its fronds. This was achieved by expression of an estradiol-inducible cyan fluorescent protein-Arabidopsis WRINKLED1 fusion protein (CFP-AtWRI1), strong constitutive expression of a mouse diacylglycerol:acyl-CoA acyltransferase2 (MmDGAT), and a sesame oleosin variant (SiOLE(*)). Individual expression of each gene increased TAG accumulation by 1- to 7-fold relative to controls, while expression of pairs of these genes increased TAG by 7- to 45-fold. In uninduced transgenics containing all three genes, TAG accumulation increased by 45-fold to 3.6% of dry weight (DW) without severely impacting growth, and by 108-fold to 8.7% of DW after incubation on medium containing 100 μm estradiol for 4 days. TAG accumulation was accompanied by an increase in total fatty acids of up to three-fold to approximately 15% of DW. Lipid droplets from fronds of all transgenic lines were visible by confocal microscopy of BODIPY-stained fronds. At a conservative 12 tonnes (dry matter) per acre and 10% (DW) TAG, duckweed could produce 350 gallons of oil/acre/year, approximately seven-fold the yield of soybean, and similar to that of oil palm. These findings provide the foundation for optimizing TAG accumulation in duckweed and present a new opportunity for producing biofuels and lipidic bioproducts.
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Affiliation(s)
- Yuanxue Liang
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | - Xiao‐Hong Yu
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | - Sanket Anaokar
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | - Hai Shi
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | | | - Yingqi Cai
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | - Guangbin Luo
- Agronomy Department, Genetics InstituteUniversity of FloridaGainesvilleFLUSA
| | - Jin Chai
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | - Yuanheng Cai
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | | | - Fredy Altpeter
- Agronomy Department, Genetics InstituteUniversity of FloridaGainesvilleFLUSA
| | - Evan Ernst
- Cold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Howard Hughes Medical InstituteCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Jorg Schwender
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
| | - Robert A. Martienssen
- Cold Spring Harbor LaboratoryCold Spring HarborNYUSA
- Howard Hughes Medical InstituteCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - John Shanklin
- Biology DepartmentBrookhaven National LaboratoryUptonNYUSA
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16
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Zhou Y, Stepanenko A, Kishchenko O, Xu J, Borisjuk N. Duckweeds for Phytoremediation of Polluted Water. PLANTS (BASEL, SWITZERLAND) 2023; 12:589. [PMID: 36771672 PMCID: PMC9919746 DOI: 10.3390/plants12030589] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/28/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Tiny aquatic plants from the Lemnaceae family, commonly known as duckweeds, are often regarded as detrimental to the environment because of their ability to quickly populate and cover the surfaces of bodies of water. Due to their rapid vegetative propagation, duckweeds have one of the fastest growth rates among flowering plants and can accumulate large amounts of biomass in relatively short time periods. Due to the high yield of valuable biomass and ease of harvest, duckweeds can be used as feedstock for biofuels, animal feed, and other applications. Thanks to their efficient absorption of nitrogen- and phosphate-containing pollutants, duckweeds play an important role in the restorative ecology of water reservoirs. Moreover, compared to other species, duckweed species and ecotypes demonstrate exceptionally high adaptivity to a variety of environmental factors; indeed, duckweeds remove and convert many contaminants, such as nitrogen, into plant biomass. The global distribution of duckweeds and their tolerance of ammonia, heavy metals, other pollutants, and stresses are the major factors highlighting their potential for use in purifying agricultural, municipal, and some industrial wastewater. In summary, duckweeds are a powerful tool for bioremediation that can reduce anthropogenic pollution in aquatic ecosystems and prevent water eutrophication in a simple, inexpensive ecologically friendly way. Here we review the potential for using duckweeds in phytoremediation of several major water pollutants: mineral nitrogen and phosphorus, various organic chemicals, and heavy metals.
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Affiliation(s)
- Yuzhen Zhou
- School of Life Science, Huaiyin Normal University, Huai’an 223300, China
| | - Anton Stepanenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Olena Kishchenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
- Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Jianming Xu
- School of Life Science, Huaiyin Normal University, Huai’an 223300, China
| | - Nikolai Borisjuk
- School of Life Science, Huaiyin Normal University, Huai’an 223300, China
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17
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Johanndrees O, Baggs EL, Uhlmann C, Locci F, Läßle HL, Melkonian K, Käufer K, Dongus JA, Nakagami H, Krasileva KV, Parker JE, Lapin D. Variation in plant Toll/Interleukin-1 receptor domain protein dependence on ENHANCED DISEASE SUSCEPTIBILITY 1. PLANT PHYSIOLOGY 2023; 191:626-642. [PMID: 36227084 PMCID: PMC9806590 DOI: 10.1093/plphys/kiac480] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 05/07/2023]
Abstract
Toll/Interleukin-1 receptor (TIR) domains are integral to immune systems across all kingdoms. In plants, TIRs are present in nucleotide-binding leucine-rich repeat (NLR) immune receptors, NLR-like, and TIR-only proteins. Although TIR-NLR and TIR signaling in plants require the ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) protein family, TIRs persist in species that have no EDS1 members. To assess whether particular TIR groups evolved with EDS1, we searched for TIR-EDS1 co-occurrence patterns. Using a large-scale phylogenetic analysis of TIR domains from 39 algal and land plant species, we identified 4 TIR families that are shared by several plant orders. One group occurred in TIR-NLRs of eudicots and another in TIR-NLRs across eudicots and magnoliids. Two further groups were more widespread. A conserved TIR-only group co-occurred with EDS1 and members of this group elicit EDS1-dependent cell death. In contrast, a maize (Zea mays) representative of TIR proteins with tetratricopeptide repeats was also present in species without EDS1 and induced EDS1-independent cell death. Our data provide a phylogeny-based plant TIR classification and identify TIRs that appear to have evolved with and are dependent on EDS1, while others have EDS1-independent activity.
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Affiliation(s)
| | | | - Charles Uhlmann
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Federica Locci
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Henriette L Läßle
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Katharina Melkonian
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kiara Käufer
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Joram A Dongus
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hirofumi Nakagami
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Jane E Parker
- Authors for correspondence: (D.L.); (J.E.P.); (K.V.K.)
| | - Dmitry Lapin
- Authors for correspondence: (D.L.); (J.E.P.); (K.V.K.)
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18
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Michael TP. Time of Day Analysis over a Field Grown Developmental Time Course in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:166. [PMID: 36616295 PMCID: PMC9823482 DOI: 10.3390/plants12010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here, an Oryza sativa (rice) expression study that followed TOD expression in the field over an entire growing season was re-analyzed. Similar to Arabidopsis thaliana, almost all rice genes have a TOD-specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs of EARLY FLOWERING 3 (ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provide a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.
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Affiliation(s)
- Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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19
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Baggs EL, Tiersma MB, Abramson BW, Michael TP, Krasileva KV. Characterization of defense responses against bacterial pathogens in duckweeds lacking EDS1. THE NEW PHYTOLOGIST 2022; 236:1838-1855. [PMID: 36052715 PMCID: PMC9828482 DOI: 10.1111/nph.18453] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/19/2022] [Indexed: 05/19/2023]
Abstract
ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) mediates the induction of defense responses against pathogens in most angiosperms. However, it has recently been shown that a few species have lost EDS1. It is unknown how defense against disease unfolds and evolves in the absence of EDS1. We utilize duckweeds; a collection of aquatic species that lack EDS1, to investigate this question. We established duckweed-Pseudomonas pathosystems and used growth curves and microscopy to characterize pathogen-induced responses. Through comparative genomics and transcriptomics, we show that the copy number of infection-associated genes and the infection-induced transcriptional responses of duckweeds differ from other model species. Pathogen defense in duckweeds has evolved along different trajectories than in other plants, including genomic and transcriptional reprogramming. Specifically, the miAMP1 domain-containing proteins, which are absent in Arabidopsis, showed pathogen responsive upregulation in duckweeds. Despite such divergence between Arabidopsis and duckweed species, we found conservation of upregulation of certain genes and the role of hormones in response to disease. Our work highlights the importance of expanding the pool of model species to study defense responses that have evolved in the plant kingdom independent of EDS1.
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Affiliation(s)
- Erin L. Baggs
- Department of Plant and Microbial BiologyUniversity of California BerkeleyBerkeleyCA94720USA
| | - Meije B. Tiersma
- Department of Plant and Microbial BiologyUniversity of California BerkeleyBerkeleyCA94720USA
| | - Brad W. Abramson
- Plant Molecular and Cellular Biology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA92037USA
| | - Todd P. Michael
- Plant Molecular and Cellular Biology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA92037USA
| | - Ksenia V. Krasileva
- Department of Plant and Microbial BiologyUniversity of California BerkeleyBerkeleyCA94720USA
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20
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Bog M, Braglia L, Morello L, Noboa Melo KI, Schubert I, Shchepin ON, Sree KS, Xu S, Lam E, Appenroth KJ. Strategies for Intraspecific Genotyping of Duckweed: Comparison of Five Orthogonal Methods Applied to the Giant Duckweed Spirodela polyrhiza. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223033. [PMID: 36432762 PMCID: PMC9696241 DOI: 10.3390/plants11223033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 06/12/2023]
Abstract
The predominantly vegetative propagating duckweeds are of growing commercial interest. Since clonal accessions within a respective species can vary considerably with respect to their physiological as well as biochemical traits, it is critical to be able to track the clones of species of interest after their characterization. Here, we compared the efficacy of five different genotyping methods for Spirodela polyrhiza, a species with very low intraspecific sequence variations, including polymorphic NB-ARC-related loci, tubulin-gene-based polymorphism (TBP), simple sequence repeat variations (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq), and low-coverage, reduced-representation genome sequencing (GBS). Four of the five approaches could distinguish 20 to 22 genotypes out of the 23 investigated clones, while TBP resolved just seven genotypes. The choice for a particular method for intraspecific genotyping can depend on the research question and the project budget, while the combination of orthogonal methods may increase the confidence and resolution for the results obtained.
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Affiliation(s)
- Manuela Bog
- Institute of Botany and Landscape Ecology, University of Greifswald, 17489 Greifswald, Germany
| | - Luca Braglia
- Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, 20131 Milano, Italy
| | - Laura Morello
- Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, 20131 Milano, Italy
| | - Karen I. Noboa Melo
- Institute of Botany and Landscape Ecology, University of Greifswald, 17489 Greifswald, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Oleg N. Shchepin
- Institute of Botany and Landscape Ecology, University of Greifswald, 17489 Greifswald, Germany
| | - K. Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Klaus J. Appenroth
- Matthias Schleiden Institute—Plant Physiology, University of Jena, 07743 Jena, Germany
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21
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Liu P, Fang Y, Tan X, Hu Z, Jin Y, Yi Z, He K, Wei C, Chen R, Zhao H. Local endocytosis of sucrose transporter 2 in duckweed reveals the role of sucrose transporter 2 in guard cells. FRONTIERS IN PLANT SCIENCE 2022; 13:996618. [PMID: 36352881 PMCID: PMC9638040 DOI: 10.3389/fpls.2022.996618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
The local endocytosis of membrane proteins is critical for many physiological processes in plants, including the regulation of growth, development, nutrient absorption, and osmotic stress response. Much of our knowledge on the local endocytosis of plasma membrane (PM) protein only focuses on the polar growth of pollen tubes in plants and neuronal axon in animals. However, the role of local endocytosis of PM proteins in guard cells has not yet been researched. Here, we first cloned duckweed SUT2 (sucrose transporter 2) protein and then conducted subcellular and histological localization of the protein. Our results indicated that LpSUT2 (Landoltia punctata 0202 SUT2) is a PM protein highly expressed on guard cells. In vitro experiments on WT (wild type) lines treated with high sucrose concentration showed that the content of ROS (reactive oxygen species) in guard cells increased and stomatal conductance decreased. We observed the same results in the lines after overexpression of the LpSUT2 gene with newfound local endocytosis of LpSUT2. The local endocytosis mainly showed that LpSUT2 was uniformly distributed on the PM of guard cells in the early stage of development, and was only distributed in the endomembrane of guard cells in the mature stage. Therefore, we found the phenomenon of guard cell LpSUT2 local endocytosis through the changes of duckweed stomata and concluded that LpSUT2 local endocytosis might be dependent on ROS accumulation in the development of duckweed guard cells. This paper might provide future references for the genetic improvement and water-use efficiency in other crops.
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Affiliation(s)
- Penghui Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Fang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiao Tan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhubin Hu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanling Jin
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhuolin Yi
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Kaize He
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Cuicui Wei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hai Zhao
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
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22
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Hoang PTN, Fuchs J, Schubert V, Tran TBN, Schubert I. Chromosome Numbers and Genome Sizes of All 36 Duckweed Species ( Lemnaceae). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202674. [PMID: 36297698 PMCID: PMC9608876 DOI: 10.3390/plants11202674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/27/2022] [Accepted: 10/08/2022] [Indexed: 06/12/2023]
Abstract
Usually, chromosome sets (karyotypes) and genome sizes are rather stable for distinct species and therefore of diagnostic value for taxonomy. In combination with (cyto)genomics, both features provide essential cues for genome evolution and phylogenetic relationship studies within and between taxa above the species level. We present for the first time a survey on chromosome counts and genome size measurement for one or more accessions from all 36 duckweed species and discuss the evolutionary impact and peculiarities of both parameters in duckweeds.
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23
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. PLANT PHYSIOLOGY 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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24
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Sestari I, Campos ML. Into a dilemma of plants: the antagonism between chemical defenses and growth. PLANT MOLECULAR BIOLOGY 2022; 109:469-482. [PMID: 34843032 DOI: 10.1007/s11103-021-01213-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/28/2021] [Indexed: 05/21/2023]
Abstract
Chemical defenses are imperative for plant survival, but their production is often associated with growth restrictions. Here we review the most recent theories to explain this complex dilemma of plants. Plants are a nutritional source for a myriad of pests and pathogens that depend on green tissues to complete their life cycle. Rather than remaining passive victims, plants utilize an arsenal of chemical defenses to fend off biotic attack. While the deployment of such barriers is imperative for survival, the production of these chemical defenses is typically associated with negative impacts on plant growth. Here we discuss the most recent theories which explain this highly dynamic growth versus defense dilemma. Firstly, we discuss the hypothesis that the antagonism between the accumulation of chemical defenses and growth is rooted in the evolutionary history of plants and may be a consequence of terrestrialization. Then, we revise the different paradigms available to explain the growth versus chemical defense antagonism, including recent findings that update these into more comprehensive and plausible theories. Finally, we highlight state-of-the-art strategies that are now allowing the activation of growth and the concomitant production of chemical barriers in plants. Growth versus chemical defense antagonism imposes large ecological and economic costs, including increased crop susceptibility to pests and pathogens. In a world where these plant enemies are the main problem to increase food production, we believe that this review will summarize valuable information for future studies aiming to breed highly defensive plants without the typical accompanying penalties to growth.
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Affiliation(s)
- Ivan Sestari
- Coordenadoria Especial de Ciências Biológicas e Agronômicas, Universidade Federal de Santa Catarina, Curitibanos, SC, Brazil
| | - Marcelo Lattarulo Campos
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
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25
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Zhao X, Yang J, Li X, Li G, Sun Z, Chen Y, Chen Y, Xia M, Li Y, Yao L, Hou H. Identification and expression analysis of GARP superfamily genes in response to nitrogen and phosphorus stress in Spirodela polyrhiza. BMC PLANT BIOLOGY 2022; 22:308. [PMID: 35751022 PMCID: PMC9233324 DOI: 10.1186/s12870-022-03696-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND GARP transcription factors perform critical roles in plant development and response to environmental stimulus, especially in the phosphorus (P) and nitrogen (N) sensing and uptake. Spirodela polyrhiza (giant duckweed) is widely used for phytoremediation and biomass production due to its rapid growth and efficient N and P removal capacities. However, there has not yet been a comprehensive analysis of the GRAP gene family in S. polyrhiza. RESULTS We conducted a comprehensive study of GRAP superfamily genes in S. polyrhiza. First, we investigated 35 SpGARP genes which have been classified into three groups based on their gene structures, conserved motifs, and phylogenetic relationship. Then, we identified the duplication events, performed the synteny analysis, and calculated the Ka/Ks ratio in these SpGARP genes. The regulatory and co-expression networks of SpGARPs were further constructed using cis-acting element analysis and weighted correlation network analysis (WGCNA). Finally, the expression pattern of SpGARP genes were analyzed using RNA-seq data and qRT-PCR, and several NIGT1 transcription factors were found to be involved in both N and P starvation responses. CONCLUSIONS The study provides insight into the evolution and function of GARP superfamily in S. polyrhiza, and lays the foundation for the further functional verification of SpGARP genes.
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Affiliation(s)
- Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaozhe Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yimeng Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lunguang Yao
- Henan Key Laboratory of Ecological Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Collaborative Innovation Center of Water Security for Water Source Region of Mid-Line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang, 473061, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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26
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Qiao X, Zhang S, Paterson AH. Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions. Comput Struct Biotechnol J 2022; 20:3248-3256. [PMID: 35782740 PMCID: PMC9237934 DOI: 10.1016/j.csbj.2022.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 01/09/2023] Open
Abstract
Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA,Corresponding author.
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27
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Isoda M, Ito S, Oyama T. Interspecific divergence of circadian properties in duckweed plants. PLANT, CELL & ENVIRONMENT 2022; 45:1942-1953. [PMID: 35201626 DOI: 10.1111/pce.14297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock system is widely conserved in plants; however, divergence in circadian rhythm properties is poorly understood. We conducted a comparative analysis of the circadian properties of closely related duckweed species. Using a particle bombardment method, a circadian bioluminescent reporter was introduced into duckweed plants. We measured bioluminescence circadian rhythms of eight species of the genus Lemna and seven species of the genus Wolffiella at various temperatures (20, 25, and 30°C) and light conditions (constant light or constant dark). Wolffiella species inhabit relatively warm areas and lack some tissues/organs found in Lemna species. Lemna species tended to show robust bioluminescence circadian rhythms under all conditions, while Wolffiella species showed lower rhythm stability, especially at higher temperatures. For Lemna, two species (L. valdiviana and L. minuta) forming a clade showed relatively lower circadian stability. For Wolffiella, two species (W. hyalina and W. repanda) forming a clade showed extremely long period lengths. These analyses reveal that the circadian properties of species primarily reflect their phylogenetic positions. The relationships between geographical and morphological factors and circadian properties are also suggested.
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Affiliation(s)
- Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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28
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Biodiversity of Duckweed (Lemnaceae) in Water Reservoirs of Ukraine and China Assessed by Chloroplast DNA Barcoding. PLANTS 2022; 11:plants11111468. [PMID: 35684242 PMCID: PMC9182681 DOI: 10.3390/plants11111468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
Monitoring and characterizing species biodiversity is essential for germplasm preservation, academic studies, and various practical applications. Duckweeds represent a group of tiny aquatic plants that include 36 species divided into 5 genera within the Lemnaceae family. They are an important part of aquatic ecosystems worldwide, often covering large portions of the water reservoirs they inhabit, and have many potential applications, including in bioremediation, biofuels, and biomanufacturing. Here, we evaluated the biodiversity of duckweeds in Ukraine and Eastern China by characterizing specimens using the two-barcode protocol with the chloroplast atpH–atpF and psbK–psbI spacer sequences. In total, 69 Chinese and Ukrainian duckweed specimens were sequenced. The sequences were compared against sequences in the NCBI database using BLAST. We identified six species from China (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, Lemna minor, Lemna turionifera, and Wolffia globosa) and six from Ukraine (S. polyrhiza, Lemna gibba, Lemna minor, Lemna trisulca, Lemna turionifera, and Wolffia arrhiza). The most common duckweed species in the samples from Ukraine were Le. minor and S. polyrhiza, accounting for 17 and 15 out of 40 specimens, respectively. The most common duckweed species in the samples from China was S. polyrhiza, accounting for 15 out of 29 specimens. La. punctata and Le. aequinoctialis were also common in China, accounting for five and four specimens, respectively. According to both atpH–atpF and psbK–psbI barcode analyses, the species identified as Le. aequinoctialis does not form a uniform taxon similar to other duckweed species, and therefore the phylogenetic status of this species requires further clarification. By monitoring duckweeds using chloroplast DNA sequencing, we not only precisely identified local species and ecotypes, but also provided background for further exploration of native varieties with diverse genetic backgrounds. These data could be useful for future conservation, breeding, and biotechnological applications.
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29
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Qian Z, Li Y, Yang J, Shi T, Li Z, Chen J. The chromosome-level genome of a free-floating aquatic weed Pistia stratiotes provides insights into its rapid invasion. Mol Ecol Resour 2022; 22:2732-2743. [PMID: 35620935 DOI: 10.1111/1755-0998.13653] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/04/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
Abstract
Pistia stratiotes (Araceae), commonly referred to as water lettuce, is one of the most notorious weeds that cause severe damage to the economy and natural ecosystems of infested areas. In order to explore the mechanism of its rapid invasion, here, we assembled a high-quality chromosome-level genome for P. stratiotes based on the Illumina sequencing, PacBio sequencing, and Hi-C scaffolding technology. The assembled genome is 311.87 Mb in size with a contig N50 of 1.08 Mb. The contigs were further anchored on 14 pseudochromosomes with a scaffold N50 of 21.21 Mb. A total of 20,356 protein-coding genes were predicted, of which 79.35% were functionally annotated here. Evolutionary analysis showed that P. stratiotes and Colocasia esculenta were clustered together as sister lineages that diverged approximately 61 Mya. The synteny analyses indicated that two whole-genome duplication (WGD) events occurred within a short period in P. stratiotes. Moreover, comparative genome analysis indicated that the expansion of gene families corresponding to disease resistance might contribute to rapid invasion in P. stratiotes. Also, we analyzed the disease-resistance gene family (NBS-LRR) involved in plant defense. A genome-wide search in P. stratiotes genome identified 85 NBS-LRR genes in this study. In conclusion, our present study provides some new insights into the evolution of the invasive aquatic plant P. stratiotes. Our reference genome will also provide valuable resources for future invasion genomics research programs.
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Affiliation(s)
- Zhihao Qian
- Key Laboratory of Aquatic Botany and Watershed Ecology, Botanical Garden, Chinese Academy of Sciences, Wuhan, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Botanical Garden, Chinese Academy of Sciences, Wuhan, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingshan Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Botanical Garden, Chinese Academy of Sciences, Wuhan, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Botanical Garden, Chinese Academy of Sciences, Wuhan, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Zhizhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Botanical Garden, Chinese Academy of Sciences, Wuhan, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Botanical Garden, Chinese Academy of Sciences, Wuhan, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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30
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Lam E, Michael TP. Wolffia, a minimalist plant and synthetic biology chassis. TRENDS IN PLANT SCIENCE 2022; 27:430-439. [PMID: 34920947 DOI: 10.1016/j.tplants.2021.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
A highly simplified species for genome engineering would facilitate rational design of a synthetic plant. A candidate species is the aquatic, non-grass monocot wolffia (Wolffia australiana) in the Lemnaceae family. Commonly known as watermeal, wolffia is a rootless ball of several thousand cells the size of a pinhead and the fastest growing plant known on Earth. Its extreme morphological reduction is coupled to transposon-mediated streamlining of its transcriptome, which represents a core set of nonredundant protein coding genes. Despite its body plan and transcriptome being highly specialized for continuous growth, wolffia retains cell types relevant to higher plants. Systems level studies with this species could enable the creation of a defined biological chassis for synthetic plant construction.
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Affiliation(s)
- Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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31
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Abramson BW, Novotny M, Hartwick NT, Colt K, Aevermann BD, Scheuermann RH, Michael TP. The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness. PLANT PHYSIOLOGY 2022; 188:879-897. [PMID: 34893913 PMCID: PMC8825320 DOI: 10.1093/plphys/kiab564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/16/2021] [Indexed: 05/13/2023]
Abstract
The ability to trace every cell in some model organisms has led to the fundamental understanding of development and cellular function. However, in plants the complexity of cell number, organ size, and developmental time makes this a challenge even in the diminutive model plant Arabidopsis (Arabidopsis thaliana). Duckweed, basal nongrass aquatic monocots, provide an opportunity to follow every cell of an entire plant due to their small size, reduced body plan, and fast clonal growth habit. Here we present a chromosome-resolved genome for the highly invasive Lesser Duckweed (Lemna minuta) and generate a preliminary cell atlas leveraging low cell coverage single-nuclei sequencing. We resolved the 360 megabase genome into 21 chromosomes, revealing a core nonredundant gene set with only the ancient tau whole-genome duplication shared with all monocots, and paralog expansion as a result of tandem duplications related to phytoremediation. Leveraging SMARTseq2 single-nuclei sequencing, which provided higher gene coverage yet lower cell count, we profiled 269 nuclei covering 36.9% (8,457) of the L. minuta transcriptome. Since molecular validation was not possible in this nonmodel plant, we leveraged gene orthology with model organism single-cell expression datasets, gene ontology, and cell trajectory analysis to define putative cell types. We found that the tissue that we computationally defined as mesophyll expressed high levels of elemental transport genes consistent with this tissue playing a role in L. minuta wastewater detoxification. The L. minuta genome and preliminary cell map provide a paradigm to decipher developmental genes and pathways for an entire plant.
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Affiliation(s)
- Bradley W Abramson
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Nolan T Hartwick
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kelly Colt
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Brian D Aevermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, California 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, California 92093, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, USA
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Author for communication: ,
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32
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Demmig-Adams B, López-Pozo M, Polutchko SK, Fourounjian P, Stewart JJ, Zenir MC, Adams WW. Growth and Nutritional Quality of Lemnaceae Viewed Comparatively in an Ecological and Evolutionary Context. PLANTS (BASEL, SWITZERLAND) 2022; 11:145. [PMID: 35050033 PMCID: PMC8779320 DOI: 10.3390/plants11020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
This review focuses on recently characterized traits of the aquatic floating plant Lemna with an emphasis on its capacity to combine rapid growth with the accumulation of high levels of the essential human micronutrient zeaxanthin due to an unusual pigment composition not seen in other fast-growing plants. In addition, Lemna's response to elevated CO2 was evaluated in the context of the source-sink balance between plant sugar production and consumption. These and other traits of Lemnaceae are compared with those of other floating aquatic plants as well as terrestrial plants adapted to different environments. It was concluded that the unique features of aquatic plants reflect adaptations to the freshwater environment, including rapid growth, high productivity, and exceptionally strong accumulation of high-quality vegetative storage protein and human antioxidant micronutrients. It was further concluded that the insensitivity of growth rate to environmental conditions and plant source-sink imbalance may allow duckweeds to take advantage of elevated atmospheric CO2 levels via particularly strong stimulation of biomass production and only minor declines in the growth of new tissue. It is proposed that declines in nutritional quality under elevated CO2 (due to regulatory adjustments in photosynthetic metabolism) may be mitigated by plant-microbe interaction, for which duckweeds have a high propensity.
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Affiliation(s)
- Barbara Demmig-Adams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (S.K.P.); (P.F.); (J.J.S.); (M.C.Z.); (W.W.A.III)
| | - Marina López-Pozo
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48049 Bilbao, Spain;
| | - Stephanie K. Polutchko
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (S.K.P.); (P.F.); (J.J.S.); (M.C.Z.); (W.W.A.III)
| | - Paul Fourounjian
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (S.K.P.); (P.F.); (J.J.S.); (M.C.Z.); (W.W.A.III)
- International Lemna Association, Denville, NJ 07832, USA
| | - Jared J. Stewart
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (S.K.P.); (P.F.); (J.J.S.); (M.C.Z.); (W.W.A.III)
| | - Madeleine C. Zenir
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (S.K.P.); (P.F.); (J.J.S.); (M.C.Z.); (W.W.A.III)
| | - William W. Adams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (S.K.P.); (P.F.); (J.J.S.); (M.C.Z.); (W.W.A.III)
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33
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Abstract
To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.
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Acosta K, Appenroth KJ, Borisjuk L, Edelman M, Heinig U, Jansen MAK, Oyama T, Pasaribu B, Schubert I, Sorrels S, Sree KS, Xu S, Michael TP, Lam E. Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era. THE PLANT CELL 2021; 33:3207-3234. [PMID: 34273173 PMCID: PMC8505876 DOI: 10.1093/plcell/koab189] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/18/2021] [Indexed: 05/05/2023]
Abstract
The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society's pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Klaus J Appenroth
- Plant Physiology, Matthias Schleiden Institute, University of Jena, Jena 07737, Germany
| | - Ljudmilla Borisjuk
- The Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
| | - Marvin Edelman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uwe Heinig
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marcel A K Jansen
- School of Biological, Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork T23 TK30, Ireland
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Buntora Pasaribu
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Ingo Schubert
- The Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
| | - Shawn Sorrels
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Münster 48149, Germany
| | | | - Eric Lam
- Author for correspondence: (E.L.), (T.P.M.)
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Yoshida A, Taoka KI, Hosaka A, Tanaka K, Kobayashi H, Muranaka T, Toyooka K, Oyama T, Tsuji H. Characterization of Frond and Flower Development and Identification of FT and FD Genes From Duckweed Lemna aequinoctialis Nd. FRONTIERS IN PLANT SCIENCE 2021; 12:697206. [PMID: 34707626 PMCID: PMC8542802 DOI: 10.3389/fpls.2021.697206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/31/2021] [Indexed: 06/12/2023]
Abstract
Duckweeds (Araceae: Lemnoideae) are aquatic monocotyledonous plants that are characterized by their small size, rapid growth, and wide distribution. Developmental processes regulating the formation of their small leaf-like structures, called fronds, and tiny flowers are not well characterized. In many plant species, flowering is promoted by the florigen activation complex, whose major components are florigen FLOWERING LOCUS T (FT) protein and transcription factor FD protein. How this complex is regulated at the molecular level during duckweed flowering is also not well understood. In this study, we characterized the course of developmental changes during frond development and flower formation in Lemna aequinoctialis Nd, a short-day plant. Detailed observations of frond and flower development revealed that cell proliferation in the early stages of frond development is active as can be seen in the separate regions corresponding to two budding pouches in the proximal region of the mother frond. L. aequinoctialis produces two stamens of different lengths with the longer stamen growing more rapidly. Using high-throughput RNA sequencing (RNA-seq) and de novo assembly of transcripts from plants induced to flower, we identified the L. aequinoctialis FT and FD genes, whose products in other angiosperms form a transcriptional complex to promote flowering. We characterized the protein-protein interaction of duckweed FT and FD in yeast and examined the functions of the two gene products by overexpression in Arabidopsis. We found that L. aequinoctialis FTL1 promotes flowering, whereas FTL2 suppresses flowering.
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Affiliation(s)
- Akiko Yoshida
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Ken-ichiro Taoka
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Aoi Hosaka
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
- Department of Embryology, Nara Medical University, Nara, Japan
| | | | - Kiminori Toyooka
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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Romano LE, Aronne G. The World Smallest Plants ( Wolffia Sp.) as Potential Species for Bioregenerative Life Support Systems in Space. PLANTS (BASEL, SWITZERLAND) 2021; 10:1896. [PMID: 34579428 PMCID: PMC8470744 DOI: 10.3390/plants10091896] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022]
Abstract
To colonise other planets, self-sufficiency of space missions is mandatory. To date, the most promising technology to support long-duration missions is the bioregenerative life support system (BLSS), in which plants as autotrophs play a crucial role in recycling wastes and producing food and oxygen. We reviewed the scientific literature on duckweed (Lemnaceae) and reported available information on plant biological traits, nutritional features, biomass production, and space applications, especially of the genus Wolffia. Results confirmed that the smallest existing higher plants are the best candidate for space BLSS. We discussed needs for further research before criticalities to be addressed to finalise the adoption of Wolffia species for space missions.
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Affiliation(s)
- Leone Ermes Romano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
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Yang J, Zhao X, Li G, Hu S, Hou H. Frond architecture of the rootless duckweed Wolffia globosa. BMC PLANT BIOLOGY 2021; 21:387. [PMID: 34416853 PMCID: PMC8377843 DOI: 10.1186/s12870-021-03165-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The plant body in duckweed species has undergone reduction and simplification from the ancient Spirodela species towards more derived Wolffia species. Among the five duckweed genera, Wolffia members are rootless and represent the smallest and most reduced species. A better understanding of Wolffia frond architecture is necessary to fully explore duckweed evolution. RESULTS We conducted a comprehensive study of the morphology and anatomy of Wolffia globosa, the only Wolffia species in China. We first used X-ray microtomography imaging to reveal the three-dimensional and internal structure of the W. globosa frond. This showed that new fronds rapidly budded from the hollow reproductive pocket of the mother fronds and that several generations at various developmental stages could coexist in a single W. globosa frond. Using light microscopy, we observed that the meristem area of the W. globosa frond was located at the base of the reproductive pocket and composed of undifferentiated cells that continued to produce new buds. A single epidermal layer surrounded the W. globosa frond, and the mesophyll cells varied from small and dense palisade-like parenchyma cells to large, vacuolated cells from the ventral to the dorsal part. Furthermore, W. globosa fronds contained all the same organelles as other angiosperms; the most prominent organelles were chloroplasts with abundant starch grains. CONCLUSIONS Our study revealed that the reproductive strategy of W. globosa plants enables the rapid accumulation of biomass and the wide distribution of this species in various habitats. The reduced body plan and size of Wolffia are consistent with our observation that relatively few cell types are present in these plants. We also propose that W. globosa plants are not only suitable for the study of structural reduction in higher plants, but also an ideal system to explore fundamental developmental processes of higher plants that cannot be addressed using other model plants.
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Affiliation(s)
- Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shiqi Hu
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Zhejiang Marine Development Research Institute, Zhoushan, 316021, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Zhao X, Yang J, Li G, Sun Z, Chen Y, Guo W, Li Y, Chen Y, Hou H. Identification, structure analysis, and transcript profiling of phosphate transporters under Pi deficiency in duckweeds. Int J Biol Macromol 2021; 188:595-608. [PMID: 34389388 DOI: 10.1016/j.ijbiomac.2021.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022]
Abstract
Phosphate transporters (PHTs) mediate the uptake and translocation of phosphate in plants. A comprehensive analysis of the PHT family in aquatic plant is still lacking. In this study, we identified 73 PHT members of six major PHT families from four duckweed species. The phylogenetic analysis, gene structure and protein characteristics analysis revealed that PHT genes are highly conserved among duckweeds. Interaction network and miRNA target prediction showed that SpPHTs could interact with the important components of the nitrate/phosphate signaling pathway, and spo-miR399 might be a central regulator that mediates phosphate signal network in giant duckweed (Spirodela polyrhiza). The modeled 3D structure of SpPHT proteins shared a high level of homology with template structures, which provide information to understand their functions at proteomic level. The expression profiles derived from transcriptome data and quantitative real-time PCR revealed that SpPHT genes are respond to exogenous stimuli and remarkably induced by phosphate starvation, phosphate is absorbed from aquatic environment by the whole duckweed plant. This study lays the foundation for further functional studies on PHT genes for genetic improvement and the promotion of phosphate uptake efficiency in duckweeds.
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Affiliation(s)
- Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Environment and Chemical Engineering, Pingdingshan University, Pingdingshan 467000, Henan, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Guo
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixian Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yimeng Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Genome of the world's smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology. Commun Biol 2021; 4:900. [PMID: 34294872 PMCID: PMC8298427 DOI: 10.1038/s42003-021-02422-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/17/2021] [Indexed: 11/17/2022] Open
Abstract
Watermeal, Wolffia australiana, is the smallest known flowering monocot and is rich in protein. Despite its great potential as a biotech crop, basic research on Wolffia is in its infancy. Here, we generated the reference genome of a species of watermeal, W. australiana, and identified the genome-wide features that may contribute to its atypical anatomy and physiology, including the absence of roots, adaxial stomata development, and anaerobic life as a turion. In addition, we found evidence of extensive genome rearrangements that may underpin the specialized aquatic lifestyle of watermeal. Analysis of the gene inventory of this intriguing species helps explain the distinct characteristics of W. australiana and its unique evolutionary trajectory. Halim Park and Jin Hwa Park et al. report the nuclear genome sequence of the duckweed Wolffia australiana, the smallest known flowering plant. The genome assembly represents an improvement over a recently published genome and highlights genome rearrangements that may be linked to its specialized aquatic adaptations.
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Stewart JJ, Adams WW, López-Pozo M, Doherty Garcia N, McNamara M, Escobar CM, Demmig-Adams B. Features of the Duckweed Lemna That Support Rapid Growth under Extremes of Light Intensity. Cells 2021; 10:1481. [PMID: 34204703 PMCID: PMC8231585 DOI: 10.3390/cells10061481] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
This study addresses the unique functional features of duckweed via comparison of Lemna gibba grown under controlled conditions of 50 versus 1000 µmol photons m-2 s-1 and of a L. minor population in a local pond with a nearby population of the biennial weed Malva neglecta. Principal component analysis of foliar pigment composition revealed that Malva was similar to fast-growing annuals, while Lemna was similar to slow-growing evergreens. Overall, Lemna exhibited traits reminiscent of those of its close relatives in the family Araceae, with a remarkable ability to acclimate to both deep shade and full sunlight. Specific features contributing to duckweed's shade tolerance included a foliar pigment composition indicative of large peripheral light-harvesting complexes. Conversely, features contributing to duckweed's tolerance of high light included the ability to convert a large fraction of the xanthophyll cycle pool to zeaxanthin and dissipate a large fraction of absorbed light non-photochemically. Overall, duckweed exhibited a combination of traits of fast-growing annuals and slow-growing evergreens with foliar pigment features that represented an exaggerated version of that of terrestrial perennials combined with an unusually high growth rate. Duckweed's ability to thrive under a wide range of light intensities can support success in a dynamic light environment with periodic cycles of rapid expansion.
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Affiliation(s)
- Jared J. Stewart
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (W.W.A.III); (M.L.-P.); (N.D.G.); (M.M.)
| | - William W. Adams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (W.W.A.III); (M.L.-P.); (N.D.G.); (M.M.)
| | - Marina López-Pozo
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (W.W.A.III); (M.L.-P.); (N.D.G.); (M.M.)
| | - Naiara Doherty Garcia
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (W.W.A.III); (M.L.-P.); (N.D.G.); (M.M.)
| | - Maureen McNamara
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (W.W.A.III); (M.L.-P.); (N.D.G.); (M.M.)
| | - Christine M. Escobar
- Department of Aerospace Engineering Sciences, University of Colorado, Boulder, CO 80309, USA;
- Space Lab Technologies, LLC, Boulder, CO 80309, USA
| | - Barbara Demmig-Adams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; (W.W.A.III); (M.L.-P.); (N.D.G.); (M.M.)
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Barragan AC, Weigel D. Plant NLR diversity: the known unknowns of pan-NLRomes. THE PLANT CELL 2021; 33:814-831. [PMID: 33793812 PMCID: PMC8226294 DOI: 10.1093/plcell/koaa002] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/23/2020] [Indexed: 05/20/2023]
Abstract
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Wolffia arrhiza as a promising producer of recombinant hirudin. 3 Biotech 2021; 11:209. [PMID: 33927997 DOI: 10.1007/s13205-021-02762-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022] Open
Abstract
The production of recombinant proteins in transgenic plants is becoming an increasingly serious alternative to classical biopharming methods as knowledge about this process grows. Wolffia arrhiza, an aquatic plant unique in its anatomy, is a promising expression system that can grow in submerged culture in bioreactors. In our study 8550 explants were subjected to Agrobacterium-mediated transformation, and 41 independent hygromycin-resistant Wolffia lines were obtained, with the transformation efficiency of 0.48%. 40 of them contained the hirudin-1 gene (codon-optimized for expression in plants) and were independent lines of nuclear-transformed Wolffia, the transgenic insertion has been confirmed by PCR and Southern blot analysis. We have analyzed the accumulation of the target protein and its expression has been proven in three transgenic lines. The maximum accumulation of recombinant hirudin was 0.02% of the total soluble protein, which corresponds to 775.5 ± 111.9 ng g-1 of fresh weight of the plant. The results will be used in research on the development of an expression system based on Wolffia plants for the production of hirudin and other recombinant pharmaceutical proteins.
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Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds. Chromosoma 2021; 130:15-25. [PMID: 33443586 PMCID: PMC7889562 DOI: 10.1007/s00412-020-00749-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.
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