1
|
Saul F, Scharmann M, Wakatake T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. NATURE PLANTS 2023; 9:2000-2015. [PMID: 37996654 DOI: 10.1038/s41477-023-01562-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.
Collapse
Affiliation(s)
- Franziska Saul
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Mathias Scharmann
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, Germany
| | - Takanori Wakatake
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Louisa Channon
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Emily Carroll
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | | | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station & Program in Ecology, Evolution, and Behavior, Michigan State University, Hickory Corners, MI, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Sachiko Masuda
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerd Vogg
- Botanical Garden, University of Würzburg, Würzburg, Germany
| | - Ken Shirasu
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany.
| |
Collapse
|
2
|
Liu S, Smith SD. Replicated radiations in the South American marsh pitcher plants (Heliamphora) lead to convergent carnivorous trap morphologies. AMERICAN JOURNAL OF BOTANY 2023; 110:e16230. [PMID: 37807697 DOI: 10.1002/ajb2.16230] [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: 04/04/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 10/10/2023]
Abstract
PREMISE The evolution of carnivorous pitcher traps across multiple angiosperm lineages represents a classic example of morphological convergence. Nevertheless, no comparative study to-date has examined pitcher evolution from a quantitative morphometric perspective. METHODS In the present study, we used comparative morphometric approaches to quantify the shape space occupied by Heliamphora pitchers and to trace evolutionary trajectories through this space to examine patterns of divergence and convergence within the genus. We also investigated pitcher development, and, how the packing of pitchers is affected by crowding, a common condition in their natural environments. RESULTS Our results showed that Heliamphora pitchers have diverged along three main axes in morphospace: (1) pitcher curvature; (2) nectar spoon elaboration; and (3) pitcher stoutness. Both curvature and stoutness are correlated with pitcher size, suggesting structural constraints in pitcher morphological evolution. Among the four traits (curvature, spoon elaboration, stoutness, and size), all but curvature lacked phylogenetic signal and showed marked convergence across the phylogeny. We also observed tighter packing of pitchers in crowded conditions, and this effect was most pronounced in curved, slender pitchers. CONCLUSIONS Overall, our study demonstrates that diversification and convergent evolution of carnivory-related traits extends to finer evolutionary timescales, reinforcing the notion that ecological specialization may not necessarily be an evolutionary dead end.
Collapse
Affiliation(s)
- Sukuan Liu
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant Street, Boulder, Colorado, 80309, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant Street, Boulder, Colorado, 80309, USA
| |
Collapse
|
3
|
Freund M, Graus D, Fleischmann A, Gilbert KJ, Lin Q, Renner T, Stigloher C, Albert VA, Hedrich R, Fukushima K. The digestive systems of carnivorous plants. PLANT PHYSIOLOGY 2022; 190:44-59. [PMID: 35604105 PMCID: PMC9434158 DOI: 10.1093/plphys/kiac232] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/08/2022] [Indexed: 05/19/2023]
Abstract
To survive in the nutrient-poor habitats, carnivorous plants capture small organisms comprising complex substances not suitable for immediate reuse. The traps of carnivorous plants, which are analogous to the digestive systems of animals, are equipped with mechanisms for the breakdown and absorption of nutrients. Such capabilities have been acquired convergently over the past tens of millions of years in multiple angiosperm lineages by modifying plant-specific organs including leaves. The epidermis of carnivorous trap leaves bears groups of specialized cells called glands, which acquire substances from their prey via digestion and absorption. The digestive glands of carnivorous plants secrete mucilage, pitcher fluids, acids, and proteins, including digestive enzymes. The same (or morphologically distinct) glands then absorb the released compounds via various membrane transport proteins or endocytosis. Thus, these glands function in a manner similar to animal cells that are physiologically important in the digestive system, such as the parietal cells of the stomach and intestinal epithelial cells. Yet, carnivorous plants are equipped with strategies that deal with or incorporate plant-specific features, such as cell walls, epidermal cuticles, and phytohormones. In this review, we provide a systematic perspective on the digestive and absorptive capacity of convergently evolved carnivorous plants, with an emphasis on the forms and functions of glands.
Collapse
Affiliation(s)
- Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Dorothea Graus
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Andreas Fleischmann
- Botanische Staatssammlung München and GeoBio-Center LMU, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan 49060, USA
| | - Qianshi Lin
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Christian Stigloher
- Imaging Core Facility of the Biocenter, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| |
Collapse
|
4
|
Galvanese EF, Costa APL, Araújo ES, Falkievicz BC, de Melo GGV, Vitule JRS, Padial AA. Community stability and seasonal biotic homogenisation emphasize the effect of the invasive tropical tanner grass on macrophytes from a highly dynamic neotropical tidal river. AQUATIC SCIENCES 2022; 84:30. [PMID: 35400976 PMCID: PMC8980772 DOI: 10.1007/s00027-022-00858-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED We described the spatial and temporal dynamics of aquatic macrophytes in a Neotropical coastal estuarine river, and identified the negative effects associated to the presence and dominance of the invasive tanner grass. We compared macrophyte beds along the Guaraguaçu River (South Brazil) over four years, using taxonomic and functional dimensions. Biodiversity descriptors were higher in the driest periods compared to the rainiest, although this difference seems to be decreasing over the studied years. Moreover, the spatial organization of biodiversity and community structure slightly changed over time. Such spatial community stability was highlighted by the dominance of the highly invasive tanner grass. In beds dominated by the invasive species, the biodiversity was reduced. As aquatic macrophytes represent an important group in water bodies, the long-term loss of seasonal differences in community structuring is of concern, mainly regarding its potential to impact other groups and ecosystem functioning. By analysing data from standardized monitoring, we were able to identify a poorly discussed facet of biotic homogenisation-the seasonal homogenisation. We also discussed the impact of massive development of invasive species and its consequences for biodiversity in a Neotropical river of outmost importance for biological conservation. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00027-022-00858-3.
Collapse
Affiliation(s)
- Elena Fukasawa Galvanese
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
- Programa de Pós-graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Ana Paula Lula Costa
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
- Programa de Pós-graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Elielton Silva Araújo
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
- Programa de Pós-graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Bruno Cesar Falkievicz
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Gabriel Garcia Valente de Melo
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Jean Ricardo Simões Vitule
- Programa de Pós-graduação em Ecologia e Conservação, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
- Laboratório de Ecologia e Conservação, Departamento de Engenharia Ambiental, Setor de Tecnologia, Programa de Pós-graduação em Engenharia Ambiental, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Andre Andrian Padial
- Laboratório de Análise e Síntese em Biodiversidade, Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
- Laboratório de Ecologia e Conservação, Departamento de Engenharia Ambiental, Setor de Tecnologia, Programa de Pós-graduação em Engenharia Ambiental, Universidade Federal do Paraná, Curitiba, PR Brazil
- Programa de Pós-graduação em Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, PR Brazil
- Programa de Pós-graduação em Ecologia de Ambientes Aquáticos Continentais, Núcleo de Pesquisa em Limnologia, Ictiologia e Aquicultura, Universidade Estadual de Maringá, Maringá, PR Brazil
| |
Collapse
|
5
|
Adamec L, Matušíková I, Pavlovič A. Recent ecophysiological, biochemical and evolutional insights into plant carnivory. ANNALS OF BOTANY 2021; 128:241-259. [PMID: 34111238 PMCID: PMC8389183 DOI: 10.1093/aob/mcab071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Carnivorous plants are an ecological group of approx. 810 vascular species which capture and digest animal prey, absorb prey-derived nutrients and utilize them to enhance their growth and development. Extant carnivorous plants have evolved in at least ten independent lineages, and their adaptive traits represent an example of structural and functional convergence. Plant carnivory is a result of complex adaptations to mostly nutrient-poor, wet and sunny habitats when the benefits of carnivory exceed the costs. With a boost in interest and extensive research in recent years, many aspects of these adaptations have been clarified (at least partly), but many remain unknown. SCOPE We provide some of the most recent insights into substantial ecophysiological, biochemical and evolutional particulars of plant carnivory from the functional viewpoint. We focus on those processes and traits in carnivorous plants associated with their ecological characterization, mineral nutrition, cost-benefit relationships, functioning of digestive enzymes and regulation of the hunting cycle in traps. We elucidate mechanisms by which uptake of prey-derived nutrients leads to stimulation of photosynthesis and root nutrient uptake. CONCLUSIONS Utilization of prey-derived mineral (mainly N and P) and organic nutrients is highly beneficial for plants and increases the photosynthetic rate in leaves as a prerequisite for faster plant growth. Whole-genome and tandem gene duplications brought gene material for diversification into carnivorous functions and enabled recruitment of defence-related genes. Possible mechanisms for the evolution of digestive enzymes are summarized, and a comprehensive picture on the biochemistry and regulation of prey decomposition and prey-derived nutrient uptake is provided.
Collapse
Affiliation(s)
- Lubomír Adamec
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 01 Třeboň, Czech Republic
| | - Ildikó Matušíková
- University of Ss. Cyril and Methodius, Department of Ecochemistry and Radioecology, J. Herdu 2, SK-917 01 Trnava, Slovak Republic
| | - Andrej Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
- For correspondence. E-mail
| |
Collapse
|