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Muthan B, Wang J, Welti R, Kosma DK, Yu L, Deo B, Khatiwada S, Vulavala VKR, Childs KL, Xu C, Durrett TP, Sanjaya SA. Mechanisms of Spirodela polyrhiza tolerance to FGD wastewater-induced heavy-metal stress: Lipidomics, transcriptomics, and functional validation. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133951. [PMID: 38492385 DOI: 10.1016/j.jhazmat.2024.133951] [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: 12/11/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Unlike terrestrial angiosperm plants, the freshwater aquatic angiosperm duckweed (Spirodela polyrhiza) grows directly in water and has distinct responses to heavy-metal stress. Plantlets accumulate metabolites, including lipids and carbohydrates, under heavy-metal stress, but how they balance metabolite levels is unclear, and the gene networks that mediate heavy-metal stress responses remain unknown. Here, we show that heavy-metal stress induced by flue gas desulfurization (FGD) wastewater reduces chlorophyll contents, inhibits growth, reduces membrane lipid biosynthesis, and stimulates membrane lipid degradation in S. polyrhiza, leading to triacylglycerol and carbohydrate accumulation. In FGD wastewater-treated plantlets, the degraded products of monogalactosyldiacylglycerol, primarily polyunsaturated fatty acids (18:3), were incorporated into triacylglycerols. Genes involved in early fatty acid biosynthesis, β-oxidation, and lipid degradation were upregulated while genes involved in cuticular wax biosynthesis were downregulated by treatment. The transcription factor gene WRINKLED3 (SpWRI3) was upregulated in FGD wastewater-treated plantlets, and its ectopic expression increased tolerance to FGD wastewater in transgenic Arabidopsis (Arabidopsis thaliana). Transgenic Arabidopsis plants showed enhanced glutathione and lower malondialdehyde contents under stress, suggesting that SpWRI3 functions in S. polyrhiza tolerance of FGD wastewater-induced heavy-metal stress. These results provide a basis for improving heavy metal-stress tolerance in plants for industrial applications.
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Affiliation(s)
- Bagyalakshmi Muthan
- Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Ruth Welti
- Division of Biology, Kansas State University, Manhattan, KS 66506-4901, USA
| | - Dylan K Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Linhui Yu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bikash Deo
- Department of Biology, Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Subhiksha Khatiwada
- Department of Biology, Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA
| | - Vijaya K R Vulavala
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Changcheng Xu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Timothy P Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Sanju A Sanjaya
- Department of Biology, Agricultural and Environmental Research Station and Energy and Environmental Science Institute, West Virginia State University, Institute, WV 25112-1000, USA.
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Chen G, Stepanenko A, Borisjuk N. Contrasting patterns of 5S rDNA repeats in European and Asian ecotypes of greater duckweed, Spirodela polyrhiza (Lemnaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1378683. [PMID: 38711607 PMCID: PMC11070557 DOI: 10.3389/fpls.2024.1378683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
Ribosomal DNA (rDNA) contains highly conserved, specifically organized sequences encoding ribosomal RNAs (rRNAs) separated by variable non-transcribed intergenic spacers (NTSs) and is abundant in eukaryotic genomes. These characteristics make the rDNA an informative molecular target to study genome organization, molecular evolution, and phylogenetics. In this study, we characterized the 5S rDNA repeats in the greater duckweed Spiroldela polyrhiza, a species known for its small size, rapid growth, highly conserved genome organization, and low mutation rate. Sequence analysis of at least 12 individually cloned PCR fragments containing the 5S rDNA units for each of six ecotypes that originated from Europe (Ukraine) and Asia (China) revealed two distinct types of 5S rDNA repeats containing NTSs of different lengths and nucleotide compositions. The shorter 5S rDNA repeat units had a highly homogeneous 400-bp NTS, with few ecotype- or region-specific single-nucleotide polymorphisms (SNPs). The longer 5S rDNA units had NTSs of 1056-1084 bp with characteristic intra- and inter-genomic variants due to specific SNPs and insertions/deletions of 4-15-bp DNA elements. We also detected significant variability in the ratio of short/long 5S rDNA variants between ecotypes of S. polyrhiza. The contrasting dynamics of the two types of 5S rDNA units, combined with the unusually low repeat copy number (for plants) in S. polyrhiza (46-220 copies per genome), shows that this species could serve as an excellent model for examining the mechanisms of concerted evolution and functional significance of rDNA variability.
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Affiliation(s)
- Guimin Chen
- School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Anton Stepanenko
- School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Molecular Genetics, Institute of Cell Biology and Genetic Engineering, Kyiv, Ukraine
| | - Nikolai Borisjuk
- School of Life Sciences, Huaiyin Normal University, Huai’an, China
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3
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Harkess A, Bewick AJ, Lu Z, Fourounjian P, Michael TP, Schmitz RJ, Meyers BC. The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza. G3 (BETHESDA, MD.) 2024; 14:jkae004. [PMID: 38190722 PMCID: PMC10989885 DOI: 10.1093/g3journal/jkae004] [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: 08/08/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
Abstract
Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.
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Affiliation(s)
- Alex Harkess
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Paul Fourounjian
- Waksman Institute of Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Todd P Michael
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri—Columbia, Columbia, MO 65211, USA
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4
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Shi H, Ernst E, Heinzel N, McCorkle S, Rolletschek H, Borisjuk L, Ortleb S, Martienssen R, Shanklin J, Schwender J. Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis. BMC PLANT BIOLOGY 2023; 23:458. [PMID: 37789269 PMCID: PMC10546790 DOI: 10.1186/s12870-023-04480-9] [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: 05/08/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions. RESULTS To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts. CONCLUSIONS Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.
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Affiliation(s)
- Hai Shi
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Evan Ernst
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Nicolas Heinzel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Sean McCorkle
- Brookhaven National Laboratory, Computational Science Initiative, Upton, NY, 11973, USA
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Stefan Ortleb
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Robert Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jorg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.
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5
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Oláh V, Appenroth KJ, Lam E, Sree KS. Sixth International Conference on Duckweed Research and Applications Presents Lemnaceae as a Model Plant System in the Genomics and Postgenomics Era. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112134. [PMID: 37299113 DOI: 10.3390/plants12112134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
The 6th International Conference on Duckweed Research and Applications (6th ICDRA) was organized at the Institute of Plant Genetics and Crop Plant Research (IPK) located in Gatersleben, Germany, from 29 May to 1 June 2022. The growing community of duckweed research and application specialists was noted with participants from 21 different countries including an increased share of newly integrated young researchers. The four-day conference focused on diverse aspects of basic and applied research together with practical applications of these tiny aquatic plants that could have an enormous potential for biomass production.
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Affiliation(s)
- Viktor Oláh
- Department of Botany, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | | | - Eric Lam
- Department Plant Biology, Rutgers State University of New Jersey, New Brunswick, NJ 08901, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
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6
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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: 5] [Impact Index Per Article: 5.0] [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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7
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Sun Z, Zhao X, Li G, Yang J, Chen Y, Xia M, Hwang I, Hou H. Metabolic flexibility during a trophic transition reveals the phenotypic plasticity of greater duckweed (Spirodela polyrhiza 7498). THE NEW PHYTOLOGIST 2023; 238:1386-1402. [PMID: 36856336 DOI: 10.1111/nph.18844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The greater duckweed (Spirodela polyrhiza 7498) exhibits trophic diversity (photoautotrophic, heterotrophic, photoheterotrophic, and mixotrophic growth) depending on the availability of exogenous organic carbon sources and light. Here, we show that the ability to transition between various trophic growth conditions is an advantageous trait, providing great phenotypic plasticity and metabolic flexibility in S. polyrhiza 7498. By comparing S. polyrhiza 7498 growth characteristics, metabolic acclimation, and cellular ultrastructure across these trophic modes, we show that mixotrophy decreases photosynthetic performance and relieves the CO2 limitation of photosynthesis by enhancing the CO2 supply through the active respiration pathway. Proteomic and metabolomic analyses corroborated that S. polyrhiza 7498 increases its intracellular CO2 and decreases reactive oxygen species under mixotrophic and heterotrophic conditions, which substantially suppressed the wasteful photorespiration and oxidative-damage pathways. As a consequence, mixotrophy resulted in a higher biomass yield than the sum of photoautotrophy and heterotrophy. Our work provides a basis for using trophic transitions in S. polyrhiza 7498 for the enhanced accumulation of value-added products.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - 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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8
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Yang L, Luo X, Sun J, Ma X, Ren Q, Wang Y, Wang W, He Y, Li Q, Han B, Yu Y, Sun J. The Antimicrobial Potential and Aquaculture Wastewater Treatment Ability of Penaeidins 3a Transgenic Duckweed. PLANTS (BASEL, SWITZERLAND) 2023; 12:1715. [PMID: 37111939 PMCID: PMC10144588 DOI: 10.3390/plants12081715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 06/19/2023]
Abstract
With the development of aquaculture, wastewater treatment and diseases have been paid more and more attention. The question of how to improve the immunity of aquatic species, as well as treat aquaculture wastewater, has become an urgent problem. In this study, duckweed with a high protein content (37.4%) (Lemna turionifera 5511) has been employed as a feedstock for aquatic wastewater treatment and the production of antimicrobial peptides. Penaeidins 3a (Pen3a), from Litopenaeus vannamei, were expressed under the control of CaMV-35S promoter in duckweed. Bacteriostatic testing using the Pen3a duckweed extract showed its antibacterial activity against Escherichia coli and Staphylococcus aureus. Transcriptome analysis of wild type (WT) duckweed and Pen3a duckweed showed different results, and the protein metabolic process was the most up-regulated by differential expression genes (DEGs). In Pen3a transgenic duckweed, the expression of sphingolipid metabolism and phagocytosis process-related genes have been significantly up-regulated. Quantitative proteomics suggested a remarkable difference in protein enrichment in the metabolic pathway. Pen3a duckweed decreased the bacterial number, and effectively inhibited the growth of Nitrospirae. Additionally, Pen3a duckweed displayed better growth in the lake. The study showed the nutritional and antibacterial value of duckweed as an animal feed ingredient.
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Affiliation(s)
- Lin Yang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Ximeng Luo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Jinge Sun
- Tianjin Nankai Xiangyu School, Tianjin 300387, China
| | - Xu Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Qiuting Ren
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Yaya Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Wenqiao Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Yuman He
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Qingqing Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Bing Han
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Yiqi Yu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
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9
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Acosta K, Sorrels S, Chrisler W, Huang W, Gilbert S, Brinkman T, Michael TP, Lebeis SL, Lam E. Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:872. [PMID: 36840219 PMCID: PMC9965182 DOI: 10.3390/plants12040872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed-associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Shawn Sorrels
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - William Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA 99354, USA
| | - Weijuan Huang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Thomas Brinkman
- 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
| | - Sarah L. Lebeis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
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10
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Pakdee O, Tshering S, Pokethitiyook P, Meetam M. Examination of the Metallothionein Gene Family in Greater Duckweed Spirodela polyrhiza. PLANTS (BASEL, SWITZERLAND) 2022; 12:plants12010125. [PMID: 36616254 PMCID: PMC9824710 DOI: 10.3390/plants12010125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 05/27/2023]
Abstract
Duckweeds are aquatic plants that proliferate rapidly in a wide range of freshwaters, and they are regarded as a potential source of sustainable biomass for various applications and the cost-effective bioremediation of heavy metal pollutants. To understand the cellular and molecular basis that underlies the high metal tolerance and accumulation capacity of duckweeds, we examined the forms and transcript profiles of the metallothionein (MT) gene family in the model duckweed Spirodela polyrhiza, whose genome has been completely sequenced. Four S. polyrhiza MT-like genes were identified and annotated as SpMT2a, SpMT2b, SpMT3, and SpMT4. All except SpMT2b showed high sequence homology including the conserved cysteine residues with the previously described MTs from flowering plants. The S. polyrhiza genome appears to lack the root-specific Type 1 MT. The transcripts of SpMT2a, SpMT2b, and SpMT3 could be detected in the vegetative whole-plant tissues. The transcript abundance of SpMT2a was upregulated several-fold in response to cadmium stress, and the heterologous expression of SpMT2a conferred copper and cadmium tolerance to the metal-sensitive ∆cup1 strain of Saccharomyces cerevisiae. Based on these results, we proposed that SpMT2a may play an important role in the metal detoxification mechanism of duckweed.
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Affiliation(s)
- Orathai Pakdee
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Shomo Tshering
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Prayad Pokethitiyook
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Metha Meetam
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
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11
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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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12
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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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13
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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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14
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Xiong J, Tang X, Wei M, Yu W. Comparative full-length transcriptome analysis by Oxford Nanopore Technologies reveals genes involved in anthocyanin accumulation in storage roots of sweet potatoes ( Ipomoea batatas L.). PeerJ 2022; 10:e13688. [PMID: 35846886 PMCID: PMC9285475 DOI: 10.7717/peerj.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/16/2022] [Indexed: 01/17/2023] Open
Abstract
Background Storage roots of sweet potatoes (Ipomoea batatas L.) with different colors vary in anthocyanin content, indicating different economically agronomic trait. As the newest DNA/RNA sequencing technology, Oxford Nanopore Technologies (ONT) have been applied in rapid transcriptome sequencing for investigation of genes related to nutrient metabolism. At present, few reports concern full-length transcriptome analysis based on ONT for study on the molecular mechanism of anthocyanin accumulation leading to color change of tuberous roots of sweet potato cultivars. Results The storage roots of purple-fleshed sweet potato (PFSP) and white-fleshed sweet potato (WFSP) at different developmental stages were subjected to anthocyanin content comparison by UV-visible spectroscopy as well as transcriptome analysis at ONT MinION platform. UV-visible spectrophotometric measurements demonstrated the anthocyanin content of PFSP was much higher than that of WFSP. ONT RNA-Seq results showed each sample generated average 2.75 GB clean data with Full-Length Percentage (FL%) over 70% and the length of N50 ranged from 1,192 to 1,395 bp, indicating reliable data for transcriptome analysis. Subsequent analysis illustrated intron retention was the most prominent splicing event present in the resulting transcripts. As compared PFSP with WFSP at the relative developmental stages with the highest (PH vs. WH) and the lowest (PL vs. WL) anthocyanin content, 282 and 216 genes were up-regulated and two and 11 genes were down-regulated respectively. The differential expression genes involved in flavonoid biosynthesis pathway include CCoAOMT, PpLDOX, DFR, Cytochrome P450, CHI, and CHS. The genes encoding oxygenase superfamily were significantly up-regulated when compared PFSP with WFSP at the relative developmental stages. Conclusions Comparative full-length transcriptome analysis based on ONT serves as an effective approach to detect the differences in anthocyanin accumulation in the storage roots of different sweet potato cultivars at transcript level, with noting that some key genes can now be closely related to flavonoids biosynthesis. This study helps to improve understanding of molecular mechanism for anthocyanin accumulation in sweet potatoes and also provides a theoretical basis for high-quality sweet potato breeding.
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Affiliation(s)
- Jun Xiong
- Agricultural College, Guangxi University, Nanning, China,Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiuhua Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Minzheng Wei
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wenjin Yu
- Agricultural College, Guangxi University, Nanning, China
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15
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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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16
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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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17
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Bog M, Appenroth KJ, Schneider P, Sree KS. Intraspecific Diversity in Aquatic Ecosystems: Comparison between Spirodela polyrhiza and Lemna minor in Natural Populations of Duckweed. PLANTS 2022; 11:plants11070968. [PMID: 35406948 PMCID: PMC9003317 DOI: 10.3390/plants11070968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022]
Abstract
Samples of two duckweed species, Spirodela polyrhiza and Lemna minor, were collected around small ponds and investigated concerning the question of whether natural populations of duckweeds constitute a single clone, or whether clonal diversity exists. Amplified fragment length polymorphism was used as a molecular method to distinguish clones of the same species. Possible intraspecific diversity was evaluated by average-linkage clustering. The main criterion to distinguish one clone from another was the 95% significance level of the Jaccard dissimilarity index for replicated samples. Within natural populations of L. minor, significant intraspecific genetic differences were detected. In each of the three small ponds harbouring populations of L. minor, based on twelve samples, between four and nine distinct clones were detected. Natural populations of L. minor consist of a mixture of several clones representing intraspecific biodiversity in an aquatic ecosystem. Moreover, identical distinct clones were discovered in more than one pond, located at a distance of 1 km and 2.4 km from each other. Evidently, fronds of L. minor were transported between these different ponds. The genetic differences for S. polyrhiza, however, were below the error-threshold of the method within a pond to detect distinct clones, but were pronounced between samples of two different ponds.
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Affiliation(s)
- Manuela Bog
- Institute of Botany and Landscape Ecology, University of Greifswald, D-17489 Greifswald, Germany;
| | - Klaus-Juergen Appenroth
- Matthias Schleiden Institute-Plant Physiology, University of Jena, D-07743 Jena, Germany;
- Correspondence: (K.-J.A.); or (K.S.S.); Tel.: +49-3641-949233 (K.-J.A.); +91-9999-672921 (K.S.S.)
| | - Philipp Schneider
- Matthias Schleiden Institute-Plant Physiology, University of Jena, D-07743 Jena, Germany;
| | - K. Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
- Correspondence: (K.-J.A.); or (K.S.S.); Tel.: +49-3641-949233 (K.-J.A.); +91-9999-672921 (K.S.S.)
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18
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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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19
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Zhong Y, Wang L, Ma Z, Du X. Physiological responses and transcriptome analysis of Spirodela polyrhiza under red, blue, and white light. PLANTA 2021; 255:11. [PMID: 34855030 DOI: 10.1007/s00425-021-03764-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Red light (RL) accelerated starch accumulation in S. polyrhiza, but higher protein content under blue light (BL) was associated with the upregulation of most DEGs enriched for specific GO terms and KEGG pathways. Red light (RL) and blue light (BL) greatly influence the growth and physiological processes of duckweed. Physiological and molecular mechanisms underlying the response of duckweed to different light qualities remain unclear. This study employed physiological and transcriptomic analyses on duckweed, Spirodela polyrhiza "5510", to elucidate its differential response mechanisms under RL, BL, and white light conditions. Changes in growth indicators, ultrastructure alterations, metabolite accumulations, and differentially expressed genes (DEGs) were measured. The results showed that BL promoted both biomass and protein accumulations, while RL promoted starch accumulation. A total of 633, 518, and 985 DEGs were found in white-vs-red, white-vs-blue, and red-vs-blue comparison groups, respectively. In Gene Ontology (GO) enrichment analysis, the DEGs in all three comparison groups were significantly enriched in two GO terms, carboxylic acid metabolic process and lyase activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the DEGs were greatly enriched in two pathways, histidine metabolism and isoquinoline alkaloid biosynthesis. Higher protein content under BL was associated with the upregulation of most DEGs enriched with the GO terms and KEGG pathways. Furthermore, the light qualities influenced the gene expression patterns of other metabolic pathways, like carotenoid biosynthesis, and the regulation of these genes may explain the level of photosynthetic pigment content. The results revealed the physiological changes and transcriptome-level responses of duckweed to three light qualities, thereby providing bases for further research studies on the ability of duckweed as a biomass energy source.
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Affiliation(s)
- Yu Zhong
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Le Wang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - ZiMing Ma
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062, China.
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20
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Lemnaceae and Orontiaceae Are Phylogenetically and Morphologically Distinct from Araceae. PLANTS 2021; 10:plants10122639. [PMID: 34961110 PMCID: PMC8704351 DOI: 10.3390/plants10122639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/18/2022]
Abstract
Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence has called into question their phylogenetic independence, with some authors asserting instead that duckweeds should be reclassified as subfamily Lemnoideae of an expanded family Araceae. Although a close phylogenetic relationship of duckweeds with traditional Araceae has been supported by multiple studies, the taxonomic disposition of duckweeds must be evaluated more critically to promote nomenclatural stability and utility. Subsuming duckweeds as a morphologically incongruent lineage of Araceae effectively eliminates the family category of Lemnaceae that has been widely used for many years. Instead, we suggest that Araceae subfamily Orontioideae should be restored to family status as Orontiaceae, which thereby would enable the recognition of three morphologically and phylogenetically distinct lineages: Araceae, Lemnaceae, and Orontiaceae.
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21
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Xie S, Leung AWS, Zheng Z, Zhang D, Xiao C, Luo R, Luo M, Zhang S. Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. Innovation (N Y) 2021; 2:100153. [PMID: 34901902 PMCID: PMC8640597 DOI: 10.1016/j.xinn.2021.100153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them. Nanopore-seq can dissect native DNA/RNA molecules from any organisms at unlimited length A wide variety of algorithms greatly increase the accuracy of signal decoding in Nanopore-Seq Nanopore-Seq significantly facilitates genome assembly and structural variant calling, and can simultaneously detect base modifications These advantages ensure its great potentials in future medical and agricultural practices
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Affiliation(s)
- Shangqian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China
| | - Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Zhenxian Zheng
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Dake Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou 510060, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Ming Luo
- Agriculture and Biotechnology Research Center, Guangdong Provincial Key Laboratory of Applied Botany, Center of Economic Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shoudong Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China.,Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
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22
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Upadhyay RK, Shao J, Mattoo AK. Genomic analysis of the polyamine biosynthesis pathway in duckweed Spirodela polyrhiza L.: presence of the arginine decarboxylase pathway, absence of the ornithine decarboxylase pathway, and response to abiotic stresses. PLANTA 2021; 254:108. [PMID: 34694486 PMCID: PMC8545783 DOI: 10.1007/s00425-021-03755-5] [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: 07/08/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Identification of the polyamine biosynthetic pathway genes in duckweed S. polyrhiza reveals presence of prokaryotic as well as land plant-type ADC pathway but absence of ODC encoding genes. Their differential gene expression and transcript abundance is shown modulated by exogenous methyl jasmonate, salinity, and acidic pH. Genetic components encoding for polyamine (PA) biosynthetic pathway are known in several land plant species; however, little is known about them in aquatic plants. We utilized recently sequenced three duckweed (Spirodela polyrhiza) genome assemblies to map PA biosynthetic pathway genes in S. polyrhiza. PA biosynthesis in most higher plants except for Arabidopsis involves two pathways, via arginine decarboxylase (ADC) and ornithine decarboxylase (ODC). ADC-mediated PA biosynthetic pathway genes, namely, one arginase (SpARG1), two arginine decarboxylases (SpADC1, SpADC2), one agmatine iminohydrolase/deiminase (SpAIH), one N-carbamoyl putrescine amidase (SpCPA), three S-adenosylmethionine decarboxylases (SpSAMDc1, 2, 3), one spermidine synthase (SpSPDS1) and one spermine synthase (SpSPMS1) in S. polyrhiza genome were identified here. However, no locus was found for ODC pathway genes in this duckweed. Hidden Markov Model protein domain analysis established that SpADC1 is a prokaryotic/biodegradative type ADC and its molecular phylogenic classification fell in a separate prokaryotic origin ADC clade with SpADC2 as a biosynthetic type of arginine decarboxylase. However, thermospermine synthase (t-SPMS)/Aculis5 genes were not found present. Instead, one of the annotated SPDS may also function as SPMS, since it was found associated with the SPMS phylogenetic clade along with known SPMS genes. Moreover, we demonstrate that S. polyrhiza PA biosynthetic gene transcripts are differentially expressed in response to unfavorable conditions, such as exogenously added salt, methyl jasmonate, or acidic pH environment as well as in extreme temperature regimes. Thus, S. polyrhiza genome encodes for complete polyamine biosynthesis pathway and the genes are transcriptionally active in response to changing environmental conditions suggesting an important role of polyamines in this aquatic plant.
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Affiliation(s)
- Rakesh K Upadhyay
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA.
| | - Jonathan Shao
- Bioinformatics-North East Area Office, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD, 20705-2350, USA.
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23
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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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24
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Chen G, Stepanenko A, Borisjuk N. Mosaic Arrangement of the 5S rDNA in the Aquatic Plant Landoltia punctata (Lemnaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:678689. [PMID: 34249048 PMCID: PMC8264772 DOI: 10.3389/fpls.2021.678689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Duckweeds are a group of monocotyledonous aquatic plants in the Araceae superfamily, represented by 37 species divided into five genera. Duckweeds are the fastest growing flowering plants and are distributed around the globe; moreover, these plants have multiple applications, including biomass production, wastewater remediation, and making pharmaceutical proteins. Dotted duckweed (Landoltia punctata), the sole species in genus Landoltia, is one of the most resilient duckweed species. The ribosomal DNA (rDNA) encodes the RNA components of ribosomes and represents a significant part of plant genomes but has not been comprehensively studied in duckweeds. Here, we characterized the 5S rDNA genes in L. punctata by cloning and sequencing 25 PCR fragments containing the 5S rDNA repeats. No length variation was detected in the 5S rDNA gene sequence, whereas the nontranscribed spacer (NTS) varied from 151 to 524 bp. The NTS variants were grouped into two major classes, which differed both in nucleotide sequence and the type and arrangement of the spacer subrepeats. The dominant class I NTS, with a characteristic 12-bp TC-rich sequence present in 3-18 copies, was classified into four subclasses, whereas the minor class II NTS, with shorter, 9-bp nucleotide repeats, was represented by two identical sequences. In addition to these diverse subrepeats, class I and class II NTSs differed in their representation of cis-elements and the patterns of predicted G-quadruplex structures, which may influence the transcription of the 5S rDNA. Similar to related duckweed species in the genus Spirodela, L. punctata has a relatively low rDNA copy number, but in contrast to Spirodela and the majority of other plants, the arrangement of the 5S rDNA units demonstrated an unusual, heterogeneous pattern in L. punctata, as revealed by analyzing clones containing double 5S rDNA neighboring units. Our findings may further stimulate the research on the evolution of the plant rDNA and discussion of the molecular forces driving homogenization of rDNA repeats in concerted evolution.
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Affiliation(s)
- Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
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25
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Jiang M, Wang P, Xu L, Ye X, Fan H, Cheng J, Chen J. In silico analysis of glycosyltransferase 2 family genes in duckweed ( Spirodela polyrhiza) and its role in salt stress tolerance. Open Life Sci 2021; 16:583-593. [PMID: 34179502 PMCID: PMC8216227 DOI: 10.1515/biol-2021-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/27/2021] [Accepted: 05/22/2021] [Indexed: 11/15/2022] Open
Abstract
Plant glycosyltransferase 2 (GT2) family genes are involved in plant abiotic stress tolerance. However, the roles of GT2 genes in the abiotic resistance in freshwater plants are largely unknown. We identified seven GT2 genes in duckweed, remarkably more than those in the genomes of Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Nymphaea tetragona, Persea americana, Zostera marina, and Ginkgo biloba, suggesting a significant expansion of this family in the duckweed genome. Phylogeny resolved the GT2 family into two major clades. Six duckweed genes formed an independent subclade in Clade I, and the other was clustered in Clade II. Gene structure and protein domain analysis showed that the lengths of the seven duckweed GT2 genes were varied, and the majority of GT2 genes harbored two conserved domains, PF04722.12 and PF00535.25. The expression of all Clade I duckweed GT2 genes was elevated at 0 h after salt treatment, suggesting a common role of these genes in rapid response to salt stress. The gene Sp01g00794 was highly expressed at 12 and 24 h after salt treatment, indicating its association with salt stress resilience. Overall, these results are essential for studies on the molecular mechanisms in stress response and resistance in aquatic plants.
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Affiliation(s)
- Mingliang Jiang
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Ligang Xu
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Hongxiang Fan
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Junxiang Cheng
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jinting Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
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26
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Kudryavtseva N, Ermolaev A, Karlov G, Kirov I, Shigyo M, Sato S, Khrustaleva L. A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps. Int J Mol Sci 2021; 22:5860. [PMID: 34070753 PMCID: PMC8215642 DOI: 10.3390/ijms22115860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps.
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Affiliation(s)
- Natalya Kudryavtseva
- Laboratory of Plant Cell Engineering, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia;
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
| | - Aleksey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Kurchatov Genomics Center of ARRIAB, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Masayoshi Shigyo
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan;
| | - Shusei Sato
- Graduate School of Life Science, Tohoku University, Miyagi 980-8577, Japan;
| | - Ludmila Khrustaleva
- Laboratory of Plant Cell Engineering, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia;
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia;
- Department of Botany, Breeding and Seed Production of Garden Plants, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
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27
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Harkess A, McLoughlin F, Bilkey N, Elliott K, Emenecker R, Mattoon E, Miller K, Czymmek K, Vierstra RD, Meyers BC, Michael TP. Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2491-2500. [PMID: 33454741 DOI: 10.1093/jxb/erab006] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 01/13/2021] [Indexed: 05/11/2023]
Abstract
Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. Here, we studied the genome and proteome of Spirodela polyrhiza, or greater duckweed, which has the largest body plan yet the smallest genome size in the family (1C=150 Mb). Using Oxford Nanopore sequencing combined with Hi-C scaffolding, we generated a highly contiguous, chromosome-scale assembly of S. polyrhiza line Sp7498 (Sp7498_HiC). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations relative to a recent PacBio assembly of Sp7498, highlighting the need for orthogonal long-range scaffolding techniques such as Hi-C and BioNano optical mapping. Shotgun proteomics of Sp7498 verified the expression of ~2250 proteins and revealed a high abundance of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome illustrates the utility of duckweed as a model for genomics- and proteomics-based education.
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Affiliation(s)
- Alex Harkess
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | | | - Natasha Bilkey
- Department of Biology, Washington University, St Louis, MO, USA
| | - Kiona Elliott
- Department of Biology, Washington University, St Louis, MO, USA
| | - Ryan Emenecker
- Department of Biology, Washington University, St Louis, MO, USA
| | - Erin Mattoon
- Department of Biology, Washington University, St Louis, MO, USA
| | - Kari Miller
- Department of Biology, Washington University, St Louis, MO, USA
| | - Kirk Czymmek
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | | | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Todd P Michael
- Department of Informatics, J. Craig Venter Institute (JCVI), San Diego, CA, USA
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
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28
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Fourounjian P, Slovin J, Messing J. Flowering and Seed Production across the Lemnaceae. Int J Mol Sci 2021; 22:2733. [PMID: 33800476 PMCID: PMC7962950 DOI: 10.3390/ijms22052733] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/23/2021] [Accepted: 03/05/2021] [Indexed: 12/16/2022] Open
Abstract
Plants in the family Lemnaceae are aquatic monocots and the smallest, simplest, and fastest growing angiosperms. Their small size, the smallest family member is 0.5 mm and the largest is 2.0 cm, as well as their diverse morphologies make these plants ideal for laboratory studies. Their rapid growth rate is partially due to the family's neotenous lifestyle, where instead of maturing and producing flowers, the plants remain in a juvenile state and continuously bud asexually. Maturation and flowering in the wild are rare in most family members. To promote further research on these unique plants, we have optimized laboratory flowering protocols for 3 of the 5 genera: Spirodela; Lemna; and Wolffia in the Lemnaceae. Duckweeds were widely used in the past for research on flowering, hormone and amino acid biosynthesis, the photosynthetic apparatus, and phytoremediation due to their aqueous lifestyle and ease of aseptic culture. There is a recent renaissance in interest in growing these plants as non-lignified biomass sources for fuel production, and as a resource-efficient complete protein source. The genome sequences of several Lemnaceae family members have become available, providing a foundation for genetic improvement of these plants as crops. The protocols for maximizing flowering described herein are based on screens testing daylength, a variety of media, supplementation with salicylic acid or ethylenediamine-N,N'-bis(2-hydroxyphenylacetic acid) (EDDHA), as well as various culture vessels for effects on flowering of verified Lemnaceae strains available from the Rutgers Duckweed Stock Cooperative.
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Affiliation(s)
- Paul Fourounjian
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Janet Slovin
- Genetic Improvement of Fruits & Vegetables Laboratory, USDA, Beltsville, MD 20705, USA;
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
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29
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Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martienssen RA, Lam E. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Res 2021; 31:225-238. [PMID: 33361111 PMCID: PMC7849404 DOI: 10.1101/gr.266429.120] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/16/2020] [Indexed: 11/24/2022]
Abstract
Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
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Affiliation(s)
- Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Evan Ernst
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nolan Hartwick
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Philomena Chu
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Douglas Bryant
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Stefan Ortleb
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Erin L Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye, Kerala 671316, India
| | | | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Florian Jupe
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Justin P Sandoval
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Ljudmylla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Joseph R Ecker
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Robert A Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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30
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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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Upadhyay RK, Edelman M, Mattoo AK. Identification, Phylogeny, and Comparative Expression of the Lipoxygenase Gene Family of the Aquatic Duckweed, Spirodela polyrhiza, during Growth and in Response to Methyl Jasmonate and Salt. Int J Mol Sci 2020; 21:E9527. [PMID: 33333747 PMCID: PMC7765210 DOI: 10.3390/ijms21249527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022] Open
Abstract
Lipoxygenases (LOXs) (EC 1.13.11.12) catalyze the oxygenation of fatty acids and produce oxylipins, including the plant hormone jasmonic acid (JA) and its methyl ester, methyl jasmonate (MeJA). Little information is available about the LOX gene family in aquatic plants. We identified a novel LOX gene family comprising nine LOX genes in the aquatic plant Spirodela polyrhiza (greater duckweed). The reduced anatomy of S. polyrhiza did not lead to a reduction in LOX family genes. The 13-LOX subfamily, with seven genes, predominates, while the 9-LOX subfamily is reduced to two genes, an opposite trend from known LOX families of other plant species. As the 13-LOX subfamily is associated with the synthesis of JA/MeJA, its predominance in the Spirodela genome raises the possibility of a higher requirement for the hormone in the aquatic plant. JA-/MeJA-based feedback regulation during culture aging as well as the induction of LOX gene family members within 6 h of salt exposure are demonstrated.
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Affiliation(s)
- Rakesh K. Upadhyay
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA
| | - Marvin Edelman
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Autar K. Mattoo
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705-2350, USA
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Yang L, Chen Y, Shi L, Yu J, Yao J, Sun J, Zhao L, Sun J. Enhanced Cd accumulation by Graphene oxide (GO) under Cd stress in duckweed. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 229:105579. [PMID: 33075615 DOI: 10.1016/j.aquatox.2020.105579] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/11/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Effective phytoremediation by aquatic plant such as duckweed could be applied to solve Cd pollution. In the present study, the impact of Graphene oxide (GO) on the accumulation of Cd in duckweed has been studied. The response of duckweed was also investigated, concluding growth, Cd2+ flux, and gene expression response. Results showed that GO promoted the accumulation of Cd in duckweed. After 6 h of Cd enrichment in duckweed, Cd content was about 1.4 times that of the control group at fronds and 1.25 times that of the control group at roots, meanwhile, Cd content in the water system was 0.67 times that of the control group. The Cd2+ influx increased significantly. 4471 genes were up-regulated and 3230 genes were down-regulated significantly as duckweed treated with GO under Cd treatment. Moreover, phagosome pathway was downregulated, some key proteins: Stx7, Rab7 and Tubastatin B (TUBB) were significantly downregulated with GO addition under Cd stress. Scanning electron microscope (SEM) observation showed that GO and Cd were attached on the cell surface of duckweed as white crystal. GO could be applied in phytoremediation by duckweed of Cd in aquatic system.
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Affiliation(s)
- Lin Yang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 300387, Tianjin, China.
| | - Yikai Chen
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 300387, Tianjin, China
| | - Leqian Shi
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 300387, Tianjin, China
| | - Jie Yu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 300387, Tianjin, China
| | - Jie Yao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 300387, Tianjin, China
| | - Jinge Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 300387, Tianjin, China
| | - Ling Zhao
- College of Life Sciences, Department of Plant Biology and Ecology, Nankai University, 300071, Tianjin, China
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, 300387, Tianjin, China.
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Edelman M, Appenroth KJ, Sree KS. Editorial: Duckweed: Biological Chemistry and Applications. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.615135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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Hoang PTN, Fiebig A, Novák P, Macas J, Cao HX, Stepanenko A, Chen G, Borisjuk N, Scholz U, Schubert I. Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. Sci Rep 2020; 10:19230. [PMID: 33154426 PMCID: PMC7645714 DOI: 10.1038/s41598-020-75728-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the monocot order Alismatales. They display the most rapid growth among flowering plants, vary ~ 14-fold in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two mainly asexually propagating species: S. polyrhiza (2n = 40; 160 Mbp/1C) and S. intermedia (2n = 36; 160 Mbp/1C). This study combined comparative cytogenetics and de novo genome assembly based on PacBio, Illumina and Oxford Nanopore (ON) reads to obtain the first genome reference for S. intermedia and to compare its genomic features with those of the sister species S. polyrhiza. Both species' genomes revealed little more than 20,000 putative protein-coding genes, very low rDNA copy numbers and a low amount of repetitive sequences, mainly Ty3/gypsy retroelements. The detection of a few new small chromosome rearrangements between both Spirodela species refined the karyotype and the chromosomal sequence assignment for S. intermedia.
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Affiliation(s)
- Phuong T N Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
- Biology Faculty, Dalat University, District 8, Dalat City, Lamdong Province, Vietnam
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany.
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Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020; 13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
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Affiliation(s)
- Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Dumschott K, Schmidt MHW, Chawla HS, Snowdon R, Usadel B. Oxford Nanopore sequencing: new opportunities for plant genomics? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5313-5322. [PMID: 32459850 PMCID: PMC7501810 DOI: 10.1093/jxb/eraa263] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 05/25/2020] [Indexed: 05/06/2023]
Abstract
DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today's long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.
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Affiliation(s)
- Kathryn Dumschott
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Maximilian H-W Schmidt
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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37
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Chen D, Zhang H, Wang Q, Shao M, Li X, Chen D, Zeng R, Song Y. Intraspecific variations in cadmium tolerance and phytoaccumulation in giant duckweed (Spirodela polyrhiza). JOURNAL OF HAZARDOUS MATERIALS 2020; 395:122672. [PMID: 32305716 DOI: 10.1016/j.jhazmat.2020.122672] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 05/25/2023]
Abstract
Duckweeds are widely recognized for the heavy metal phytoremediation. However, the intraspecific variations in biological responses of duckweeds to heavy metal remain largely unknown. Here, the toxicity and phytoaccumulation of cadmium (Cd) were synchronously evaluated in 30 accessions of giant duckweed (Spirodela polyrhiza) collected from different provenances in Southern China. Exposure to 1 μM Cd decreased relative growth rates of dry weight, fronds number and fronds area, as well as photosynthetic pigment contents, while it increased H2O2 accumulation, lipid peroxidation and activities of anti-oxidant enzymes in the majority of accessions. Cd treatment led to remarkable Cd accumulation but little changes in the starch content in giant duckweed. The biological responses to Cd varied among the accessions. Further correlation analysis indicated that growth traits and Cd concentration were positively correlated with Cd accumulation, while the contents of chlorophyll, H2O2 and MDA were negatively associated with Cd accumulation. Our results proved the great intraspecific variation in Cd tolerance of giant duckweed, suggesting a valuable natural resource for Cd phytoremediation. Moreover, different mechanisms may be exploited by S. polyrhiza for phytoaccumulation, but growth maintenance, Cd uptake and antioxidative enzyme-independent ROS-scavenging under Cd exposure are the common mechanisms contributing to Cd accumulation ability.
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Affiliation(s)
- Daoqian Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Hao Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Qiongli Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Min Shao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Xinyu Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Dongmei Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China.
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Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:74-83. [PMID: 32344371 DOI: 10.1016/j.pbi.2020.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/19/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA.
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39
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Zhang Y, An D, Li C, Zhao Z, Wang W. The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation. BMC Genomics 2020; 21:76. [PMID: 31992185 PMCID: PMC6986005 DOI: 10.1186/s12864-020-6499-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
Background Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles. Results Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956 bp circular genome is composed of a pair of inverted repeats of 31,844 bp, a large single copy of 91,210 bp and a small single copy of 14,058 bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli. Conclusions The understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.
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Affiliation(s)
- Yating Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Changsheng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhixuan Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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40
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Bog M, Appenroth KJ, Sree KS. Duckweed (Lemnaceae): Its Molecular Taxonomy. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00117] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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41
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Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Göker M, Murray AE, Lindemann SR, Klenk HP, O'Malley R, Zane M, Cheng JF, Copeland A, Daum C, Singer E, Woyke T. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Sci Data 2019; 6:285. [PMID: 31772173 PMCID: PMC6879543 DOI: 10.1038/s41597-019-0287-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/31/2019] [Indexed: 11/17/2022] Open
Abstract
Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2–7.2 Mbp, 40–73% GC content, and 1.5–7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel. Measurement(s) | metagenomic data • sequence_assembly | Technology Type(s) | ONT MinION • Illumina sequencing • PacBio RS II | Factor Type(s) | sequencing platform | Sample Characteristic - Organism | Bacteria | Sample Characteristic - Environment | mock community |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.10260740
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Affiliation(s)
- Volkan Sevim
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Juna Lee
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Robert Egan
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hope Hundley
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Janey Lee
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - R Craig Everroad
- NASA Ames Research Center, Exobiology Branch, Moffett Field, CA, 94035, USA
| | - Angela M Detweiler
- NASA Ames Research Center, Exobiology Branch, Moffett Field, CA, 94035, USA.,Bay Area Environmental Research Institute, Moffett Field, CA, 94035, USA
| | - Brad M Bebout
- NASA Ames Research Center, Exobiology Branch, Moffett Field, CA, 94035, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Nuclear and Chemical Science Division, 7000 East Ave, Livermore, CA, 94550-9234, USA
| | - Markus Göker
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Alison E Murray
- Desert Research Institute, Division of Earth and Ecosystem Sciences, 2215 Raggio Pkwy, Reno, NV, 89512, USA
| | | | - Hans-Peter Klenk
- Newcastle University, School of Natural and Environmental Sciences, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Ronan O'Malley
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Matthew Zane
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Alex Copeland
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Christopher Daum
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Esther Singer
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
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Liu Y, Wang Y, Xu S, Tang X, Zhao J, Yu C, He G, Xu H, Wang S, Tang Y, Fu C, Ma Y, Zhou G. Efficient genetic transformation and CRISPR/Cas9-mediated genome editing in Lemna aequinoctialis. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2143-2152. [PMID: 30972865 PMCID: PMC6790374 DOI: 10.1111/pbi.13128] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 05/13/2023]
Abstract
The fast growth, ease of metabolic labelling and potential for feedstock and biofuels production make duckweeds not only an attractive model system for understanding plant biology, but also a potential future crop. However, current duckweed research is constrained by the lack of efficient genetic manipulation tools. Here, we report a case study on genome editing in a duckweed species, Lemna aequinoctialis, using a fast and efficient transformation and CRISPR/Cas9 tool. By optimizing currently available transformation protocols, we reduced the duration time of Agrobacterium-mediated transformation to 5-6 weeks with a success rate of over 94%. Based on the optimized transformation protocol, we generated 15 (14.3% success rate) biallelic LaPDS mutants that showed albino phenotype using a CRISPR/Cas9 system. Investigations on CRISPR/Cas9-mediated mutation spectrum among mutated L. aequinoctialis showed that most of mutations were short insertions and deletions. This study presents the first example of CRISPR/Cas9-mediated genome editing in duckweeds, which will open new research avenues in using duckweeds for both basic and applied research.
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Affiliation(s)
- Yu Liu
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Yu Wang
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Shuqing Xu
- Institute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
| | - Xianfeng Tang
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Jinshan Zhao
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
| | - Changjiang Yu
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Guo He
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Hua Xu
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Shumin Wang
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Yali Tang
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Chunxiang Fu
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Yubin Ma
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
| | - Gongke Zhou
- College of Resources and EnvironmentQingdao Agricultural UniversityQingdaoChina
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentShandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
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Kono N, Arakawa K. Nanopore sequencing: Review of potential applications in functional genomics. Dev Growth Differ 2019; 61:316-326. [DOI: 10.1111/dgd.12608] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
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Hoang PTN, Schubert V, Meister A, Fuchs J, Schubert I. Variation in genome size, cell and nucleus volume, chromosome number and rDNA loci among duckweeds. Sci Rep 2019; 9:3234. [PMID: 30824726 PMCID: PMC6397220 DOI: 10.1038/s41598-019-39332-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/18/2019] [Indexed: 12/01/2022] Open
Abstract
Duckweeds are small, free-floating, largely asexual and highly neotenous organisms. They display the most rapid growth among flowering plants and are of growing interest in aquaculture and genome biology. Genomic and chromosomal data are still rare. Applying flow-cytometric genome size measurement, microscopic determination of frond, cell and nucleus morphology, as well as fluorescence in situ hybridization (FISH) for localization of ribosomal DNA (rDNA), we compared eleven species, representative for the five duckweed genera to search for potential correlations between genome size, cell and nuclei volume, simplified body architecture (neoteny), chromosome numbers and rDNA loci. We found a ~14-fold genome size variation (from 160 to 2203 Mbp), considerable differences in frond size and shape, highly variable guard cell and nucleus size, chromosome number (from 2n = 36 to 82) and number of 5S and 45S rDNA loci. In general, genome size is positively correlated with guard cell and nucleus volume (p < 0.001) and with the neoteny level and inversely with the frond size. In individual cases these correlations could be blurred for instance by particular body and cell structures which seem to be linked to specific floating styles. Chromosome number and rDNA loci variation between the tested species was independent of the genome size. We could not confirm previously reported intraspecific variation of chromosome numbers between individual clones of the genera Spirodela and Landoltia.
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Affiliation(s)
- Phuong T N Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany.,Dalat University, Lamdong Province, Vietnam
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Armin Meister
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany.
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