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van Veen H, Müller JT, Bartylla MM, Akman M, Sasidharan R, Mustroph A. Phylotranscriptomics provides a treasure trove of flood-tolerance mechanisms in the Cardamineae tribe. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39012097 DOI: 10.1111/pce.15033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/10/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
Flooding events are highly detrimental to most terrestrial plant species. However, there is an impressive diversity of plant species that thrive in flood-prone regions and represent a treasure trove of unexplored flood-resilience mechanisms. Here we surveyed a panel of four species from the Cardamineae tribe representing a broad tolerance range. This included the flood-tolerant Cardamine pratensis, Rorippa sylvestris and Rorippa palustris and the flood-sensitive species Cardamine hirsuta. All four species displayed a quiescent strategy, evidenced by the repression of shoot growth underwater. Comparative transcriptomics analyses between the four species and the sensitive model species Arabidopsis thaliana were facilitated via de novo transcriptome assembly and identification of 16 902 universal orthogroups at a high resolution. Our results suggest that tolerance likely evolved separately in the Cardamine and Rorippa species. While the Rorippa response was marked by a strong downregulation of cell-cycle genes, Cardamine minimized overall transcriptional regulation. However, a weak starvation response was a universal trait of tolerant species, potentially achieved in multiple ways. It could result from a strong decline in cell-cycle activity, but is also intertwined with autophagy, senescence, day-time photosynthesis and night-time fermentation capacity. Our data set provides a rich source to study adaptational mechanisms of flooding tolerance.
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Affiliation(s)
- Hans van Veen
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
- Evolutionary Plant Ecophysiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jana T Müller
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Malte M Bartylla
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Melis Akman
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Rashmi Sasidharan
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Angelika Mustroph
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
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Chumová Z, Monier Z, Šemberová K, Havlíčková E, Euston-Brown D, Muasya AM, Bergh NG, Trávníček P. Diploid and tetraploid cytotypes of the flagship Cape species Dicerothamnus rhinocerotis (Asteraceae): variation in distribution, ecological niche, morphology and genetics. ANNALS OF BOTANY 2024; 133:851-870. [PMID: 37410810 PMCID: PMC11082512 DOI: 10.1093/aob/mcad084] [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: 04/29/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND AND AIMS The Greater Cape Floristic Region is one of the world's biodiversity hotspots and is considered poor in polyploids. To test this assumption, ploidy variation was investigated in a widespread Cape shrub, Dicerothamnus rhinocerotis (renosterbos, Asteraceae). The aim was to elucidate the cytotype distribution and population composition across the species range, and to assess differences in morphology, environmental niches and genetics. METHODS Ploidy level and genome size were determined via flow cytometry and cytotype assignment was confirmed by chromosome counting. Restriction site-associated DNA sequencing (RADseq) analyses were used to infer genetic relationships. Cytotype climatic and environmental niches were compared using a range of environmental layers and a soil model, while morphological differences were examined using multivariate methods. KEY RESULTS The survey of 171 populations and 2370 individuals showed that the species comprises diploid and tetraploid cytotypes, no intermediates and only 16.8 % of mixed populations. Mean 2C values were 1.80-2.06 pg for diploids and 3.48-3.80 pg for tetraploids, with very similar monoploid genome sizes. Intra-cytotype variation showed a significant positive correlation with altitude and longitude in both cytotypes and with latitude in diploids. Although niches of both cytotypes were highly equivalent and similar, their optima and breadth were shifted due to differences mainly in isothermality and available water capacity. Morphometric analyses showed significant differences in the leaves and corolla traits, the number of florets per capitulum, and cypsela dimensions between the two cytotypes. Genetic analyses revealed four groups, three of them including both cytotypes. CONCLUSIONS Dicerothamnus rhinocerotis includes two distinct cytotypes that are genetically similar. While tetraploids arise several times independently within different genetic groups, morphological and ecological differences are evident between cytotypes. Our results open up new avenues for questions regarding the importance of ploidy in the megadiverse Cape flora, and exemplify the need for population-based studies focused on ploidy variation.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Zafar Monier
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, 7707, South Africa
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Eliška Havlíčková
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, 120 00, Czech Republic
| | | | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, 7707, South Africa
| | - Nicola G Bergh
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Cape Town, 7707, South Africa
- The Compton Herbarium, Kirstenbosch National Botanical Gardens, Cape Town, 7735, South Africa
| | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
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Katayama N, Yamamoto T, Aiuchi S, Watano Y, Fujiwara T. Subgenome evolutionary dynamics in allotetraploid ferns: insights from the gene expression patterns in the allotetraploid species Phegopteris decursivepinnata (Thelypteridacea, Polypodiales). FRONTIERS IN PLANT SCIENCE 2024; 14:1286320. [PMID: 38264021 PMCID: PMC10803465 DOI: 10.3389/fpls.2023.1286320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern-Phegopteris decursivepinnata-and its diploid parental species, P. koreana (K) and P. taiwaniana (T). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T-dominance and a slight increase in K-dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T- or K-subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns.
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Affiliation(s)
- Natsu Katayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Takuya Yamamoto
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Sakura Aiuchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Yasuyuki Watano
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Tao Fujiwara
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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Bejerman N, Dietzgen R, Debat H. Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses. Viruses 2023; 15:2402. [PMID: 38140643 PMCID: PMC10747219 DOI: 10.3390/v15122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.
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Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| | - Ralf Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
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Wang S, Wu M. The Draft Genome of the "Golden Tide" Seaweed, Sargassum horneri: Characterization and Comparative Analysis. Genes (Basel) 2023; 14:1969. [PMID: 37895318 PMCID: PMC10606923 DOI: 10.3390/genes14101969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive "golden tide", causing severe damage to the local economy and coastal ecosystems. In this study, we carried out de novo whole-genome sequencing of S. horneri using next-generation sequencing to unravel the genetic information of this alga. By utilizing a reference-guided de novo assembly pipeline with a closely related species, we successfully established a final assembled genome with a total length of 385 Mb. Repetitive sequences made up approximately 30.6% of this genome. Among the identified putative genes, around 87.03% showed homology with entries in the NCBI non-redundant protein database, with Ectocarpus siliculosus being the most closely related species for approximately one-third of these genes. One gene encoding an alkaline phosphatase family protein was found to exhibit positive selection, which could give a clue for the formation of S. horneri golden tides. Additionally, we characterized putative genes involved in fucoidan biosynthesis metabolism, a significant pathway in S. horneri. This study represents the first genome-wide characterization of a S. horneri species, providing crucial insights for future investigations, such as ecological genomic analyses.
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Affiliation(s)
- Shengqin Wang
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou 325035, China;
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Mingjiang Wu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou 325035, China;
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
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Sun J, Okada M, Tameshige T, Shimizu-Inatsugi R, Akiyama R, Nagano A, Sese J, Shimizu K. A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat. NAR Genom Bioinform 2023; 5:lqad067. [PMID: 37448590 PMCID: PMC10336777 DOI: 10.1093/nargab/lqad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 06/12/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Although allopolyploid species are common among natural and crop species, it is not easy to distinguish duplicated genes, known as homeologs, during their genomic analysis. Yet, cost-efficient RNA sequencing (RNA-seq) is to be developed for large-scale transcriptomic studies such as time-series analysis and genome-wide association studies in allopolyploids. In this study, we employed a 3' RNA-seq utilizing 3' untranslated regions (UTRs) containing frequent mutations among homeologous genes, compared to coding sequence. Among the 3' RNA-seq protocols, we examined a low-cost method Lasy-Seq using an allohexaploid bread wheat, Triticum aestivum. HISAT2 showed the best performance for 3' RNA-seq with the least mapping errors and quick computational time. The number of detected homeologs was further improved by extending 1 kb of the 3' UTR annotation. Differentially expressed genes in response to mild cold treatment detected by the 3' RNA-seq were verified with high-coverage conventional RNA-seq, although the latter detected more differentially expressed genes. Finally, downsampling showed that even a 2 million sequencing depth can still detect more than half of expressed homeologs identifiable by the conventional 32 million reads. These data demonstrate that this low-cost 3' RNA-seq facilitates large-scale transcriptomic studies of allohexaploid wheat and indicate the potential application to other allopolyploid species.
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Affiliation(s)
- Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Moeko Okada
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, Kanagawa 244-0813, Japan
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, Kanagawa 244-0813, Japan
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
| | - Jun Sese
- Humanome Lab, Inc., 2-4-10, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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7
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Quintanilla LG, Aranda I, Clemente-Moreno MJ, Pons-Perpinyà J, Gago J. Ecophysiological Differentiation among Two Resurrection Ferns and Their Allopolyploid Derivative. PLANTS (BASEL, SWITZERLAND) 2023; 12:1529. [PMID: 37050155 PMCID: PMC10096763 DOI: 10.3390/plants12071529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Theoretically, the coexistence of diploids and related polyploids is constrained by reproductive and competitive mechanisms. Although niche differentiation can explain the commonly observed co-occurrence of cytotypes, the underlying ecophysiological differentiation among cytotypes has hardly been studied. We compared the leaf functional traits of the allotetraploid resurrection fern Oeosporangium tinaei (HHPP) and its diploid parents, O. hispanicum (HH) and O. pteridioides (PP), coexisting in the same location. Our experimental results showed that all three species can recover physiological status after severe leaf dehydration, which confirms their 'resurrection' ability. However, compared with PP, HH had much higher investment per unit area of light-capturing surface, lower carbon assimilation rate per unit mass for the same midday water potential, higher non-enzymatic antioxidant capacity, higher carbon content, and lower contents of nitrogen, phosphorus, and other macronutrients. These traits allow HH to live in microhabitats with less availability of water and nutrients (rock crevices) and to have a greater capacity for resurrection. The higher assimilation capacity and lower antioxidant capacity of PP explain its more humid and nutrient-rich microhabitats (shallow soils). HHPP traits were mostly intermediate between those of HH and PP, and they allow the allotetraploid to occupy the free niche space left by the diploids.
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Affiliation(s)
- Luis G. Quintanilla
- School of Environmental Sciences and Technology (ESCET), University Rey Juan Carlos, 28922 Móstoles, Spain
| | - Ismael Aranda
- National Institute for Agricultural and Food Research and Technology (INIA), Spanish National Research Council, 28040 Madrid, Spain
| | - María José Clemente-Moreno
- Agro-Environmental and Water Economics Institute (INAGEA), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Joan Pons-Perpinyà
- Agro-Environmental and Water Economics Institute (INAGEA), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Jorge Gago
- Agro-Environmental and Water Economics Institute (INAGEA), University of the Balearic Islands, 07122 Palma de Mallorca, Spain
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8
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Kauai F, Mortier F, Milosavljevic S, Van de Peer Y, Bonte D. Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems. Proc Biol Sci 2023; 290:20222456. [PMID: 36946113 PMCID: PMC10031433 DOI: 10.1098/rspb.2022.2456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Polyploidy, i.e. the occurrence of multiple sets of chromosomes, is regarded as an important phenomenon in plant ecology and evolution, with all flowering plants likely having a polyploid ancestry. Owing to genome shock, minority cytotype exclusion and reduced fertility, polyploids emerging in diploid populations are expected to face significant challenges to successful establishment. Their establishment and persistence are often explained by possible fitness or niche differences that would relieve the competitive pressure with diploid progenitors. Experimental evidence for such advantages is, however, not unambiguous, and considerable niche overlap exists among most polyploid species and their diploid counterparts. Here, we develop a neutral spatially explicit eco-evolutionary model to understand whether neutral processes can explain the eco-evolutionary patterns of polyploids. We present a general mechanism for polyploid establishment by showing that sexually reproducing organisms assemble in space in an iterative manner, reducing frequency-dependent mating disadvantages and overcoming potential reduced fertility issues. Moreover, we construct a mechanistic theoretical framework that allows us to understand the long-term evolution of mixed-ploidy populations and show that our model is remarkably consistent with recent phylogenomic estimates of species extinctions in the Brassicaceae family.
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Affiliation(s)
- Felipe Kauai
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Frederik Mortier
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Silvija Milosavljevic
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, BE-9000 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Dries Bonte
- Department of Biology, Terrestrial Ecology Unit, Ghent University, BE-9000 Ghent, Belgium
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Shimizu-Inatsugi R, Morishima A, Mourato B, Shimizu KK, Sato Y. Phenotypic variation of a new synthetic allotetraploid Arabidopsis kamchatica enhanced in natural environment. FRONTIERS IN PLANT SCIENCE 2023; 13:1058522. [PMID: 36684772 PMCID: PMC9846130 DOI: 10.3389/fpls.2022.1058522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The phenotypic variation of vegetative organs and reproductive organs of newly synthesized and natural Arabidopsis kamchatica genotypes was investigated in both a controlled environment and a natural environment in an experimental garden. When we compared the variation of their leaf shape as a vegetative organ, the synthetic A. kamchatica individuals grown in the garden showed larger variation compared with the individuals incubated in a growth chamber, suggesting enhanced phenotypic variation in a natural fluctuating environment. In contrast, the natural A. kamchatica genotypes did not show significant change in variation by growth condition. The phenotypic variation of floral organs by growth condition was much smaller in both synthetic and natural A. kamchatica genotypes, and the difference in variation width between the growth chamber and the garden was not significant in each genotype as well as among genotypes. The higher phenotypic variation in synthetic leaf may imply flexible transcriptomic regulation of a newly synthesized polyploid compared with a natural polyploid.
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Affiliation(s)
- Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Aki Morishima
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Beatriz Mourato
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Yasuhiro Sato
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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Zhong DL, Li YC, Zhang JQ. Allopolyploid origin and niche expansion of Rhodiola integrifolia (Crassulaceae). PLANT DIVERSITY 2023; 45:36-44. [PMID: 36876317 PMCID: PMC9975476 DOI: 10.1016/j.pld.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/18/2023]
Abstract
Polyploidy after hybridization between species can lead to immediate post-zygotic isolation, causing saltatory origin of new species. Although the incidence of polyploidization in plants is high, it is thought that a new polyploid lineage can succeed only if it establishes a new ecological niche divergent from its progenitor lineages. We tested the hypothesis that Rhodiola integrifolia from North America is an allopolyploid produced by R. rhodantha and R. rosea and determined whether its survival can be explained by the niche divergence hypothesis. To this end, we sequenced two low-copy nuclear genes (ncpGS and rpb2) in a phylogenetic analysis of 42 Rhodiola species and tested for niche equivalency and similarity using Schoener's D as the index of niche overlap. Our phylogeny-based approach showed that R. integrifolia possesses alleles from both R. rhodantha and R. rosea. Dating analysis showed that the hybridization event that led to R. integrifolia occurred ca. 1.67 Mya and niche modeling analysis showed that at this time, both R. rosea and R. rhodantha may have been present in Beringia, providing the opportunity for the hybridization event. We also found that the niche of R. integrifolia differs from that of its progenitors in both niche breadth and optimum. Taken together, these results confirm the hybrid origin of R. integrifolia and support the niche divergence hypothesis for this tetraploid species. Our results underscore the fact that lineages with no current overlapping distribution could produce hybrid descendants in the past, when climate oscillations made their distributions overlap.
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Dong PB, Wang LJ, Jia Y, Li ZH, Wang HY, Guo FX, Chen Y. Niche divergence at the intraspecific level in an endemic rare peony ( Paeonia rockii): A phylogenetic, climatic and environmental survey. FRONTIERS IN PLANT SCIENCE 2022; 13:978011. [PMID: 36388470 PMCID: PMC9663928 DOI: 10.3389/fpls.2022.978011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Ecological factors have received increasing attention as drivers of speciation but also in the maintenance of postspeciation divergence. However, the relative significance of the responses of species to climate oscillations for driving niche divergence or conservatism in the evolution of many species that pass through diverse environments and limited geographical boundaries remains poorly understood. Paeonia rockii (one of the ancient species of Paeonia) comprising two subspecies called Paeonia rockii subsp. rockii and Paeonia rockii subsp. taibaishanica is an endemic, rare, and endangered medicinal plant in China. In this study, we integrated whole chloroplast genomes, and ecological factors to obtain insights into ecological speciation and species divergence in this endemic rare peony. RAxML analysis indicated that the topological trees recovered from three different data sets were identical, where P. rockii subsp. rockii and P. rockii subsp. taibaishanica clustered together, and molecular dating analyses suggested that the two subspecies diverged 0.83 million years ago. In addition, ecological niche modeling showed that the predicted suitable distribution areas for P. rockii subsp. rockii and P. rockii subsp. taibaishanica differed considerably, although the predicted core distribution areas were similar, where the population contracted in the last interglacial and expanded in the last glacial maximum. Under the emissions scenarios for the 2050s and 2070s, the suitable distribution areas were predicted to contract significantly, where the migration routes of the two subspecies tended to migrate toward high latitudes and elevations, thereby suggesting strong responses of the distributions of the two subspecies to climate change. These findings combined with the phylogeographic relationships provide comprehensive insights into niche variation and differentiation in this endemic rare peony, and they highlight the importance of geological and climatic changes for species divergence and changes in the population geographic patterns of rare and endangered medicinal plants in East Asia.
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Affiliation(s)
- Peng-Bin Dong
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Ling-Juan Wang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Jia
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) College of Life Sciences, Northwest University, Xi’an, China
| | - Hong-Yan Wang
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Feng-Xia Guo
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Chen
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
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Shimizu KK. Robustness and the generalist niche of polyploid species: Genome shock or gradual evolution? CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102292. [PMID: 36063635 DOI: 10.1016/j.pbi.2022.102292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/01/2022] [Accepted: 07/27/2022] [Indexed: 05/26/2023]
Abstract
The prevalence of polyploidy in wild and crop species has stimulated debate over its evolutionary advantages and disadvantages. Previous studies have focused on changes occurring at the polyploidization events, including genome-wide changes termed "genome shock," as well as ancient polyploidy. Recent bioinformatics advances and empirical studies of Arabidopsis and wheat relatives are filling a research gap: the functional evolutionary study of polyploid species using RNA-seq, DNA polymorphism, and epigenomics. Polyploid species can become generalists in natura through environmental robustness by inheriting and merging parental stress responses. Their evolvability is enhanced by mutational robustness working on inherited standing variation. The identification of key genes responsible for gradual adaptive evolution will encourage synthetic biological approaches to transfer polyploid advantages to other species.
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Affiliation(s)
- Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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13
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Hörandl E. Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020204. [PMID: 35050093 PMCID: PMC8781807 DOI: 10.3390/plants11020204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/08/2023]
Abstract
Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Göttingen, Germany
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Akiyama R, Briskine RV, Gan X, Hatakeyama M, Kudoh H, Lischer HEL, Sese J, Shimizu KK, Shimizu‐Inatsugi R, Sun J. Corrigendum. THE NEW PHYTOLOGIST 2021; 231:500. [PMID: 34060666 PMCID: PMC8451049 DOI: 10.1111/nph.17320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
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