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Whitener MR, Mangelson H, Sweigart AL. Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis. Evolution 2024; 78:1464-1477. [PMID: 38766685 DOI: 10.1093/evolut/qpae079] [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: 09/17/2023] [Revised: 03/12/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer Mimulus nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both Mimulus decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid's predisposition to self-fertilize.
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Affiliation(s)
- Makenzie R Whitener
- Department of Genetics, University of Georgia, Athens, GA 30602, United States
| | | | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, GA 30602, United States
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2
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Mostow RS, Barreto FS, Hacker SD. A hybrid beachgrass (Ammophila arenaria × A. breviligulata) is more productive and outcompetes its non-native parent species. Oecologia 2024; 205:81-94. [PMID: 38687376 DOI: 10.1007/s00442-024-05548-5] [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: 10/19/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024]
Abstract
The ability of non-native species to successfully invade new ecosystems sometimes involves evolutionary processes such as hybridization. Hybridization can produce individuals with superior traits that give them a competitive advantage over their parent species, allowing for rapid spread. Here we assess growth, functional morphology, and species interactions between two non-native beachgrass species (Ammophila arenaria and A. breviligulata) and their recently discovered hybrid (A. arenaria × A. breviligulata) on the U.S. Pacific Northwest coast. We asked whether the hybrid beachgrass differs from its parent species in morphology and growth, whether it competes with its parent species, and, if so, what are the potential mechanisms of competition. Plant taxa were grown in low- and high-density monocultures and in two-way interactions in a common garden environment. We show that the hybrid grew taller and more densely, with greater total biomass, than either parent species. The hybrid was also the better competitor, resulting in the model prediction of competitive exclusion against A. breviligulata and, depending on its relative abundance, A. arenaria. The hybrid displays a mixed 'guerilla-phalanx' growth form that allows it to spread laterally and achieve high shoot densities, giving it a competitive advantage. Given the current dominance of A. breviligulata compared to A. arenaria in most of the region where these taxa co-occur, we suggest that the hybrid will grow, compete, and spread quickly with potentially widespread consequences for the two non-native Ammophila congeners and the dunes they build.
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Affiliation(s)
- Rebecca S Mostow
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331-2914, USA
| | - Felipe S Barreto
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331-2914, USA
| | - Sally D Hacker
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331-2914, USA.
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3
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Sha Y, Li Y, Zhang D, Lv R, Wang H, Wang R, Ji H, Li S, Gong L, Li N, Liu B. Genome shock in a synthetic allotetraploid wheat invokes subgenome-partitioned gene regulation, meiotic instability, and karyotype variation. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5547-5563. [PMID: 37379452 DOI: 10.1093/jxb/erad247] [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: 03/14/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
It is becoming increasingly evident that interspecific hybridization at the homoploid level or coupled with whole-genome duplication (i.e. allopolyploidization) has played a major role in biological evolution. However, the direct impacts of hybridization and allopolyploidization on genome structure and function, phenotype, and fitness remains to be fully understood. Synthetic hybrids and allopolyploids are trackable experimental systems that can be used to address this issue. In this study, we resynthesized a pair of reciprocal F1 hybrids and corresponding reciprocal allotetraploids using the two diploid progenitor species of bread wheat (Triticum aestivum, BBAADD), namely T. urartu (AA) and Aegilops tauschii (DD). By comparing phenotypes related to growth, development, and fitness, and by analysing genome expression in both hybrids and allotetraploids in relation to the parents, we found that the types and trends of karyotype variation in the immediately formed allotetraploids were correlated with both instability of meiosis and chromosome- and subgenome-biased expression. We determined clear advantages of allotetraploids over diploid F1 hybrids in several morphological traits including fitness that mirrored the tissue- and developmental stage-dependent subgenome-partitioning of the allotetraploids. The allotetraploids were meiotically unstable primarily due to homoeologous pairing that varied dramatically among the chromosomes. Nonetheless, the manifestation of organismal karyotype variation and the occurrence of meiotic irregularity were not concordant, suggesting a role of functional constraints probably imposed by subgenome- and chromosome-biased gene expression. Our results provide new insights into the direct impacts and consequences of hybridization and allopolyploidization that are relevant to evolution and likely to be informative for future crop improvement approaches using synthetic polyploids.
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Affiliation(s)
- Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Deshi Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Han Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Heyu Ji
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Shuhang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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de Jong GW, Adams KL. Subgenome-dominant expression and alternative splicing in response to Sclerotinia infection in polyploid Brassica napus and progenitors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:142-158. [PMID: 36710652 DOI: 10.1111/tpj.16127] [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: 03/14/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both resynthesized and natural lines of polyploid Brassica napus, along with the progenitors Brassica rapa and Brassica oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12 709 DAS events) and lower in resynthesized B. napus (8863 DAS events). Natural B. napus had more upregulated events and fewer downregulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus, this resulted in a disproportionate C subgenome contribution to the pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in resynthesized and natural B. napus.
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Affiliation(s)
- Grant W de Jong
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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Cavé-Radet A, Salmon A, Tran Van Canh L, Moyle RL, Pretorius LS, Lima O, Ainouche ML, El Amrani A. Recent allopolyploidy alters Spartina microRNA expression in response to xenobiotic-induced stress. PLANT MOLECULAR BIOLOGY 2023; 111:309-328. [PMID: 36581792 DOI: 10.1007/s11103-022-01328-y] [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: 06/08/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Environmental contamination by xenobiotics represents a major threat for natural ecosystems and public health. In response, xenobiotic detoxification is a fundamental trait of organisms for developmental plasticity and stress tolerance, but the underlying molecular mechanisms remain poorly understood in plants. To decipher this process, we explored the consequences of allopolyploidy on xenobiotic tolerance in the genus Spartina Schreb. Specifically, we focused on microRNAs (miRNAs) owing to their central function in the regulation of gene expression patterns, including responses to stress. Small RNA-Seq was conducted on the parents S. alterniflora and S. maritima, their F1 hybrid S. x townsendii and the allopolyploid S. anglica under phenanthrene-induced stress (phe), a model Polycyclic Aromatic Hydrocarbon (PAH) compound. Differentially expressed miRNAs in response to phe were specifically identified within species. In complement, the respective impacts of hybridization and genome doubling were detected, through changes in miRNA expression patterns between S. x townsendii, S. anglica and the parents. The results support the impact of allopolyploidy in miRNA-guided regulation of plant response to phe. In total, we identified 17 phe-responsive miRNAs in Spartina among up-regulated MIR156 and down-regulated MIR159. We also describe novel phe-responsive miRNAs as putative Spartina-specific gene expression regulators in response to stress. Functional validation using Arabidopsis (L.) Heynh. T-DNA lines inserted in homologous MIR genes was performed, and the divergence of phe-responsive miRNA regulatory networks between Arabidopsis and Spartina was discussed.
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Affiliation(s)
- Armand Cavé-Radet
- Université de Rennes 1, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, OSUR, Campus de Beaulieu, Bâtiment 14A, 35042, Rennes Cedex, France.
| | - Armel Salmon
- Université de Rennes 1, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, OSUR, Campus de Beaulieu, Bâtiment 14A, 35042, Rennes Cedex, France
| | - Loup Tran Van Canh
- Université de Rennes 1, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, OSUR, Campus de Beaulieu, Bâtiment 14A, 35042, Rennes Cedex, France
| | - Richard L Moyle
- Nexgen Plants Pty Ltd., School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Lara-Simone Pretorius
- Nexgen Plants Pty Ltd., School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Oscar Lima
- Université de Rennes 1, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, OSUR, Campus de Beaulieu, Bâtiment 14A, 35042, Rennes Cedex, France
| | - Malika L Ainouche
- Université de Rennes 1, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, OSUR, Campus de Beaulieu, Bâtiment 14A, 35042, Rennes Cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, UMR CNRS 6553, Ecosystèmes-Biodiversité-Evolution, OSUR, Campus de Beaulieu, Bâtiment 14A, 35042, Rennes Cedex, France.
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Sattler MC, de Oliveira SC, Mendonça MAC, Clarindo WR. Coffea cytogenetics: from the first karyotypes to the meeting with genomics. PLANTA 2022; 255:112. [PMID: 35501619 DOI: 10.1007/s00425-022-03898-z] [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: 09/23/2021] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Coffea karyotype organization and evolution has been uncovered by classical cytogenetics and cytogenomics. We revisit these discoveries and present new karyotype data. Coffea possesses ~ 124 species, including C. arabica and C. canephora responsible for commercial coffee production. We reviewed the Coffea cytogenetics, from the first chromosome counting, encompassing the karyotype characterization, chromosome DNA content, and mapping of chromosome portions and DNA sequences, until the integration with genomics. We also showed new data about Coffea karyotype. The 2n chromosome number evidenced the diploidy of almost all Coffea, and the C. arabica tetraploidy, as well as the polyploidy of other hybrids. Since then, other genomic similarities and divergences among the Coffea have been shown by karyotype morphology, nuclear and chromosomal C-value, AT and GC rich chromosome portions, and repetitive sequence and gene mapping. These cytogenomic data allowed us to know and understand the phylogenetic relations in Coffea, as well as their ploidy level and genomic origin, highlighting the relatively recent allopolyploidy. In addition to the euploidy, the role of the mobile elements in Coffea diversification is increasingly more evident, and the comparative analysis of their structure and distribution on the genome of different species is in the spotlight for future research. An integrative look at all these data is fundamental for a deeper understanding of Coffea karyotype evolution, including the key role of polyploidy in C. arabica origin. The 'Híbrido de Timor', a recent natural allotriploid, is also in the spotlight for its potential as a source of resistance genes and model for plant polyploidy research. Considering this, we also present some unprecedented results about the exciting evolutionary history of these polyploid Coffea.
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Affiliation(s)
- Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, ZIP 36.570-900, Brazil.
| | - Stéfanie Cristina de Oliveira
- Laboratório de Citogenética e Cultura de Tecidos Vegetais, Campus de Alegre, Universidade Federal Do Espírito Santo, Alegre, ES, ZIP 29.500-000, Brazil
| | | | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, ZIP 36.570-900, Brazil
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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Guo J, Richards CL, Holsinger KE, Fox GA, Zhang Z, Zhou C. Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity. AMERICAN JOURNAL OF BOTANY 2021; 108:2371-2387. [PMID: 34636406 DOI: 10.1002/ajb2.1771] [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: 06/04/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species because they create and define ecological communities, contributing disproportionately to ecosystem function. METHODS We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages. We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass Leymus chinensis. We examined the relationship between genetic and clonal diversities, their variation with patch size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species. RESULTS Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single multilocus lineages. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three. CONCLUSIONS We found strong genetic structure among patches of L. chinensis. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.
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Affiliation(s)
- Jian Guo
- School of Life Science, Liaoning University, Shenyang, 110036, P.R. China
- School of Environmental Engineering, Xuzhou University of Technology, Xuzhou, 221018, P.R. China
| | - Christina L Richards
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
- Plant Evolutionary Ecology group, University of Tübingen, Tübingen, D-72076, Germany
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, Connecticut, 06269, USA
| | - Gordon A Fox
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Zhuo Zhang
- School of Life Science and Bioengineering, Shenyang University, Shenyang, 110044, P.R. China
| | - Chan Zhou
- School of Life Science, Liaoning University, Shenyang, 110036, P.R. China
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Lorenz J, Heinrich R, Schneider A, Schwager M, Herklotz V, Wesche K, Ritz CM. Invasive populations of Spiraea tomentosa (Rosaceae) are genetically diverse but decline during succession in forest habitats. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:749-759. [PMID: 33899992 DOI: 10.1111/plb.13275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
Population genetic and ecological data may help to control invasive plants, which are considered a major threat to natural habitats. In contrast to expected bottleneck events, genetic diversity of such invasive populations may be high due to extensive propagule pressure or admixture. The ecological impact of invasive species has been broadly evaluated in the field; however, long-term studies on the fate of invasive plants are scarce. We analysed genetic diversity and structure in invasive Spiraea tomentosa populations in eastern Germany and western Poland using Amplified Fragment Length Polymorphism. Potential hybridization between co-occurring diploid Sp. tomentosa and tetraploid Sp. douglasii was investigated using Flow Cytometry. The genetic analyses were complemented by data from a 13-year vegetation study in an area invaded by these Spiraea species. We found no evidence for hybridization between Spiraea species. In populations of Sp. tomentosa both genetic diversity (He = 0.26) and genetic structure (ΦPT = 0.27) were high and comparable to other outcrossing woody plants. Low levels of clonality, presence of seedlings and new patches in sites that had been colonized over the last 13 years imply that populations spread via sexual reproduction. In all habitat types, native species diversity declined following Sp. tomentosa invasion. However, detailed aerial mapping of a forest reserve with ongoing succession revealed that Spiraea spp. populations have declined over a 10-year period. Despite its potential for dispersal and negative effects on native plant communities, invasive Spiraea populations may be controlled by increasing canopy cover in forest habitats.
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Affiliation(s)
- J Lorenz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Zittau, Germany
| | - R Heinrich
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- NABU - Naturschutzstation Ebersbach, Ebersbach-Neugersdorf, Germany
| | - A Schneider
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - M Schwager
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - V Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - K Wesche
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Zittau, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Halle-Jena-Leipzig, Germany
| | - C M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute (IHI) Zittau, Chair of Biodiversity of Higher Plants, Zittau, Germany
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Mounger J, Ainouche ML, Bossdorf O, Cavé-Radet A, Li B, Parepa M, Salmon A, Yang J, Richards CL. Epigenetics and the success of invasive plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200117. [PMID: 33866809 PMCID: PMC8059582 DOI: 10.1098/rstb.2020.0117] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
| | - Malika L. Ainouche
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armand Cavé-Radet
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Madalin Parepa
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Campus Scientifique de Beaulieu, Rennes, France
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Christina L. Richards
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33617, USA
- Plant Evolutionary Ecology, University of Tübingen, 72076 Tübingen, Germany
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Giraud D, Lima O, Rousseau-Gueutin M, Salmon A, Aïnouche M. Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae). Front Genet 2021; 12:589160. [PMID: 33841492 PMCID: PMC8027259 DOI: 10.3389/fgene.2021.589160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploid Spartina species (Poaceae, Chloridoideae) that successively diverged in the last 6-10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploids Spartina alterniflora (2n = 6x = 62) and S. maritima (2n = 6x = 60) that resulted in two sterile F1 hybrids: Spartina × townsendii (2n = 6x = 62) in England and Spartina × neyrautii (2n = 6x = 62) in France. Whole genome duplication of S. × townsendii gave rise to the invasive neo-allododecaploid species Spartina anglica (2n = 12x = 124). New transcriptome assemblies and annotations for tetraploids and the enrichment of previously published reference transcriptomes for hexaploids and the allododecaploid allowed identifying 42,423 clusters of orthologs and distinguishing 21 transcribed transposable element (TE) lineages across the seven investigated Spartina species. In 4x and 6x mesopolyploids, gene and TE expression changes were consistent with phylogenetic relationships and divergence, revealing weak expression differences in the tetraploid sister species Spartina bakeri and Spartina versicolor (<2 my divergence time) compared to marked transcriptome divergence between the hexaploids S. alterniflora and S. maritima that diverged 2-4 mya. Differentially expressed genes were involved in glycolysis, post-transcriptional protein modifications, epidermis development, biosynthesis of carotenoids. Most detected TE lineages (except SINE elements) were found more expressed in hexaploids than in tetraploids, in line with their abundance in the corresponding genomes. Comparatively, an astonishing (52%) expression repatterning and deviation from parental additivity were observed following recent reticulate evolution (involving the F1 hybrids and the neo-allododecaploid S. anglica), with various patterns of biased homoeologous gene expression, including genes involved in epigenetic regulation. Downregulation of TEs was observed in both hybrids and accentuated in the neo-allopolyploid. Our results reinforce the view that allopolyploidy represents springboards to new regulatory patterns, offering to worldwide invasive species, such as S. anglica, the opportunity to colonize stressful and fluctuating environments on saltmarshes.
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Affiliation(s)
- Delphine Giraud
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | - Oscar Lima
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | | | - Armel Salmon
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
| | - Malika Aïnouche
- UMR CNRS 6553 Ecosystèmes, Biodiversité, Evolution (ECOBIO), Université de Rennes 1, Rennes, France
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12
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Sun J, Shimizu-Inatsugi R, Hofhuis H, Shimizu K, Hay A, Shimizu KK, Sese J. A Recently Formed Triploid Cardamine insueta Inherits Leaf Vivipary and Submergence Tolerance Traits of Parents. Front Genet 2020; 11:567262. [PMID: 33133153 PMCID: PMC7573311 DOI: 10.3389/fgene.2020.567262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/18/2020] [Indexed: 12/03/2022] Open
Abstract
Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, Cardamine amara and Cardamine rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.
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Affiliation(s)
- Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Hugo Hofhuis
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,Humanome Lab, Inc., Tokyo, Japan
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13
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Mason AS, Wendel JF. Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution. Front Genet 2020; 11:1014. [PMID: 33005183 PMCID: PMC7485112 DOI: 10.3389/fgene.2020.01014] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023] Open
Abstract
Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early stages of allopolyploid stabilization. Homoeologous exchanges (HEs) have been reported in young allopolyploids from across the angiosperms. Although all lineages undergo karyotype change via chromosome rearrangements over time, the early generations after allopolyploid formation are predicted to show an accelerated rate of genomic change. HEs can also cause changes in allele dosage, genome-wide methylation patterns, and downstream phenotypes, and can hence be responsible for speciation and genome stabilization events. Additionally, we propose that fixation of duplication - deletion events resulting from HEs could lead to the production of genomes which appear to be a mix of autopolyploid and allopolyploid segments, sometimes termed "segmental allopolyploids." We discuss the implications of these findings for our understanding of the relationship between genome instability in novel polyploids and genome evolution.
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Affiliation(s)
- Annaliese S. Mason
- Plant Breeding Department, Justus Liebig University Giessen, Giessen, Germany
| | - Jonathan F. Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, United States
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14
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Gallego-Tévar B, Peinado-Torrubia P, Álvarez R, Grewell BJ, Castillo JM. From physiology to salt marsh management challenges with sea level rise: the case of native Spartina foliosa, invasive S. densiflora and their hybrid. CONSERVATION PHYSIOLOGY 2020; 8:coaa053. [PMID: 32685163 PMCID: PMC7327128 DOI: 10.1093/conphys/coaa053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
Sea level rise (SLR) imposes increasing salinity and inundation stresses in salt marshes which simultaneously face invasions by exotic plant species. We aimed to improve and apply knowledge on the ecophysiological responses of halophytes to SLR to conservation management of salt marshes. In a mesocosm experiment, we measured and compared phosphoenolpyruvate carboxylase (PEPC) activity and related functional traits of the California-native Spartina foliosa, invasive S. densiflora and their hybrid S. densiflora × foliosa in response to increasing levels of salinity and inundation. S. foliosa was moderately sensitive to salinity, showing a 57% reduction in PEPC specific activity from freshwater to hypersalinity. This native species compensated for the reduction of PEPC activity with increased salinity through 80% higher enzyme activation by phosphorylation. PEPC functional trait responses of S. foliosa were mostly independent of inundation depth. In view of these results, managers should conserve undeveloped lands for accommodation space above current high tide lines to facilitate colonization of stress-tolerant S. foliosa. Our results on functional responses of PEPC traits recorded high sensitivity to salinity for S. densiflora. This was reflected by 65% lower PEPC specific activity together with increasing accumulation of free proline (+96%) and total proteins (+23%) with elevated salinity. These results suggest prioritized eradication of S. densiflora populations in brackish habitats. Measured PEPC responses support the high stress tolerance of the S. densiflora × foliosa hybrid. PEPC traits for the hybrid were mostly independent of salinity and inundation. The hybrid showed higher PEPC-specific activity than S. foliosa (+70%) and S. densiflora (+15%) in freshwater under intermediate inundation. Results suggest that eradication of the hybrid should be the highest management priority. Our study shows that the responses of key functional physiological traits to environmental stresses serve as biological indicators that can guide ecosystem management practices in a scenario of climate change.
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Affiliation(s)
- Blanca Gallego-Tévar
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap 1095, 41080 Sevilla, Spain
| | | | - Rosario Álvarez
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap 1095, 41080 Sevilla, Spain
| | - Brenda J Grewell
- USDA-ARS, Invasive Species and Pollinator Health Research Unit, Department of Plant Sciences MS-4, 1 Shields Avenue, University of California, Davis, CA 95616, USA
| | - Jesús M Castillo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap 1095, 41080 Sevilla, Spain
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15
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Azibi T, Hadj-Arab H, Lodé M, Ferreira de Carvalho J, Trotoux G, Nègre S, Gilet MM, Boutte J, Lucas J, Vekemans X, Chèvre AM, Rousseau-Gueutin M. Impact of whole genome triplication on the evolutionary history and the functional dynamics of regulatory genes involved in Brassica self-incompatibility signalling pathway. PLANT REPRODUCTION 2020; 33:43-58. [PMID: 32080762 DOI: 10.1007/s00497-020-00385-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Polyploidy or whole genome duplication is a frequent and recurrent phenomenon in flowering plants that has played a major role in their diversification, adaptation and speciation. The adaptive success of polyploids relates to the different evolutionary fates of duplicated genes. In this study, we explored the impact of the whole genome triplication (WGT) event in the Brassiceae tribe on the genes involved in the self-incompatibility (SI) signalling pathway, a mechanism allowing recognition and rejection of self-pollen in hermaphrodite plants. By taking advantage of the knowledge acquired on this pathway as well as of several reference genomes in Brassicaceae species, we determined copy number of the different genes involved in this pathway and investigated their structural and functional evolutionary dynamics. We could infer that whereas most genes involved in the SI signalling returned to single copies after the WGT event (i.e. ARC1, JDP1, THL1, THL2, Exo70A01) in diploid Brassica species, a few were retained in duplicated (GLO1 and PLDα) or triplicated copies (MLPK). We also carefully studied the gene structure of these latter duplicated genes (including the conservation of functional domains and active sites) and tested their transcription in the stigma to identify which copies seem to be involved in the SI signalling pathway. By taking advantage of these analyses, we then explored the putative origin of a contrasted SI phenotype between two Brassica rapa varieties that have been fully sequenced and shared the same S-allele (S60).
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Affiliation(s)
- Thanina Azibi
- University of Sciences and Technology Houari Boumedienne USTHB, Faculty of Biological Sciences FSB, Laboratory of Biology and Physiology of Organisms LBPO, Bab-Ezzouar, El-Alia, BP 32, 16111, Algiers, Algeria
- INRAE, Agrocampus Ouest, Université de Rennes, UMR IGEPP, 35650, Le Rheu, France
| | - Houria Hadj-Arab
- University of Sciences and Technology Houari Boumedienne USTHB, Faculty of Biological Sciences FSB, Laboratory of Biology and Physiology of Organisms LBPO, Bab-Ezzouar, El-Alia, BP 32, 16111, Algiers, Algeria.
| | - Maryse Lodé
- INRAE, Agrocampus Ouest, Université de Rennes, UMR IGEPP, 35650, Le Rheu, France
| | | | - Gwenn Trotoux
- INRAE, Agrocampus Ouest, Université de Rennes, UMR IGEPP, 35650, Le Rheu, France
| | - Sylvie Nègre
- INRAE, Agrocampus Ouest, Université de Rennes, UMR IGEPP, 35650, Le Rheu, France
| | | | - Julien Boutte
- INRAE, Agrocampus Ouest, Université de Rennes, UMR IGEPP, 35650, Le Rheu, France
| | - Jérémy Lucas
- INRAE, Agrocampus Ouest, Université de Rennes, UMR IGEPP, 35650, Le Rheu, France
| | - Xavier Vekemans
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, 59000, Lille, France
| | - Anne-Marie Chèvre
- INRAE, Agrocampus Ouest, Université de Rennes, UMR IGEPP, 35650, Le Rheu, France
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16
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Garcia S, Wendel JF, Borowska-Zuchowska N, Aïnouche M, Kuderova A, Kovarik A. The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants. FRONTIERS IN PLANT SCIENCE 2020; 11:41. [PMID: 32117380 PMCID: PMC7025596 DOI: 10.3389/fpls.2020.00041] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups. RESULTS (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures. CONCLUSION We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC - Ajuntament de Barcelona), Barcelona, Spain
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Jonathan F. Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, United States
| | - Natalia Borowska-Zuchowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, Rennes, France
| | - Alena Kuderova
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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17
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Yang J, Fu W, Xu H, Song Z, Zhang W, Yang J, Wang Y. An Empirical Analysis Rejects the Hybrid Speciation Hypothesis of a Crucial Kiwifruit Species, Despite Genomic Evidence of Frequent Interspecific Gene Flow in the Genus. Front Genet 2020; 10:1250. [PMID: 32117405 PMCID: PMC7011101 DOI: 10.3389/fgene.2019.01250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/13/2019] [Indexed: 11/13/2022] Open
Abstract
Hybrid speciation is an important way to generate species diversity. In general, however, interspecific hybridization is easily confused with the formation of hybrid species. Using the genomic resequencing data of the kiwifruit genus (Actinidia), at least ten species were documented recently as homoploid hybrid species, and thus a two-layer mode of species diversification has been proposed. As a crucial piece of evidence, Actinidia fulvicoma was identified as a hybrid derivative of Actinidia eriantha × Actinidia cylindrica, representing a rare case of hybrid species in kiwifruit that won the competition of ecological niches with one of its putative parental species, A. cylindrica. However, the hypothesized hybrid origin of A. fulvicoma is inconsistent with our specimen observations. Here, we present multiple lines of evidence to reject the hybrid speciation hypothesis for this species, despite genomic evidence for frequent interspecific gene flow. We collected the samples of A. fulvicoma in type locality and neighboring regions to contrast them with type specimen, and sequenced nuclear ribosomal DNA ITS, chloroplast trnL-trnF and mitochondrial nad2-i3, as well as four single-copy nuclear genes explored from kiwifruit genomes, to infer phylogenetic relationships among A. fulvicoma, its putative parental species, and their relatives. Our data definitely reveal that A. fulvicoma occupies an independent backbone lineage and it is not a hybrid. This study suggests that correct evolutionary applications on extensive surveys of the putative hybrid and its possible parents with strict criteria are necessary in the documentation of hybrid speciation to advance our understanding of the genomic basis of hybrid species.
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Affiliation(s)
| | | | | | | | | | | | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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18
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Pan Q, Zhu B, Zhang D, Tong C, Ge X, Liu S, Li Z. Gene Expression Changes During the Allo-/Deallopolyploidization Process of Brassica napus. Front Genet 2020; 10:1279. [PMID: 31921314 PMCID: PMC6931035 DOI: 10.3389/fgene.2019.01279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/21/2019] [Indexed: 11/21/2022] Open
Abstract
Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted Brassica rapa (RBR, AeAe, 2n = 20) obtained from Brassica napus (AnAnCnCn, 2n = 38) to analyze the gene expression changes and its potential mechanism during the process of allo-/deallopolyploidization. RNA-seq-based transcriptome profiling identified a large number of differentially expressed genes (DEGs) between RBR and natural B. rapa (ArAr), suggesting potential effects of allopolyploidization/domestication of AA component of B. napus at the tetrapolyploid level. Meanwhile, it was revealed that up to 20% of gene expressions were immediately altered when compared with those in the An-subgenome. Interestingly, one fifth of these changes are in fact indicative of the recovery of antecedent gene expression alternations occurring since the origin of B. napus and showed association with homoeologous expression bias between An and Cn subgenomes. Enrichment of distinct gene ontology (GO) categories of the above sets of genes further indicated potential functional cooperation of the An and Cn subgenome of B. napus. Whole genome methylation analysis revealed a small number of DEGs were identified in the differentially methylated regions.
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Affiliation(s)
- Qi Pan
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bin Zhu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dawei Zhang
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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19
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Cavé-Radet A, Giraud D, Lima O, El Amrani A, Aïnouche M, Salmon A. Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae). PLANT MOLECULAR BIOLOGY 2020; 102:55-72. [PMID: 31748889 DOI: 10.1007/s11103-019-00931-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina. The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.
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Affiliation(s)
- Armand Cavé-Radet
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Delphine Giraud
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Oscar Lima
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Malika Aïnouche
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Armel Salmon
- Université de Rennes 1, Centre National de la Recherche Scientifique, UMR CNRS 6553 ECOBIO, Campus de Beaulieu, 35042, Rennes Cedex, France.
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20
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Chrtek J, Mráz P, Belyayev A, Paštová L, Mrázová V, Caklová P, Josefiová J, Zagorski D, Hartmann M, Jandová M, Pinc J, Fehrer J. Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str.: morphological versus genomic features. AMERICAN JOURNAL OF BOTANY 2020; 107:66-90. [PMID: 31903548 DOI: 10.1002/ajb2.1413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 11/13/2019] [Indexed: 05/02/2023]
Abstract
PREMISE The origin of allopolyploids is believed to shape their evolutionary potential, ecology, and geographical ranges. Morphologically distinct apomictic types sharing the same parental species belong to the most challenging groups of polyploids. We evaluated the origins and variation of two triploid taxa (Hieracium pallidiflorum, H. picroides) presumably derived from the same diploid parental pair (H. intybaceum, H. prenanthoides). METHODS We used a suite of approaches ranging from morphological, phylogenetic (three unlinked molecular markers), and cytogenetic analyses (in situ hybridization) to genome size screening and genome skimming. RESULTS Genotyping proved the expected parentage of all analyzed accessions of H. pallidiflorum and H. picroides and revealed that nearly all of them originated independently. Genome sizes and genome dosage largely corresponded to morphology, whereas the maternal origin of the allopolyploids had no discernable effect. Polyploid accessions of both parental species usually contained genetic material from other species. Given the phylogenetic distance of the parents, their chromosomes appeared only weakly differentiated in genomic in situ hybridization (GISH), as well as in overall comparisons of the repetitive fraction of their genomes. Furthermore, the repeatome of a phylogenetically more closely related species (H. umbellatum) differed significantly more. CONCLUSIONS We proved (1) multiple origins of hybridogeneous apomicts from the same diploid parental taxa, and (2) allopolyploid origins of polyploid accessions of the parental species. We also showed that the evolutionary dynamics of very fast evolving markers such as satellite DNA or transposable elements does not necessarily follow patterns of speciation.
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Affiliation(s)
- Jindřich Chrtek
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Patrik Mráz
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Ladislava Paštová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Viera Mrázová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Petra Caklová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Jiřina Josefiová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Danijela Zagorski
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Matthias Hartmann
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Michaela Jandová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Jan Pinc
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Judith Fehrer
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
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21
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Bortolus A, Adam P, Adams JB, Ainouche ML, Ayres D, Bertness MD, Bouma TJ, Bruno JF, Caçador I, Carlton JT, Castillo JM, Costa CSB, Davy AJ, Deegan L, Duarte B, Figueroa E, Gerwein J, Gray AJ, Grosholz ED, Hacker SD, Hughes AR, Mateos-Naranjo E, Mendelssohn IA, Morris JT, Muñoz-Rodríguez AF, Nieva FJJ, Levin LA, Li B, Liu W, Pennings SC, Pickart A, Redondo-Gómez S, Richardson DM, Salmon A, Schwindt E, Silliman BR, Sotka EE, Stace C, Sytsma M, Temmerman S, Turner RE, Valiela I, Weinstein MP, Weis JS. Supporting Spartina: Interdisciplinary perspective shows Spartina as a distinct solid genus. Ecology 2019; 100:e02863. [PMID: 31398280 DOI: 10.1002/ecy.2863] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 11/11/2022]
Abstract
In 2014, a DNA-based phylogenetic study confirming the paraphyly of the grass subtribe Sporobolinae proposed the creation of a large monophyletic genus Sporobolus, including (among others) species previously included in the genera Spartina, Calamovilfa, and Sporobolus. Spartina species have contributed substantially (and continue contributing) to our knowledge in multiple disciplines, including ecology, evolutionary biology, molecular biology, biogeography, experimental ecology, biological invasions, environmental management, restoration ecology, history, economics, and sociology. There is no rationale so compelling to subsume the name Spartina as a subgenus that could rival the striking, global iconic history and use of the name Spartina for over 200 yr. We do not agree with the subjective arguments underlying the proposal to change Spartina to Sporobolus. We understand the importance of both the objective phylogenetic insights and of the subjective formalized nomenclature and hope that by opening this debate we will encourage positive feedback that will strengthen taxonomic decisions with an interdisciplinary perspective. We consider that the strongly distinct, monophyletic clade Spartina should simply and efficiently be treated as the genus Spartina.
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Affiliation(s)
- Alejandro Bortolus
- Grupo de Ecología en Ambientes Costeros (GEAC), Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC), CONICET, Boulevard Brown 2915, Puerto Madryn (U9120ACD), Chubut, Argentina
| | - Paul Adam
- School of Biological, Earth and Environmental Science, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Janine B Adams
- Department of Botany, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Malika L Ainouche
- UMR CNRS 6553 Ecosystems, Biodiversity Evolution (ECOBIO), University of Rennes 1, Campus de Beaulieu, 35 042, Rennes Cedex, France
| | - Debra Ayres
- Evolution and Ecology, University of California, Davis, California, 95616, USA
| | - Mark D Bertness
- Department of Ecology and Evolutionary Biology, Brown University, 02901, Providence, Rhode Island, USA
| | - Tjeerd J Bouma
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, P.O. Box 140, 4400 AC, Yerseke, The Netherlands.,Faculty of Geosciences, Department of Physical Geography, Utrecht University, 3584 CS, Utrecht, The Netherlands
| | - John F Bruno
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, 27599-3280, USA
| | - Isabel Caçador
- MARE - Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - James T Carlton
- Maritime Studies Program, Williams College, Mystic Seaport, Mystic, Connecticut, 96355, USA
| | - Jesus M Castillo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Cesar S B Costa
- Universidade Federal do Rio Grande-FURG, Campus Carreiros, Rio Grande, RS, 96203-900, Brazil
| | - Anthony J Davy
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Linda Deegan
- Woods Hole Research Center, 129 Woods Hole Road, Falmouth, Massachusetts, 02543, USA
| | - Bernardo Duarte
- MARE - Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Enrique Figueroa
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Joel Gerwein
- California State Coastal Conservancy, Oakland, California, 94612-1401, USA
| | - Alan J Gray
- Centre for Ecology and Hydrology, Edinburgh Research Station, Penicuik, Midlothian, EH26 0QB, United Kingdom
| | - Edwin D Grosholz
- Department of Environmental Science and Policy, University of California, Davis, California, 95616, USA
| | - Sally D Hacker
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, Oregon, 97331, USA
| | - A Randall Hughes
- Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts, 01908, USA
| | - Enrique Mateos-Naranjo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Irving A Mendelssohn
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - James T Morris
- Belle Baruch Institute for Marine and Coastal Sciences, University of South Carolina, Columbia, South Carolina, 29208, USA
| | | | - Francisco J J Nieva
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, California, 92093, USA
| | - Lisa A Levin
- Integrative Oceanography Division and Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, California, 92093, USA
| | - Bo Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wenwen Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Fujian, 361102, China
| | - Steven C Pennings
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204, USA
| | - Andrea Pickart
- U.S. Fish and Wildlife Service, Humboldt Bay National Wildlife Refuge, 6800 Lanphere Road, Arcata, California, 95521, USA
| | - Susana Redondo-Gómez
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, 41080, Sevilla, Spain
| | - David M Richardson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland, 7602, South Africa
| | - Armel Salmon
- UMR CNRS 6553 Ecosystems, Biodiversity Evolution (ECOBIO), University of Rennes 1, Campus de Beaulieu, 35 042, Rennes Cedex, France
| | - Evangelina Schwindt
- Instituto de Biología de Organismos Marinos (IBIOMAR-CONICET), U9120 ACD, Puerto Madryn, Argentina
| | - Brian R Silliman
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, 28516, USA
| | - Erik E Sotka
- Grice Marine Laboratory and the Department of Biology, College of Charleston, Charleston, South Carolina, 29412, USA
| | - Clive Stace
- Apletree House, Larters Lane, Middlewood Green, Sufolk, IP14 5HB, United Kingdom
| | - Mark Sytsma
- Portland State University, Portland, Oregon, 97207, USA
| | - Stijn Temmerman
- Ecosystem Management Research Group, University of Antwerp, Antwerp, BE-2610, Belgium
| | - R Eugene Turner
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Ivan Valiela
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, 02543, USA
| | | | - Judith S Weis
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, 07102, USA
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22
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Cavé-Radet A, Salmon A, Lima O, Ainouche ML, El Amrani A. Increased tolerance to organic xenobiotics following recent allopolyploidy in Spartina (Poaceae). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:143-154. [PMID: 30823992 DOI: 10.1016/j.plantsci.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 10/28/2018] [Accepted: 11/10/2018] [Indexed: 06/09/2023]
Abstract
Genome doubling or polyploidy is a widespread phenomenon in plants where it has important evolutionary consequences affecting the species distribution and ecology. PAHs are ubiquitous organic pollutants, which represent a major environmental concern. Recent data showed that tolerance to organic xenobiotics involve specific signaling pathways, and detoxifying gene sets referred as 'the xenome'. However, no data are available about how polyploidy impacts tolerance to organic xenobiotics. In the present paper, we investigated PAH tolerance following allopolyploidization in Spartina alterniflora, S. maritima and their derived allopolyploid species S. anglica. We performed comparative analyses of cellular compartmentalization, photosynthetic indices, and oxidative stress markers under phenanthrene-induced stress, and found that S. anglica exhibit increased tolerance compared to its parents. Based on 52 genes potentially involved in phenanthrene detoxification previously identified in A. thaliana, we investigated the Spartina xenome using genomic and transcriptomic available resources. Subsequently, we focused on GSTs, a ubiquitous enzymes class involved in organic xenobiotic detoxification. We examined expression profiles of selected genes by RT-qPCR, and revealed various patterns of parental expression alteration in the allopolyploid. The impacts of allopolyploidization on phenanthrene-induced stress and their potential ecological implications are discussed. The neo-allopolyploid S. anglica appears as a potential candidate for phytoremediation in PAH-polluted marshes.
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Affiliation(s)
- Armand Cavé-Radet
- Université de Rennes 1, OSUR/CNRS-UMR 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, Bâtiment 14A, 35042 Rennes Cedex, France
| | - Armel Salmon
- Université de Rennes 1, OSUR/CNRS-UMR 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, Bâtiment 14A, 35042 Rennes Cedex, France
| | - Oscar Lima
- Université de Rennes 1, OSUR/CNRS-UMR 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, Bâtiment 14A, 35042 Rennes Cedex, France
| | - Malika L Ainouche
- Université de Rennes 1, OSUR/CNRS-UMR 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, Bâtiment 14A, 35042 Rennes Cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, OSUR/CNRS-UMR 6553, Ecosystèmes-Biodiversité-Evolution, Campus de Beaulieu, Bâtiment 14A, 35042 Rennes Cedex, France.
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23
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Gallego-Tévar B, Rubio-Casal AE, de Cires A, Figueroa E, Grewell BJ, Castillo JM. Phenotypic plasticity of polyploid plant species promotes transgressive behaviour in their hybrids. AOB PLANTS 2018; 10:ply055. [PMID: 30377487 PMCID: PMC6201833 DOI: 10.1093/aobpla/ply055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 09/20/2018] [Indexed: 05/13/2023]
Abstract
Hybridization is a frequent process that leads to relevant evolutionary consequences, but there is a lack of studies regarding the relationships of the variability of the response of parental plant species to environmental gradients and the responses of their hybrids at a phenotypic level. We designed an experiment in which we exposed two reciprocal cordgrass hybrids, Spartina maritima × densiflora and S. densiflora × maritima, and their parental species to four salinity concentrations for 30 days. The main objectives were to compare the performance of the hybrids with that of their parents, to distinguish the phenotypic inheritance operating in the hybrids and to analyse the relationships between the variability in the responses of the parents and the responses of their hybrids to salinity. We characterized the responses and the degree of variability for 37 foliar traits. Both hybrids presented greater salinity tolerance than their parents, showing their highest percentage of transgressive traits at both extremes of the salinity gradient. When the parental plants themselves showed a more plastic response for a given trait, there was a greater chance that their hybrid developed a transgressive behaviour for this trait. This finding supports a new focus to be applied for the artificial development of vigorous hybrid crops.
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Affiliation(s)
- Blanca Gallego-Tévar
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap, Sevilla, Spain
- Corresponding author’s e-mail address:
| | - Alfredo E Rubio-Casal
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap, Sevilla, Spain
| | - Alfonso de Cires
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap, Sevilla, Spain
| | - Enrique Figueroa
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap, Sevilla, Spain
| | - Brenda J Grewell
- USDA-ARS Invasive Species and Pollinator Health Unit, University of California, Davis, CA, USA
| | - Jesús M Castillo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap, Sevilla, Spain
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24
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Gallego-Tévar B, Curado G, Grewell BJ, Figueroa ME, Castillo JM. Realized niche and spatial pattern of native and exotic halophyte hybrids. Oecologia 2018; 188:849-862. [DOI: 10.1007/s00442-018-4251-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 08/20/2018] [Indexed: 11/28/2022]
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25
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Pelé A, Rousseau-Gueutin M, Chèvre AM. Speciation Success of Polyploid Plants Closely Relates to the Regulation of Meiotic Recombination. FRONTIERS IN PLANT SCIENCE 2018; 9:907. [PMID: 30002669 PMCID: PMC6031745 DOI: 10.3389/fpls.2018.00907] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/08/2018] [Indexed: 05/18/2023]
Abstract
Polyploidization is a widespread phenomenon, especially in flowering plants that have all undergone at least one event of whole genome duplication during their evolutionary history. Consequently, a large range of plants, including many of the world's crops, combines more than two sets of chromosomes originating from the same (autopolyploids) or related species (allopolyploids). Depending on the polyploid formation pathway, different patterns of recombination will be promoted, conditioning the level of heterozygosity. A polyploid population harboring a high level of heterozygosity will produce more genetically diverse progenies. Some of these individuals may show a better adaptability to different ecological niches, increasing their chance for successful establishment through natural selection. Another condition for young polyploids to survive corresponds to the formation of well-balanced gametes, assuring a sufficient level of fertility. In this review, we discuss the consequences of polyploid formation pathways, meiotic behavior and recombination regulation on the speciation success and maintenance of polyploid species.
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Affiliation(s)
- Alexandre Pelé
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Mathieu Rousseau-Gueutin
- Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Rennes, France
| | - Anne-Marie Chèvre
- Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Rennes, France
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27
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Castillo JM, Gallego-Tévar B, Figueroa E, Grewell BJ, Vallet D, Rousseau H, Keller J, Lima O, Dréano S, Salmon A, Aïnouche M. Low genetic diversity contrasts with high phenotypic variability in heptaploid Spartina densiflora populations invading the Pacific coast of North America. Ecol Evol 2018; 8:4992-5007. [PMID: 29876076 PMCID: PMC5980529 DOI: 10.1002/ece3.4063] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/06/2018] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
Species can respond to environmental pressures through genetic and epigenetic changes and through phenotypic plasticity, but few studies have evaluated the relationships between genetic differentiation and phenotypic plasticity of plant species along changing environmental conditions throughout wide latitudinal ranges. We studied inter‐ and intrapopulation genetic diversity (using simple sequence repeats and chloroplast DNA sequencing) and inter‐ and intrapopulation phenotypic variability of 33 plant traits (using field and common‐garden measurements) for five populations of the invasive cordgrass Spartina densiflora Brongn. along the Pacific coast of North America from San Francisco Bay to Vancouver Island. Studied populations showed very low genetic diversity, high levels of phenotypic variability when growing in contrasted environments and high intrapopulation phenotypic variability for many plant traits. This intrapopulation phenotypic variability was especially high, irrespective of environmental conditions, for those traits showing also high phenotypic plasticity. Within‐population variation represented 84% of the total genetic variation coinciding with certain individual plants keeping consistent responses for three plant traits (chlorophyll b and carotenoid contents, and dead shoot biomass) in the field and in common‐garden conditions. These populations have most likely undergone genetic bottleneck since their introduction from South America; multiple introductions are unknown but possible as the population from Vancouver Island was the most recent and one of the most genetically diverse. S. densiflora appears as a species that would not be very affected itself by climate change and sea‐level rise as it can disperse, establish, and acclimate to contrasted environments along wide latitudinal ranges.
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Affiliation(s)
- Jesús M Castillo
- Departamento de Biología Vegetal y Ecología Universidad de Sevilla Sevilla Spain
| | - Blanca Gallego-Tévar
- Departamento de Biología Vegetal y Ecología Universidad de Sevilla Sevilla Spain
| | - Enrique Figueroa
- Departamento de Biología Vegetal y Ecología Universidad de Sevilla Sevilla Spain
| | - Brenda J Grewell
- Department of Plant Sciences MS-4 USDA-ARS Exotic & Invasive Weeds Research Unit University of California Davis California
| | | | | | - Jean Keller
- UMR CNRS 6553 ECOBIO Université Rennes 1 Rennes France
| | - Oscar Lima
- UMR CNRS 6553 ECOBIO Université Rennes 1 Rennes France
| | - Stéphane Dréano
- Faculté de Médecine Institut de génétique et Développement de Rennes (IGDR) UMR6290, CNRS Université de Rennes1 Rennes France
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO Université Rennes 1 Rennes France
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28
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Folk RA, Soltis PS, Soltis DE, Guralnick R. New prospects in the detection and comparative analysis of hybridization in the tree of life. AMERICAN JOURNAL OF BOTANY 2018; 105:364-375. [PMID: 29683488 DOI: 10.1002/ajb2.1018] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/12/2017] [Indexed: 05/03/2023]
Abstract
Assessing the relative importance of the various pathways to diversification is a central goal of biodiversity researchers. For plant biologists, and increasingly across the spectrum of biological sciences, among these pathways of interest is hybridization. New methodological developments are moving the field away from questions of whether natural hybridization occurs or hybrids can persist and toward more direct assessments of the long-term impact of hybridization on diversification and genome organization. Advances in theory and new data, especially phylogenomic data, have changed the face of this field, revealing extensive occurrences of hybridization at both shallow and deep levels, but lacking is a synthesis of these advancements. Here we provide an overview of methods that have been proposed for detecting hybridization with molecular data and advocate a time-extended, comparative view of reticulate evolution. In particular, we pose three overarching questions, newly placed within reach, that are critical for advancing our understanding of hybridization pattern and process: (1) How often is introgression biased toward certain genomes and loci, and is this bias selectively neutral? (2) What are the relative rates of formation of hybrid species and introgressants, and how does this compare to their subsequent fates? (3) Has the frequency of hybridization increased under historical periods of greater dynamism in climate and geographic range, such as the Pleistocene?
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Affiliation(s)
- Ryan A Folk
- Florida Museum of Natural History, 1659 Museum Road, Gainesville, Florida, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, 1659 Museum Road, Gainesville, Florida, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, Florida, 32611, USA
| | - Robert Guralnick
- Florida Museum of Natural History, 1659 Museum Road, Gainesville, Florida, 32611, USA
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29
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Folk RA, Mandel JR, Freudenstein JV. Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms. Syst Biol 2018; 66:320-337. [PMID: 27637567 DOI: 10.1093/sysbio/syw083] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/04/2016] [Indexed: 11/12/2022] Open
Abstract
While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord. [Ancient hybridization; chloroplast capture; incongruence; phylogenomics; reticulation.].
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Affiliation(s)
- Ryan A Folk
- Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA and
| | - Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - John V Freudenstein
- Herbarium, Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43212, USA and
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Rousseau H, Rousseau-Gueutin M, Dauvergne X, Boutte J, Simon G, Marnet N, Bouchereau A, Guiheneuf S, Bazureau JP, Morice J, Ravanel S, Cabello-Hurtado F, Ainouche A, Salmon A, Wendel JF, Ainouche ML. Evolution of DMSP (dimethylsulfoniopropionate) biosynthesis pathway: Origin and phylogenetic distribution in polyploid Spartina (Poaceae, Chloridoideae). Mol Phylogenet Evol 2017; 114:401-414. [PMID: 28694102 DOI: 10.1016/j.ympev.2017.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022]
Abstract
DMSP (dimethylsulfoniopropionate) is an ecologically important sulfur metabolite commonly produced by marine algae and by some higher plant lineages, including the polyploid salt marsh genus Spartina (Poaceae). The molecular mechanisms and genes involved in the DMSP biosynthesis pathways are still unknown. In this study, we performed comparative analyses of DMSP amounts and molecular phylogenetic analyses to decipher the origin of DMSP in Spartina that represents one of the major source of terrestrial DMSP in coastal marshes. DMSP content was explored in 14 Spartina species using 1H Nuclear Magnetic Resonance (NMR) spectroscopy and Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS). Putative genes encoding the four enzymatic steps of the DMSP biosynthesis pathway in Spartina were examined and their evolutionary dynamics were studied. We found that the hexaploid lineage containing S. alterniflora, S. foliosa and S. maritima and their derived hybrids and allopolyploids are all able to produce DMSP, in contrast to species in the tetraploid clade. Thus, examination of DMSP synthesis in a phylogenetic context implicated a single origin of this physiological innovation, which occurred in the ancestor of the hexaploid Spartina lineage, 3-6MYA. Candidate genes specific to the Spartina DMSP biosynthesis pathway were also retrieved from Spartina transcriptomes, and provide a framework for future investigations to decipher the molecular mechanisms involved in this plant phenotypic novelty that has major ecological impacts in saltmarsh ecosystems.
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Affiliation(s)
- Hélène Rousseau
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Mathieu Rousseau-Gueutin
- UMR IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, F-35653 Le Rheu Cedex, France
| | - Xavier Dauvergne
- EA 2219 Géoarchitecture, Université de Bretagne Occidentale, 6 av. le Gorgeu - CS93837, 29238 Brest Cedex 3, France
| | - Julien Boutte
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Gaëlle Simon
- Plateforme technologique de Résonance Magnétique Nucléaire, Résonance Paramagnétique Electronique et Spectrométrie de Masse, 6, av. Victor Le Gorgeu, CS93837, 29238 Brest Cedex 3, France
| | - Nathalie Marnet
- Plateau de Profilage Métabolique et Métabolomique (P2M2), Centre de Recherche Angers Nantes BIA, INRA de Rennes, F-35653 Le Rheu, France
| | - Alain Bouchereau
- UMR IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, F-35653 Le Rheu Cedex, France
| | - Solène Guiheneuf
- UMR CNRS 6226, Groupe Ingénierie Chimique & Molécules pour le Vivant (ICMV), Sciences Chimiques de Rennes, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jean-Pierre Bazureau
- UMR CNRS 6226, Groupe Ingénierie Chimique & Molécules pour le Vivant (ICMV), Sciences Chimiques de Rennes, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jérôme Morice
- UMR IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, F-35653 Le Rheu Cedex, France
| | - Stéphane Ravanel
- Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168 CNRS-CEA-UMR 1417 INRA-Université Grenoble Alpes, Grenoble, France
| | | | - Abdelkader Ainouche
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Armel Salmon
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Malika L Ainouche
- UMR CNRS 6553 Ecobio, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes Cedex, France.
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Koop-Jakobsen K, Fischer J, Wenzhöfer F. Survey of sediment oxygenation in rhizospheres of the saltmarsh grass - Spartina anglica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 589:191-199. [PMID: 28262356 DOI: 10.1016/j.scitotenv.2017.02.147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 02/17/2017] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
Although transport of oxygen via the aerenchyma tissue and subsequent oxygen loss across root surfaces is well-documented for salt marsh grasses, only few studies have measured the oxygenation of sediment surrounding roots and rhizomes. In this study, sediment oxygenation was assessed in situ in rhizospheres of the intertidal salt marsh grass, Spartina anglica - an invading species, vigorously spreading in many wetlands around the world. The rhizospheres of two populations of S. anglica with differing plant morphology growing in different sediment types were investigated in situ using a novel multifiber optode system with 100 oxygen probes. No oxygen was detected inside the rhizospheres at any depth in either location, indicating a limited impact of plant-mediated sediment oxygenation on the bulk anoxic sediment. Subsequent planar optode studies imaging the oxygen content around the roots substantiated these findings showing that sediment oxygenation was present in both locations, but it was confined only to the immediate vicinity of the root tips. The size of the oxic zones surrounding the root tips differed between sediment-types: in S. anglica growing in permeable sandy sediment, oxic root zones extended 1.5mm away from the roots surface compared to only 0.4mm in muddy tidal flat deposit, which had a substantially higher oxygen demand. The oxygen concentration inside the oxic root zones remained stable during continuous light and air-exposure of the aboveground biomass. In comparison, sediment oxygenation generated by burrowing infauna (Hediste diversicolor) showed to be markedly more temporally variability, reaching anoxic conditions multiple times during a 5-h period.
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Affiliation(s)
- Ketil Koop-Jakobsen
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Leobener Str., D-28359 Bremen, Germany; HGF MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.
| | - Jan Fischer
- HGF MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Frank Wenzhöfer
- HGF MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany; HGF MPG Joint Research Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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Migdałek G, Nowak J, Saługa M, Cieślak E, Szczepaniak M, Ronikier M, Marcussen T, Słomka A, Kuta E. No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola, Violaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:542-551. [PMID: 28402054 DOI: 10.1111/plb.12571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations. For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH-psbA. Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species-specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among-population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana. The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana.
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Affiliation(s)
- G Migdałek
- Department of Plant Physiology, Pedagogical University of Cracow, Cracow, Poland
| | - J Nowak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - M Saługa
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - E Cieślak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - M Szczepaniak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - M Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - T Marcussen
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - A Słomka
- Department of Plant Cytology and Embryology, Jagiellonian University, Cracow, Poland
| | - E Kuta
- Department of Plant Cytology and Embryology, Jagiellonian University, Cracow, Poland
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Blaine Marchant D, Soltis DE, Soltis PS. Patterns of abiotic niche shifts in allopolyploids relative to their progenitors. THE NEW PHYTOLOGIST 2016; 212:708-718. [PMID: 27399976 DOI: 10.1111/nph.14069] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/23/2016] [Indexed: 05/05/2023]
Abstract
Polyploidy has extensive genetic, physiological, morphological, and ecological ramifications. While the patterns underlying the genetic and morphological consequences of polyploidy are being rapidly elucidated, the effects on ecological niche are still largely unknown. This study investigated 13 allopolyploid systems in North America (10 ferns and three angiosperms) using digitized natural history museum specimens. The abiotic niches of the allopolyploids were compared with those of their diploid progenitors using ecological niche modeling, niche analyses, and multivariate analyses. We identified four patterns of niche shifts through our analyses: niche expansion, niche contraction, niche intermediacy, and niche novelty. The classification of these shifts depended on the amount of niche overlap and breadth between the polyploid and progenitors. The most common niche shift was niche intermediacy in which the polyploid inhabited a geographic range between that of the progenitors and had a high degree of niche overlap. Each polyploid had at least partial geographic sympatry and abiotic niche overlap with one of its progenitors, suggesting that biotic and/or microclimate factors may play a larger role in polyploid establishment than previously hypothesized. This study provides a baseline for future comparisons of the diverse outcomes of genome merger and duplication on abiotic niche preference.
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Affiliation(s)
- D Blaine Marchant
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Florida Museum of Natural History, Gainesville, FL, 32611, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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Boutte J, Ferreira de Carvalho J, Rousseau-Gueutin M, Poulain J, Da Silva C, Wincker P, Ainouche M, Salmon A. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). Genome Biol Evol 2016; 8:3030-3044. [PMID: 27614235 PMCID: PMC5633685 DOI: 10.1093/gbe/evw209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2016] [Indexed: 01/19/2023] Open
Abstract
In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.
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Affiliation(s)
- Julien Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Julie Ferreira de Carvalho
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Mathieu Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France UMR Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique, Le Rheu Cedex, France
| | | | | | | | - Malika Ainouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Armel Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
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Phenotypic plasticity and population differentiation in response to salinity in the invasive cordgrass Spartina densiflora. Biol Invasions 2016. [DOI: 10.1007/s10530-015-1041-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Huska D, Leitch IJ, de Carvalho JF, Leitch AR, Salmon A, Ainouche M, Kovarik A. Persistence, dispersal and genetic evolution of recently formed Spartina homoploid hybrids and allopolyploids in Southern England. Biol Invasions 2016. [DOI: 10.1007/s10530-015-0956-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Soltis DE, Visger CJ, Marchant DB, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. AMERICAN JOURNAL OF BOTANY 2016; 103:1146-66. [PMID: 27234228 DOI: 10.3732/ajb.1500501] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/25/2016] [Indexed: 05/22/2023]
Abstract
Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.
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Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - D Blaine Marchant
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 USA
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Zozomová-Lihová J, Mandáková T, Kovaříková A, Mühlhausen A, Mummenhoff K, Lysak MA, Kovařík A. When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine × schulzii trigenomic allopolyploid. THE NEW PHYTOLOGIST 2014; 203:1096-1108. [PMID: 24916080 DOI: 10.1111/nph.12873] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/29/2014] [Indexed: 05/20/2023]
Abstract
Recently formed allopolyploids represent an excellent system to study the impacts of hybridization and genomic duplication on genome structure and evolution. Here we explored the 35SrRNA genes (rDNA) in the Cardamine × schulzii allohexaploid that was formed by two subsequent hybridization events within the past c. 150 yr. The rDNA loci were analyzed by cloning, next generation sequencing (NGS), RT-PCR and FISH methods. The primary C. × insueta triploid hybrid derived from C. rivularis (♀) and C. amara (♂) had gene ratios highly skewed towards maternal sequences. Similarly, C. × schulzii, originating from the secondary hybridization event involving C. × insueta (♀) and C. pratensis (♂), showed a reduction in paternal rDNA homeologs despite an excess of chromosomes inherited from C. pratensis. We also identified novel rDNA loci in C. × schulzii, suggesting that lost loci might be slowly reinstalled by translocation (but not recombination) of genes from partner genomes. Prevalent clonal propagation of allopolyploids, C. × insueta and C. × schulzii, indicates that concerted evolution of rDNA may occur in the absence of extensive meiotic cycles. Adoption of NGS in rDNA variant analysis is highly informative for deciphering the evolutionary histories of allopolyploid species with ongoing homogenization processes.
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Affiliation(s)
| | - Terezie Mandáková
- RG Plant Cytogenomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Alena Kovaříková
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | | | - Klaus Mummenhoff
- Department of Biology, University Osnabrueck, Osnabrueck, Germany
| | - Martin A Lysak
- RG Plant Cytogenomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Ramsey J, Ramsey TS. Ecological studies of polyploidy in the 100 years following its discovery. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130352. [PMID: 24958925 PMCID: PMC4071525 DOI: 10.1098/rstb.2013.0352] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Polyploidy is a mutation with profound phenotypic consequences and thus hypothesized to have transformative effects in plant ecology. This is most often considered in the context of geographical and environmental distributions-as achieved from divergence of physiological and life-history traits-but may also include species interactions and biological invasion. This paper presents a historical overview of hypotheses and empirical data regarding the ecology of polyploids. Early researchers of polyploidy (1910 s-1930 s) were geneticists by training but nonetheless savvy to its phenotypic effects, and speculated on the importance of genome duplication to adaptation and crop improvement. Cytogenetic studies in the 1930 s-1950 s indicated that polyploids are larger (sturdier foliage, thicker stems and taller stature) than diploids while cytogeographic surveys suggested that polyploids and diploids have allopatric or parapatric distributions. Although autopolyploidy was initially regarded as common, influential writings by North American botanists in the 1940 s and 1950 s argued for the principle role of allopolyploidy; according to this view, genome duplication was significant for providing a broader canvas for hybridization rather than for its phenotypic effects per se. The emphasis on allopolyploidy had a chilling effect on nascent ecological work, in part due to taxonomic challenges posed by interspecific hybridization. Nonetheless, biosystematic efforts over the next few decades (1950s-1970s) laid the foundation for ecological research by documenting cytotype distributions and identifying phenotypic correlates of polyploidy. Rigorous investigation of polyploid ecology was achieved in the 1980s and 1990 s by population biologists who leveraged flow cytometry for comparative work in autopolyploid complexes. These efforts revealed multi-faceted ecological and phenotypic differences, some of which may be direct consequences of genome duplication. Several classical hypotheses about the ecology of polyploids remain untested, however, and allopolyploidy--regarded by most botanists as the primary mode of genome duplication--is largely unstudied in an ecological context.
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Affiliation(s)
- Justin Ramsey
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Tara S Ramsey
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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Winterfeld G, Schneider J, Perner K, Röser M. Polyploidy and hybridization as main factors of speciation: complex reticulate evolution within the grass genus Helictochloa. Cytogenet Genome Res 2014; 142:204-25. [PMID: 24731950 DOI: 10.1159/000361002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2013] [Indexed: 11/19/2022] Open
Abstract
To study the origin and evolution of naturally occurring polyploids, we performed phylogenetic analyses of nuclear ribosomal DNA spacers combined with molecular cytogenetics in 55 accessions of 27 taxa of the oat genus Helictochloa. A complex pattern of reticulate evolution was revealed with many diploid species and extensive polyploidy up to 20x. Altogether 11 groups of internal transcribed spacer (ITS) sequences can be distinguished. Sequences from 1-3 different ITS lineages were detected in polyploids. Cytogenetic data allow reconstruction of 8 basic monoploid chromosome sets. Six of these genomes occur in different combinations in the polyploid species. Two genomes are only found in diploids. Our sequence and karyological data highlight the occurrence of autopolyploidy and allopolyploidy, provide new information about the evolutionary history of taxa, and allow a more accurate systematic treatment of the concerned species. The geographical distribution of the 11 ITS lineages distinguished is highly structured and points to an origin of the genus in western Asia, presumably in grasslands like steppes or mountain steppes and meadows. The evolutionary basal lineages are of Asian, Minor Asian and east Mediterranean distribution and are present also in North America. The western and central parts of the Mediterranean and northern Europe harbor the modern lineages.
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Affiliation(s)
- G Winterfeld
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
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Zozomová-Lihová J, Krak K, Mandáková T, Shimizu KK, Španiel S, Vít P, Lysak MA. Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy. ANNALS OF BOTANY 2014; 113:817-30. [PMID: 24577071 PMCID: PMC3962249 DOI: 10.1093/aob/mcu012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Recently formed allopolyploid species represent excellent subjects for exploring early stages of polyploid evolution. The hexaploid Cardamine schulzii was regarded as one of the few nascent allopolyploid species formed within the past ∼150 years that presumably arose by autopolyploidization of a triploid hybrid, C. × insueta; however, the most recent investigations have shown that it is a trigenomic hybrid. The aims of this study were to explore the efficiency of progenitor-specific microsatellite markers in detecting the hybrid origins and genome composition of these two allopolyploids, to estimate the frequency of polyploid formation events, and to outline their evolutionary potential for long-term persistence and speciation. METHODS Flow-cytometric ploidy-level screening and genotyping by progenitor-specific microsatellite markers (20 microsatellite loci) were carried out on samples focused on hybridizing populations at Urnerboden, Switzerland, but also including comparative material of the parental species from other sites in the Alps and more distant areas. KEY RESULTS It was confirmed that hybridization between the diploids C. amara and C. rivularis auct. gave rise to triploid C. × insueta, and it is inferred that this has occurred repeatedly. Evidence is provided that C. schulzii comprises three parental genomes and supports its origin from hybridization events between C. × insueta and the locally co-occurring hypotetraploid C. pratensis, leading to two cytotypes of C. schulzii: hypopentaploid and hypohexaploid. Each cytotype of C. schulzii is genetically uniform, suggesting their single origins. CONCLUSIONS Persistence of C. schulzii has presumably been achieved only by perennial growth and clonal reproduction. This contrasts with C. × insueta, in which multiple origins and occasional sexual reproduction have generated sufficient genetic variation for long-term survival and evolutionary success. This study illustrates a complex case of recurrent hybridization and polyploidization events, and highlights the role of triploids that promoted the origin of trigenomic hybrids.
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Affiliation(s)
- Judita Zozomová-Lihová
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
- For correspondence. E-mail
| | - Karol Krak
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Switzerland
| | - Stanislav Španiel
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha, Czech Republic
| | - Petr Vít
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
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Near-absent levels of segregational variation suggest limited opportunities for the introduction of genetic variation via homeologous chromosome pairing in synthetic neoallotetraploid Mimulus. G3-GENES GENOMES GENETICS 2014; 4:509-22. [PMID: 24470218 PMCID: PMC3962489 DOI: 10.1534/g3.113.008441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genetic variation is the fundamental medium of evolution. In allopolyploids, which are the product of hybridization and whole genome duplication, if homologous chromosomes always pair, then all descendants of a single diploid F1 hybrid lineage will be genetically identical. Contrarily, genetic variation among initially isogenic lineages is augmented when homeologous chromosomes pair; this added variation may contribute to phenotypic evolution. Mimulus sookensis is a naturally occurring, small-flowered allotetraploid derived from the large-flowered Mimulus guttatus and small-flowered Mimulus nasutus. Because diploid F1 hybrids between M. guttatus and M. nasutus have large flowers, phenotypic evolution post-polyploidization is implied in M. sookensis. Here, we present genetic and phenotypic analyses of synthetic neoallotetraploid Mimulus derived from a cross between M. guttatus and M. nasutus. Genetic marker data from S2 and BC1N progeny suggest that chromosomes regularly pair with their homologous counterpart. By measuring the phenotype of synthetic neoallotetraploids, we demonstrate that polyploidization per se does not induce the small flowers of M. sookensis. Moreover, phenotypic measurements of synthetic allotetraploid F2s and S4 families suggest that rare homeologous recombination events have a negligible phenotypic effect in the first few generations. In total, the results are consistent with either exceedingly rare homeologous pairing and recombination or spontaneous fragment loss. The low levels of fragment loss and phenotypic variation in neoallotetraploids suggest that homeologous recombination after polyploidization is not a major mechanism of phenotypic evolution in M. sookensis. Rather, it may be that spontaneous mutations or epigenetic changes after allopolyploidization have driven phenotypic evolution in M. sookensis.
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Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol 2014; 6:559-71. [PMID: 24558256 PMCID: PMC3971588 DOI: 10.1093/gbe/evu037] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/25/2022] Open
Abstract
Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼ 2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Joseph P. Gallagher
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Emmanuel Szadkowski
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia
| | | | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
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Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B. Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Mol Biol Evol 2014; 31:1066-76. [PMID: 24577842 PMCID: PMC3995341 DOI: 10.1093/molbev/msu085] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed “transcriptomic shock.” To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis-factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of “whole genome doubling” has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.
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Affiliation(s)
- Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Mandáková T, Marhold K, Lysak MA. The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure. THE NEW PHYTOLOGIST 2014; 201:982-992. [PMID: 24400905 DOI: 10.1111/nph.12567] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 09/23/2013] [Indexed: 05/18/2023]
Abstract
The origin of Cardamine flexuosa (Wavy Bittercress) has been a conundrum for more than six decades. Here we identify its parental species, analyse its genome structure in comparison to parental genomes and describe intergenomic structural variations in C. flexuosa. Genomic in situ hybridization (GISH) and comparative chromosome painting (CCP) uncovered the parental genomes and the chromosome composition of C. flexuosa and its presumed diploid progenitors. Cardamine flexuosa is an allotetraploid (2n = 4x = 32), originating from two diploid species, Cardamine amara and Cardamine hirsuta (2n = 2x = 16). The two parental species display almost perfectly conserved chromosomal collinearity for seven out of the eight chromosomes. A 13 Mb pericentric inversion distinguishes chromosome CA1 from CH1. A comparative cytomolecular map was established for C. flexuosa by CCP/GISH. Whereas conserved chromosome collinearity between the C. amara and C. hirsuta subgenomes might have promoted intergenomic rearrangements through homeologous recombination, only one reciprocal translocation between two homeologues has occurred since the origin of C. flexuosa. The genome of C. flexuosa demonstrates that allopolyploids can maintain remarkably stable subgenomes over 10(4) -10(5) yr throughout a wide distribution range. By contrast, the rRNA genes underwent genome-specific elimination towards a diploid-like number of loci.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
| | - Karol Marhold
- Institute of Botany, Slovak Academy of Sciences, SK-84523, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic
| | - Martin A Lysak
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
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Eliášová A, Trávníček P, Mandák B, Münzbergová Z. Autotetraploids of Vicia cracca show a higher allelic richness in natural populations and a higher seed set after artificial selfing than diploids. ANNALS OF BOTANY 2014; 113:159-70. [PMID: 24232383 PMCID: PMC3864723 DOI: 10.1093/aob/mct252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 09/11/2013] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Despite the great importance of autopolyploidy in the evolution of angiosperms, relatively little attention has been devoted to autopolyploids in natural polyploid systems. Several hypotheses have been proposed to explain why autopolyploids are so common and successful, for example increased genetic diversity and heterozygosity and the transition towards selfing. However, case studies on patterns of genetic diversity and on mating systems in autopolyploids are scarce. In this study allozymes were employed to investigate the origin, population genetic diversity and mating system in the contact zone between diploid and assumed autotetraploid cytotypes of Vicia cracca in Central Europe. METHODS Four enzyme systems resolved in six putative loci were investigated in ten diploid, ten tetraploid and five mixed-ploidy populations. Genetic diversity and heterozygosity, partitioning of genetic diversity among populations and cytotypes, spatial genetic structure and fixed heterozygosity were analysed. These studies were supplemented by a pollination experiment and meiotic chromosome observation. KEY RESULTS AND CONCLUSIONS Weak evidence of fixed heterozygosity, a low proportion of unique alleles and genetic variation between cytotypes similar to the variation among populations within cytotypes supported the autopolyploid origin of tetraploids, although no multivalent formation was observed. Tetraploids possessed more alleles than diploids and showed higher observed zygotic heterozygosity than diploids, but the observed gametic heterozygosity was similar to the value observed in diploids and smaller than expected under panmixis. Values of the inbreeding coefficient and differentiation among populations (ρST) suggested that the breeding system in both cytotypes of V. cracca is mixed mating with prevailing outcrossing. The reduction in seed production of tetraploids after selfing was less than that in diploids. An absence of correlation between genetic and geographic distances and high differentiation among neighbouring tetraploid populations supports the secondary contact hypothesis with tetraploids of several independent origins in Central Europe. Nevertheless, the possibility of a recent in situ origin of tetraploids through a triploid bridge in some regions is also discussed.
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Affiliation(s)
- Anežka Eliášová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic
| | - Pavel Trávníček
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Bohumil Mandák
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
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Ferreira de Carvalho J, Chelaifa H, Boutte J, Poulain J, Couloux A, Wincker P, Bellec A, Fourment J, Bergès H, Salmon A, Ainouche M. Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis. PLANT MOLECULAR BIOLOGY 2013; 83:591-606. [PMID: 23877482 DOI: 10.1007/s11103-013-0111-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/13/2013] [Indexed: 06/02/2023]
Abstract
Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91% of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67%). Non-LTR retrotransposons represent 0.75%, DNA transposons 0.99%, whereas small RNA, simple repeats and low-complexity sequences account for 1.38% of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1% of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6% of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family.
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Affiliation(s)
- J Ferreira de Carvalho
- UMR CNRS 6553 ECOBIO, OSUR, University of Rennes 1, Bât 14A Campus Scientifique de Beaulieu, 35042, Rennes Cedex, France
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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Phylogeny of a genomically diverse group of elymus (poaceae) allopolyploids reveals multiple levels of reticulation. PLoS One 2013; 8:e78449. [PMID: 24302986 PMCID: PMC3840256 DOI: 10.1371/journal.pone.0078449] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/11/2013] [Indexed: 11/19/2022] Open
Abstract
The grass tribe Triticeae (=Hordeeae) comprises only about 300 species, but it is well known for the economically important crop plants wheat, barley, and rye. The group is also recognized as a fascinating example of evolutionary complexity, with a history shaped by numerous events of auto- and allopolyploidy and apparent introgression involving diploids and polyploids. The genus Elymus comprises a heterogeneous collection of allopolyploid genome combinations, all of which include at least one set of homoeologs, designated St, derived from Pseudoroegneria. The current analysis includes a geographically and genomically diverse collection of 21 tetraploid Elymus species, and a single hexaploid species. Diploid and polyploid relationships were estimated using four molecular data sets, including one that combines two regions of the chloroplast genome, and three from unlinked nuclear genes: phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I. Four gene trees were generated using maximum likelihood, and the phylogenetic placement of the polyploid sequences reveals extensive reticulation beyond allopolyploidy alone. The trees were interpreted with reference to numerous phenomena known to complicate allopolyploid phylogenies, and introgression was identified as a major factor in their history. The work illustrates the interpretation of complicated phylogenetic results through the sequential consideration of numerous possible explanations, and the results highlight the value of careful inspection of multiple independent molecular phylogenetic estimates, with particular focus on the differences among them.
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