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Vroom R, Smolders A, Van de Riet BP, Lamers L, Güngör E, Krosse S, Verheggen-Kleinheerenbrink GM, Van der Wal NR, Kosten S. Azolla cultivation enables phosphate extraction from inundated former agricultural soils. WATER RESEARCH 2024; 254:121411. [PMID: 38457945 DOI: 10.1016/j.watres.2024.121411] [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: 10/17/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
To combat the global loss of wetlands and their essential functions, the restoration and creation of wetlands is imperative. However, wetland development is challenging when soils have been in prolonged agricultural use, often resulting in a substantial nutrient legacy, especially of phosphorous (P). Inundating these soils typically leads to P mobilization, resulting in poor water quality and low biodiversity recovery. As a potential novel means to overcome this challenge, we tested whether cultivation of the floating fern Azolla filiculoides could simultaneously extract and recycle P, and provide a commercial product. Azolla has high growth rates due to the nitrogen fixing capacity of its microbiome and is capable of luxury consumption of P. Azolla cultivation may also accelerate soil P mobilization and subsequent extraction by causing surface water anoxia and the release of iron-bound P. To test this approach, we cultivated Azolla on 15 P-rich former agricultural soils in an indoor mesocosm experiment. Soils were inundated and either left unvegetated or inoculated with A. filiculoides during two 8-week cultivation periods. Biomass was harvested at different intervals (weekly/monthly/bimonthly) to investigate the effect of harvesting frequency on oxygen (O2) and nutrient dynamics. We found that Azolla attained high growth rates only on soils with high mobilization of labile P, as plant cover did not reduce surface water O2 concentrations in the first phase after inundation. This concurred with low porewater iron to P ratios (<10) and high porewater P concentrations. A. filiculoides cultivation substantially reduced surface water nutrient concentrations and extracted P at rates up to 122 kg ha-1 yr-1. We conclude that rapid P extraction by A. filiculoides cultivation is possible on soils rich in labile P, offering new perspectives for wetland rehabilitation. Additional field trials are recommended to investigate long-term feasibility, seasonal variations, and the influence of potential grazers and pathogens.
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Affiliation(s)
- Rje Vroom
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Ajp Smolders
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands; B-WARE Research Centre, Toernooiveld 1, Nijmegen 6525 ED, The Netherlands
| | - B P Van de Riet
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands; B-WARE Research Centre, Toernooiveld 1, Nijmegen 6525 ED, The Netherlands
| | - Lpm Lamers
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - E Güngör
- Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - S Krosse
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands; B-WARE Research Centre, Toernooiveld 1, Nijmegen 6525 ED, The Netherlands
| | - G M Verheggen-Kleinheerenbrink
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - N R Van der Wal
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - S Kosten
- Department of Ecology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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Abstract
BACKGROUND The LEAFY (LFY) transcription factors are present in algae and across land plants. The available expression and functional data of these genes in embryophytes suggest that LFY genes control a plethora of processes including the first zygotic cell division in bryophytes, shoot cell divisions of the gametophyte and sporophyte in ferns, cone differentiation in gymnosperms and floral meristem identity in flowering plants. However, their putative plesiomorphic role in plant reproductive transition in vascular plants remains untested. RESULTS We perform Maximum Likelihood (ML) phylogenetic analyses for the LFY gene lineage in embryophytes with expanded sampling in lycophytes and ferns. We recover the previously identified seed plant duplication that results in LEAFY and NEEDLY paralogs. In addition, we recover multiple species-specific duplications in ferns and lycophytes and large-scale duplications possibly correlated with the occurrence of whole genome duplication (WGD) events in Equisetales and Salviniales. To test putative roles in diverse ferns and lycophytes we perform LFY expression analyses in Adiantum raddianum, Equisetum giganteum and Selaginella moellendorffii. Our results show that LFY genes are active in vegetative and reproductive tissues, with higher expression in early fertile developmental stages and during sporangia differentiation. CONCLUSIONS Our data point to previously unrecognized roles of LFY genes in sporangia differentiation in lycophytes and ferns and suggests that functions linked to reproductive structure development are not exclusive to seed plant LFY homologs.
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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5
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Costarelli A, Cannavò S, Cerri M, Pellegrino RM, Reale L, Paolocci F, Pasqualini S. Light and Temperature Shape the Phenylpropanoid Profile of Azolla filiculoides Fronds. FRONTIERS IN PLANT SCIENCE 2021; 12:727667. [PMID: 34745161 PMCID: PMC8567065 DOI: 10.3389/fpls.2021.727667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/16/2021] [Indexed: 05/12/2023]
Abstract
Azolla is a genus of floating freshwater ferns. By their high growth and N2 fixation rates, Azolla species have been exploited for centuries by populations of South-east Asia as biofertilizers in rice paddies. The use of Azolla species as a sustainable plant material for diverse applications, such as feeding, biofuel production, and bioremediation, has encountered a growing interest over the last few years. However, high levels of feed deterrent flavonoids in their fronds have discouraged the use of these ferns as a sustainable protein source for animal consumption. Additionally, information on how and to what extent environmental determinants affect the accumulation of secondary metabolites in these organisms remains poorly understood. Moving from these considerations, here, we investigated by an untargeted metabolomics approach the profiles of phenylpropanoid compounds in the fronds of Azolla filiculoides sampled under control and pigment-inducing stress conditions. In parallel, we assayed the expression of essential structural genes of the phenylpropanoid pathway by quantitative RT-PCR. This study provides novel information concerning A. filiculoides phenylpropanoid compounds and their temporal profiling in response to environmental stimuli. In particular, we show that besides the already known 3-deoxyanthocyanidins, anthocyanidins, and proanthocyanidins, this fern can accumulate additional secondary metabolites of outstanding importance, such as chemoattractants, defense compounds, and reactive oxygen species (ROS) scavengers, and crucial as dietary components for humans, such as dihydrochalcones, stilbenes, isoflavones, and phlobaphenes. The findings of this study open an opportunity for future research studies to unveil the interplay between genetic and environmental determinants underlying the elicitation of the secondary metabolites in ferns and exploit these organisms as sustainable sources of beneficial metabolites for human health.
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Affiliation(s)
- Alma Costarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Sara Cannavò
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Martina Cerri
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | | | - Lara Reale
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Francesco Paolocci
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Perugia, Italy
- *Correspondence: Francesco Paolocci
| | - Stefania Pasqualini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
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6
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Dijkhuizen LW, Tabatabaei BES, Brouwer P, Rijken N, Buijs VA, Güngör E, Schluepmann H. Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition. FRONTIERS IN PLANT SCIENCE 2021; 12:693039. [PMID: 34456937 PMCID: PMC8386757 DOI: 10.3389/fpls.2021.693039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/22/2021] [Indexed: 05/02/2023]
Abstract
Water ferns of the genus Azolla and the filamentous cyanobacteria Nostoc azollae constitute a model symbiosis that enabled the colonization of the water surface with traits highly desirable for the development of more sustainable crops: their floating mats capture CO2 and fix N2 at high rates using light energy. Their mode of sexual reproduction is heterosporous. The regulation of the transition from the vegetative phase to the spore forming phase in ferns is largely unknown, yet a prerequisite for Azolla domestication, and of particular interest as ferns represent the sister lineage of seed plants. Sporocarps induced with far red light could be crossed so as to verify species attribution of strains from the Netherlands but not of the strain from the Anzali lagoon in Iran; the latter strain was assigned to a novel species cluster from South America. Red-dominated light suppresses the formation of dissemination stages in both gametophyte- and sporophyte-dominated lineages of plants, the response likely is a convergent ecological strategy to open fields. FR-responsive transcripts included those from MIKCC homologues of CMADS1 and miR319-controlled GAMYB transcription factors in the fern, transporters in N. azollae, and ycf2 in chloroplasts. Loci of conserved microRNA (miRNA) in the fern lineage included miR172, yet FR only induced miR529 and miR535, and reduced miR319 and miR159. Phylogenomic analyses of MIKCC TFs suggested that the control of flowering and flower organ specification may have originated from the diploid to haploid phase transition in the homosporous common ancestor of ferns and seed plants.
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Affiliation(s)
- Laura W. Dijkhuizen
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Paul Brouwer
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Niels Rijken
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Valerie A. Buijs
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Erbil Güngör
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Henriette Schluepmann
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
- *Correspondence: Henriette Schluepmann
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Miranda AF, Kumar NR, Spangenberg G, Subudhi S, Lal B, Mouradov A. Aquatic Plants, Landoltia punctata, and Azolla filiculoides as Bio-Converters of Wastewater to Biofuel. PLANTS (BASEL, SWITZERLAND) 2020; 9:E437. [PMID: 32244834 PMCID: PMC7238415 DOI: 10.3390/plants9040437] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/17/2022]
Abstract
The aquatic plants, Azolla filiculoides, and Landoltia punctate, were used as complementing phytoremediators of wastewater containing high levels of phosphate, which simulates the effluents from textile, dyeing, and laundry detergent industries. Their complementarities are based on differences in capacities to uptake nitrogen and phosphate components from wastewater. Sequential treatment by L. punctata followed by A. filiculoides led to complete removal of NH4, NO3, and up to 93% reduction of PO4. In experiments where L. punctata treatment was followed by fresh L. punctata, PO4 concentration was reduced by 65%. The toxicity of wastewater assessed by shrimps, Paratya australiensis, showed a four-fold reduction of their mortality (LC50 value) after treatment. Collected dry biomass was used as an alternative carbon source for heterotrophic marine protists, thraustochytrids, which produced up to 35% dry weight of lipids rich in palmitic acid (50% of total fatty acids), the key fatty acid for biodiesel production. The fermentation of treated L. punctata biomass by Enterobacter cloacae yielded up to 2.14 mol H2/mole of reduced sugar, which is comparable with leading terrestrial feedstocks. A. filiculoides and L. punctata can be used as a new generation of feedstock, which can treat different types of wastewater and represent renewable and sustainable feedstock for bioenergy production.
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Affiliation(s)
- Ana F. Miranda
- School of Sciences, RMIT University, Bundoora West Campus, Bundoora VIC 3083, Australia;
| | - N. Ram Kumar
- The Energy and Resources Institute, New Delhi 110 003, India; (N.R.K.); (S.S.); (B.L.)
| | - German Spangenberg
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora VIC 3083, Australia;
- School of Applied Systems Biology, La Trobe University, Bundoora VIC 3086, Australia
| | - Sanjukta Subudhi
- The Energy and Resources Institute, New Delhi 110 003, India; (N.R.K.); (S.S.); (B.L.)
| | - Banwari Lal
- The Energy and Resources Institute, New Delhi 110 003, India; (N.R.K.); (S.S.); (B.L.)
| | - Aidyn Mouradov
- School of Sciences, RMIT University, Bundoora West Campus, Bundoora VIC 3083, Australia;
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8
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Marchant DB, Sessa EB, Wolf PG, Heo K, Barbazuk WB, Soltis PS, Soltis DE. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly. Sci Rep 2019; 9:18181. [PMID: 31796775 PMCID: PMC6890710 DOI: 10.1038/s41598-019-53968-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023] Open
Abstract
Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
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Affiliation(s)
- D Blaine Marchant
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, 84322, USA
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Kweon Heo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
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10
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de Vries S, de Vries J, Teschke H, von Dahlen JK, Rose LE, Gould SB. Jasmonic and salicylic acid response in the fern Azolla filiculoides and its cyanobiont. PLANT, CELL & ENVIRONMENT 2018; 41:2530-2548. [PMID: 29314046 DOI: 10.1111/pce.13131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/05/2017] [Accepted: 12/21/2017] [Indexed: 05/16/2023]
Abstract
Plants sense and respond to microbes utilizing a multilayered signalling cascade. In seed plants, the phytohormones jasmonic and salicylic acid (JA and SA) are key denominators of how plants respond to certain microbes. Their interplay is especially well-known for tipping the scales in plants' strategies of dealing with phytopathogens. In non-angiosperm lineages, the interplay is less well understood, but current data indicate that it is intertwined to a lesser extent and the canonical JA/SA antagonism appears to be absent. Here, we used the water fern Azolla filiculoides to gain insights into the fern's JA/SA signalling and the molecular communication with its unique nitrogen fixing cyanobiont Nostoc azollae, which the fern inherits both during sexual and vegetative reproduction. By mining large-scale sequencing data, we demonstrate that Azolla has most of the genetic repertoire to produce and sense JA and SA. Using qRT-PCR on the identified biosynthesis and signalling marker genes, we show that Azolla is responsive to exogenously applied SA. Furthermore, exogenous SA application influenced the abundance and gene expression of Azolla's cyanobiont. Our data provide a framework for JA/SA signalling in ferns and suggest that SA might be involved in Azolla's communication with its vertically inherited cyanobiont.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
- Institute of Molecular Evolution, Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Hendrik Teschke
- Institute of Molecular Evolution, Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Janina K von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Sven B Gould
- Institute of Molecular Evolution, Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
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Abstract
Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools has made it possible to conduct genetic mapping and population genetic studies to unravel the molecular underpinnings of domestication and crop evolution in diverse crop species. We propose three future avenues for the study of crop evolution: establishment of high-quality reference genomes for crops and their wild relatives; genomic characterization of germplasm collections; and the adoption of novel methodologies such as archaeogenetics, epigenomics, and genome editing.
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Affiliation(s)
- Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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12
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Li FW, Brouwer P, Carretero-Paulet L, Cheng S, de Vries J, Delaux PM, Eily A, Koppers N, Kuo LY, Li Z, Simenc M, Small I, Wafula E, Angarita S, Barker MS, Bräutigam A, dePamphilis C, Gould S, Hosmani PS, Huang YM, Huettel B, Kato Y, Liu X, Maere S, McDowell R, Mueller LA, Nierop KGJ, Rensing SA, Robison T, Rothfels CJ, Sigel EM, Song Y, Timilsena PR, Van de Peer Y, Wang H, Wilhelmsson PKI, Wolf PG, Xu X, Der JP, Schluepmann H, Wong GKS, Pryer KM. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. NATURE PLANTS 2018; 4:460-472. [PMID: 29967517 PMCID: PMC6786969 DOI: 10.1038/s41477-018-0188-8] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 05/18/2023]
Abstract
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.
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Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Paul Brouwer
- Molecular Plant Physiology Department, Utrecht University, Utrecht, the Netherlands
| | - Lorenzo Carretero-Paulet
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Shifeng Cheng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet Tolosan, France
| | - Ariana Eily
- Department of Biology, Duke University, Durham, NC, USA
| | - Nils Koppers
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Mathew Simenc
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Eric Wafula
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Stephany Angarita
- Department of Biological Science, California State University, Fullerton, CA, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Claude dePamphilis
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Sven Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Dusseldorf, Germany
| | | | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding, Cologne, Germany
| | - Yoichiro Kato
- Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Tokyo, Japan
| | - Xin Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Steven Maere
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rose McDowell
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Klaas G J Nierop
- Geolab, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands
| | | | - Tanner Robison
- Department of Biology, Utah State University, Logan, UT, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Erin M Sigel
- Department of Biology, University of Louisiana, Lafayette, LA, USA
| | - Yue Song
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Prakash R Timilsena
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yves Van de Peer
- Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Hongli Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, USA
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Joshua P Der
- Department of Biological Science, California State University, Fullerton, CA, USA
| | | | - Gane K-S Wong
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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13
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Bioremediation of effluent from a uranium mill tailings repository in South China by Azolla–Anabaena. J Radioanal Nucl Chem 2018. [DOI: 10.1007/s10967-018-5934-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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14
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Pereira AL. The Unique Symbiotic System between a Fern and a Cyanobacterium, Azolla-Anabaena azollae: Their Potential as Biofertilizer, Feed, and Remediation. Symbiosis 2018. [DOI: 10.5772/intechopen.70466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Temmink RJM, Harpenslager SF, Smolders AJP, van Dijk G, Peters RCJH, Lamers LPM, van Kempen MML. Azolla along a phosphorus gradient: biphasic growth response linked to diazotroph traits and phosphorus-induced iron chlorosis. Sci Rep 2018. [PMID: 29535346 PMCID: PMC5849758 DOI: 10.1038/s41598-018-22760-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Azolla spp., a water fern often used for phytoremediation, is a strong phosphorus (P) accumulator due to its high growth rate and N2 fixing symbionts (diazotrophs). It is known that plant growth is stimulated by P, but the nature of the interactive response of both symbionts along a P gradient, and related changes in growth-limiting factors, are unclear. We determined growth, and N and P sequestration rates of Azolla filiculoides in N-free water at different P concentrations. The growth response appeared to be biphasic and highest at levels ≥10 P µmol l−1. Diazotrophic N sequestration increased upon P addition, and rates were three times higher at high P than at low P. At 10 µmol P l−1, N sequestration rates reached its maximum and A. filiculoides growth became saturated. Due to luxury consumption, P sequestration rates increased until 50 µmol P l−1. At higher P concentrations (≥50 µmol l−1), however, chlorosis occurred that seems to be caused by iron- (Fe-), and not by N-deficiency. We demonstrate that traits of the complete symbiosis in relation to P and Fe availability determine plant performance, stressing the role of nutrient stoichiometry. The results are discussed regarding Azolla’s potential use in a bio-based economy.
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Affiliation(s)
- Ralph J M Temmink
- Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Sarah F Harpenslager
- Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,School of Biological and Chemical Sciences, Queen Mary University, E1 4NS, London, United Kingdom
| | - Alfons J P Smolders
- Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,B-WARE Research Centre, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Gijs van Dijk
- Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,B-WARE Research Centre, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Roy C J H Peters
- Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Leon P M Lamers
- Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,B-WARE Research Centre, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Monique M L van Kempen
- Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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16
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Miranda AF, Liu Z, Rochfort S, Mouradov A. Lipid production in aquatic plant Azolla at vegetative and reproductive stages and in response to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 124:117-125. [PMID: 29366971 DOI: 10.1016/j.plaphy.2018.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/13/2018] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
The aquatic plant Azolla became increasingly popular as bioenergy feedstock because of its high growth rate, production of biomass with high levels of biofuel-producing molecules and ability to grow on marginal lands. In this study, we analysed the contribution of all organs of Azolla to the total yield of lipids at vegetative and reproductive stages and in response to stress. Triacylglycerol-containing lipid droplets were detected in all (vegetative and reproductive) organs with the highest level in the male microsporocarps and microspores. As a result, significantly higher total yields of lipids were detected in Azolla filiculoides and Azolla pinnata at the reproductive stage. Starving changed the yield and composition of the fatty acid as a result of re-direction of carbon flow from fatty acid to anthocyanin pathways. The composition of lipids, in regard the length and degree of unsaturation of fatty acids, in Azolla meets most of the important requirements for biodiesel standards. The ability of Azolla to grow on wastewaters, along with their high productivity rate, makes it an attractive feedstock for the production of biofuels.
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Affiliation(s)
- Ana F Miranda
- School of Sciences, RMIT University, Melbourne, VIC, Australia.
| | - Zhiqian Liu
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3083, Australia.
| | - Simone Rochfort
- AgriBio, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3083, Australia.
| | - Aidyn Mouradov
- School of Sciences, RMIT University, Melbourne, VIC, Australia.
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17
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Dijkhuizen LW, Brouwer P, Bolhuis H, Reichart G, Koppers N, Huettel B, Bolger AM, Li F, Cheng S, Liu X, Wong GK, Pryer K, Weber A, Bräutigam A, Schluepmann H. Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify. THE NEW PHYTOLOGIST 2018; 217:453-466. [PMID: 29084347 PMCID: PMC5901025 DOI: 10.1111/nph.14843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 09/05/2017] [Indexed: 05/18/2023]
Abstract
Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. 15 N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.
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Affiliation(s)
- Laura W. Dijkhuizen
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
| | - Paul Brouwer
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and BiogeochemistryNetherlands Institute for Sea Research (NIOZ)Utrecht UniversityDen Hoorn1797SZthe Netherlands
| | - Gert‐Jan Reichart
- Department of Earth SciencesUtrecht UniversityUtrecht3508TAthe Netherlands
| | - Nils Koppers
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding ADIS/DNA Core FacilityCologne50829Germany
| | - Anthony M. Bolger
- Institute of Botany and Molecular Genetics IBMGIRWTH Aachen University52074AachenGermany
| | - Fay‐Wei Li
- Department of BiologyDuke UniversityDurhamNC27708USA
- Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNY14853USA
| | - Shifeng Cheng
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
| | - Xin Liu
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
| | - Gane Ka‐Shu Wong
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
- Department of Biological SciencesUniversity of AlbertaEdmontonABT6G 2E9Canada
| | | | - Andreas Weber
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Andrea Bräutigam
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Henriette Schluepmann
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
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18
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Brouwer P, Bräutigam A, Buijs VA, Tazelaar AOE, van der Werf A, Schlüter U, Reichart GJ, Bolger A, Usadel B, Weber APM, Schluepmann H. Metabolic Adaptation, a Specialized Leaf Organ Structure and Vascular Responses to Diurnal N 2 Fixation by Nostoc azollae Sustain the Astonishing Productivity of Azolla Ferns without Nitrogen Fertilizer. FRONTIERS IN PLANT SCIENCE 2017; 8:442. [PMID: 28408911 PMCID: PMC5374210 DOI: 10.3389/fpls.2017.00442] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/14/2017] [Indexed: 05/02/2023]
Abstract
Sustainable agriculture demands reduced input of man-made nitrogen (N) fertilizer, yet N2 fixation limits the productivity of crops with heterotrophic diazotrophic bacterial symbionts. We investigated floating ferns from the genus Azolla that host phototrophic diazotrophic Nostoc azollae in leaf pockets and belong to the fastest growing plants. Experimental production reported here demonstrated N-fertilizer independent production of nitrogen-rich biomass with an annual yield potential per ha of 1200 kg-1 N fixed and 35 t dry biomass. 15N2 fixation peaked at noon, reaching 0.4 mg N g-1 dry weight h-1. Azolla ferns therefore merit consideration as protein crops in spite of the fact that little is known about the fern's physiology to enable domestication. To gain an understanding of their nitrogen physiology, analyses of fern diel transcript profiles under differing nitrogen fertilizer regimes were combined with microscopic observations. Results established that the ferns adapted to the phototrophic N2-fixing symbionts N. azollae by (1) adjusting metabolically to nightly absence of N supply using responses ancestral to ferns and seed plants; (2) developing a specialized xylem-rich vasculature surrounding the leaf-pocket organ; (3) responding to N-supply by controlling transcripts of genes mediating nutrient transport, allocation and vasculature development. Unlike other non-seed plants, the Azolla fern clock is shown to contain both the morning and evening loops; the evening loop is known to control rhythmic gene expression in the vasculature of seed plants and therefore may have evolved along with the vasculature in the ancestor of ferns and seed plants.
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Affiliation(s)
- Paul Brouwer
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Andrea Bräutigam
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorf, Germany
| | - Valerie A. Buijs
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Anne O. E. Tazelaar
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | | | - Urte Schlüter
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorf, Germany
| | | | - Anthony Bolger
- Institute for Botany and Molecular Genetics, Bioeconomy Science Center, RWTH Aachen UniversityAachen, Germany
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, Bioeconomy Science Center, RWTH Aachen UniversityAachen, Germany
| | - Andreas P. M. Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorf, Germany
| | - Henriette Schluepmann
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
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19
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Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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20
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The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. Sci Rep 2016; 6:30444. [PMID: 27457880 PMCID: PMC4960570 DOI: 10.1038/srep30444] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Abstract
Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT). The conservation of both C/S1 bZIP interactions and SIRT remains poorly characterized in non-model species, leaving their evolutionary origin uncertain and limiting crop research. In this work, we explored recently published plant sequencing data to establish a detailed phylogeny of C and S1 bZIPs, investigating their intertwined role in plant evolution, and the origin of SIRT. Our analyses clarified C and S1 bZIP orthology relationships in angiosperms, and identified S1 sequences in gymnosperms. We experimentally showed that the gymnosperm orthologs are regulated by SIRT, tracing back the origin of this unique regulatory mechanism to the ancestor of seed plants. Additionally, we discovered an earlier S ortholog in the charophyte algae Klebsormidium flaccidum, together with a C ortholog. This suggests that C and S groups originated by duplication from a single algal proto-C/S ancestor. Based on our observations, we propose a model wherein the C/S1 bZIP dimer network evolved in seed plants from pre-existing C/S bZIP interactions.
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21
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de Vries J, Fischer AM, Roettger M, Rommel S, Schluepmann H, Bräutigam A, Carlsbecker A, Gould SB. Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots. THE NEW PHYTOLOGIST 2016; 209:705-20. [PMID: 26358624 PMCID: PMC5049668 DOI: 10.1111/nph.13630] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/04/2015] [Indexed: 05/10/2023]
Abstract
The phytohormones cytokinin and auxin orchestrate the root meristem development in angiosperms by determining embryonic bipolarity. Ferns, having the most basal euphyllophyte root, form neither bipolar embryos nor permanent embryonic primary roots but rather an adventitious root system. This raises the questions of how auxin and cytokinin govern fern root system architecture and whether this can tell us something about the origin of that root. Using Azolla filiculoides, we characterized the influence of IAA and zeatin on adventitious fern root meristems and vasculature by Nomarski microscopy. Simultaneously, RNAseq analyses, yielding 36,091 contigs, were used to uncover how the phytohormones affect root tip gene expression. We show that auxin restricts Azolla root meristem development, while cytokinin promotes it; it is the opposite effect of what is observed in Arabidopsis. Global gene expression profiling uncovered 145 genes significantly regulated by cytokinin or auxin, including cell wall modulators, cell division regulators and lateral root formation coordinators. Our data illuminate both evolution and development of fern roots. Promotion of meristem size through cytokinin supports the idea that root meristems of euphyllophytes evolved from shoot meristems. The foundation of these roots was laid in a postembryonically branching shoot system.
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Affiliation(s)
- Jan de Vries
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Angela Melanie Fischer
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Mayo Roettger
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Sophie Rommel
- Population GeneticsHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Henriette Schluepmann
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 83584CH Utrechtthe Netherlands
| | - Andrea Bräutigam
- Plant BiochemistryHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological BotanyUppsala BioCenterLinnean Centre for Plant BiologyUppsala UniversityUlls väg 24ESE‐756 51UppsalaSweden
| | - Sven Bernhard Gould
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
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22
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Plackett ARG, Di Stilio VS, Langdale JA. Ferns: the missing link in shoot evolution and development. FRONTIERS IN PLANT SCIENCE 2015; 6:972. [PMID: 26594222 PMCID: PMC4635223 DOI: 10.3389/fpls.2015.00972] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/23/2015] [Indexed: 05/02/2023]
Abstract
Shoot development in land plants is a remarkably complex process that gives rise to an extreme diversity of forms. Our current understanding of shoot developmental mechanisms comes almost entirely from studies of angiosperms (flowering plants), the most recently diverged plant lineage. Shoot development in angiosperms is based around a layered multicellular apical meristem that produces lateral organs and/or secondary meristems from populations of founder cells at its periphery. In contrast, non-seed plant shoots develop from either single apical initials or from a small population of morphologically distinct apical cells. Although developmental and molecular information is becoming available for non-flowering plants, such as the model moss Physcomitrella patens, making valid comparisons between highly divergent lineages is extremely challenging. As sister group to the seed plants, the monilophytes (ferns and relatives) represent an excellent phylogenetic midpoint of comparison for unlocking the evolution of shoot developmental mechanisms, and recent technical advances have finally made transgenic analysis possible in the emerging model fern Ceratopteris richardii. This review compares and contrasts our current understanding of shoot development in different land plant lineages with the aim of highlighting the potential role that the fern C. richardii could play in shedding light on the evolution of underlying genetic regulatory mechanisms.
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Affiliation(s)
- Andrew R. G. Plackett
- Department of Plant Sciences, University of OxfordOxford, UK
- *Correspondence: Andrew R. G. Plackett,
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23
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Li FW, Pryer KM. Crowdfunding the Azolla fern genome project: a grassroots approach. Gigascience 2014; 3:16. [PMID: 25276348 PMCID: PMC4178311 DOI: 10.1186/2047-217x-3-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/18/2014] [Indexed: 11/13/2022] Open
Abstract
Much of science progresses within the tight boundaries of what is often seen as a “black box”. Though familiar to funding agencies, researchers and the academic journals they publish in, it is an entity that outsiders rarely get to peek into. Crowdfunding is a novel means that allows the public to participate in, as well as to support and witness advancements in science. Here we describe our recent crowdfunding efforts to sequence the Azolla genome, a little fern with massive green potential. Crowdfunding is a worthy platform not only for obtaining seed money for exploratory research, but also for engaging directly with the general public as a rewarding form of outreach.
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Affiliation(s)
- Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
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24
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Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li FW, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG. Between two fern genomes. Gigascience 2014; 3:15. [PMID: 25324969 PMCID: PMC4199785 DOI: 10.1186/2047-217x-3-15] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/18/2014] [Indexed: 11/10/2022] Open
Abstract
Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
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Affiliation(s)
- Emily B Sessa
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, 1041 East Lowell Street, Tucson, AZ 85721, USA
| | - Joshua P Der
- Department of Biology, Penn State University, 201 Life Science Building, University Park, PA 16801, USA ; Current address: Department of Biological Science, California State University, 800 N. State College Blvd., Fullerton, CA 92831, USA
| | - Aaron M Duffy
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 3529-6720 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, 38 Nishigounaka, Myo-daiji-cho, Okazaki 444-8585, Japan
| | - Jane Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Fay-Wei Li
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - D Blaine Marchant
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Carl J Rothfels
- Department of Zoology, University of British Columbia, 2329 W. Mall, WAITING Vancouver, BC V6T 1Z4, Canada ; Current address: University Herbarium and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, Berkeley, CA 94720, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Mari L Salmi
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Erin M Sigel
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Douglas E Soltis
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Dennis W Stevenson
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Paul G Wolf
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
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