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Shan S, Gitzendanner MA, Boatwright JL, Spoelhof JP, Ethridge CL, Ji L, Liu X, Soltis PS, Schmitz RJ, Soltis DE. Genome-wide DNA methylation dynamics following recent polyploidy in the allotetraploid Tragopogon miscellus (Asteraceae). THE NEW PHYTOLOGIST 2024; 242:1363-1376. [PMID: 38450804 DOI: 10.1111/nph.19655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/15/2024] [Indexed: 03/08/2024]
Abstract
Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome-wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids. The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95-100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole-genome bisulfite sequencing. Genome-wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized. This study provides the first assessment of both overall and locus-specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.
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Affiliation(s)
- Shengchen Shan
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - J Lucas Boatwright
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA
| | - Jonathan P Spoelhof
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Xiaoxian Liu
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Bioinformatics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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All Ways Lead to Rome—Meiotic Stabilization Can Take Many Routes in Nascent Polyploid Plants. Genes (Basel) 2022; 13:genes13010147. [PMID: 35052487 PMCID: PMC8775444 DOI: 10.3390/genes13010147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/01/2023] Open
Abstract
Newly formed polyploids often show extensive meiotic defects, resulting in aneuploid gametes, and thus reduced fertility. However, while many neopolyploids are meiotically unstable, polyploid lineages that survive in nature are generally stable and fertile; thus, those lineages that survive are those that are able to overcome these challenges. Several genes that promote polyploid stabilization are now known in plants, allowing speculation on the evolutionary origin of these meiotic adjustments. Here, I discuss results that show that meiotic stability can be achieved through the differentiation of certain alleles of certain genes between ploidies. These alleles, at least sometimes, seem to arise by novel mutation, while standing variation in either ancestral diploids or related polyploids, from which alleles can introgress, may also contribute. Growing evidence also suggests that the coevolution of multiple interacting genes has contributed to polyploid stabilization, and in allopolyploids, the return of duplicated genes to single copies (genome fractionation) may also play a role in meiotic stabilization. There is also some evidence that epigenetic regulation may be important, which can help explain why some polyploid lineages can partly stabilize quite rapidly.
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3
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Reis AC, Chester M, de Sousa SM, Campos VR, de Queiroz Nascimento LS, Pacheco Júnior S, Franco AL, Viccini LF. Chromosomal view of Lippia alba, a tropical polyploid complex under genome stabilization process. PROTOPLASMA 2022; 259:33-46. [PMID: 33760982 DOI: 10.1007/s00709-021-01636-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Lippia alba is a phenotypically variable tropical shrub thought to comprise a young autopolyploid complex. Chromosome numbers in L. alba include 2n = 30, 38, 45, 60, and 90. High levels of chemical and phenotypic variation associated with economic and medicinal importance were reported. However, the genetic background including chromosome composition remains under-explored. Furthermore, the occurrence of at least four ploidal levels in L. alba and the lack of data for polyploid plants in tropical areas also merit further study of L. alba. Here we assessed the chromosome composition using two new satellite repeats (CL98 and CL66) applied as FISH probes to mitotic chromosomes, and we proposed to calculate the degree of homozygosis for CL66 satDNA (named as index h) and to associate it to meiotic instability. The CL98 mapping showed few variations in both number of signals and position. However, the levels of structural homozygosity for a satellite repeat CL66 were very variable. The numbers of CL66-bearing-chromosomes were under-represented in tetraploids relative to diploids implying that CL66 arrays have been lost in tetraploid lineages as a result of increased meiotic instability. High percentage of irregularities was observed in meiotic cells, especially in polyploids. L. alba complex comprised a mixture of homomorphic and heteromorphic chromosomes. Overall, the polyploid complex presents features typical of both young and older stable polyploids. It seems that L. alba genome is still in the process of stabilization.
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Affiliation(s)
- Aryane Campos Reis
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | - Saulo Marçal de Sousa
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Victória Rabelo Campos
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | | | - Ana Luiza Franco
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
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Morgan C, White MA, Franklin FCH, Zickler D, Kleckner N, Bomblies K. Evolution of crossover interference enables stable autopolyploidy by ensuring pairwise partner connections in Arabidopsis arenosa. Curr Biol 2021; 31:4713-4726.e4. [PMID: 34480856 PMCID: PMC8585506 DOI: 10.1016/j.cub.2021.08.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/23/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022]
Abstract
Polyploidy is a major driver of evolutionary change. Autopolyploids, which arise by within-species whole-genome duplication, carry multiple nearly identical copies of each chromosome. This presents an existential challenge to sexual reproduction. Meiotic chromosome segregation requires formation of DNA crossovers (COs) between two homologous chromosomes. How can this outcome be achieved when more than two essentially equivalent partners are available? We addressed this question by comparing diploid, neo-autotetraploid, and established autotetraploid Arabidopsis arenosa using new approaches for analysis of meiotic CO patterns in polyploids. We discover that crossover interference, the classical process responsible for patterning of COs in diploid meiosis, is defective in the neo-autotetraploid but robust in the established autotetraploid. The presented findings suggest that, initially, diploid-like interference fails to act effectively on multivalent pairing and accompanying pre-CO recombination interactions and that stable autopolyploid meiosis can emerge by evolution of a “supercharged” interference process, which can now act effectively on such configurations. Thus, the basic interference mechanism responsible for simplifying CO patterns along chromosomes in diploid meiosis has evolved the capability to also simplify CO patterns among chromosomes in autopolyploids, thereby promoting bivalent formation. We further show that evolution of stable autotetraploidy preadapts meiosis to higher ploidy, which in turn has interesting mechanistic and evolutionary implications. In a neo-autotetraploid, aberrant crossover interference confers aberrant meiosis In a stable autotetraploid, regular crossover interference confers regular meiosis Crossover and synaptic patterns point to evolution of “supercharged” interference Accordingly, evolution of stable autotetraploidy preadapts to higher ploidies
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Affiliation(s)
- Chris Morgan
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Martin A White
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | | | - Denise Zickler
- University Paris-Saclay, Commissariat à l'Energie Atomique at aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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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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6
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Walczyk AM, Hersch-Green EI. Impacts of soil nitrogen and phosphorus levels on cytotype performance of the circumboreal herb Chamerion angustifolium: implications for polyploid establishment. AMERICAN JOURNAL OF BOTANY 2019; 106:906-921. [PMID: 31283844 DOI: 10.1002/ajb2.1321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Although polyploidy commonly occurs in angiosperms, not all polyploidization events lead to successful lineages, and environmental conditions could influence cytotype dynamics and polyploid success. Low soil nitrogen and/or phosphorus concentrations often limit ecosystem primary productivity, and changes in these nutrients might differentially favor some cytotypes over others, thereby influencing polyploid establishment. METHODS We grew diploid, established tetraploid, and neotetraploid Chamerion angustifolium (fireweed) in a greenhouse under low and high soil nitrogen and phosphorus conditions and different competition treatments and measured plant performance (height, biomass, flower production, and root bud production) and insect damage responses. By comparing neotetraploids to established tetraploids, we were able to examine traits and responses that might directly arise from polyploidization before they are modified by natural selection and/or genetic drift. RESULTS We found that (1) neopolyploids were the least likely to survive and flower and experienced the most herbivore damage, regardless of nutrient conditions; (2) both neo- and established tetraploids had greater biomass and root bud production under nutrient-enriched conditions, whereas diploid biomass and root bud production was not significantly affected by nutrients; and (3) intra-cytotype competition more negatively affected diploids and established tetraploids than it did neotetraploids. CONCLUSIONS Following polyploidization, biomass and clonal growth might be more immediately affected by environmental nutrient availabilities than plant survival, flowering, and/or responses to herbivory, which could influence competitive dynamics. Specifically, polyploids might have competitive and colonizing advantages over diploids under nutrient-enriched conditions favoring their establishment, although establishment may also depend upon the density and occurrences of other related cytotypes in a population.
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Affiliation(s)
- Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA
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7
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Göbel U, Arce AL, He F, Rico A, Schmitz G, de Meaux J. Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids. Genome Biol Evol 2018; 10:1403-1415. [PMID: 29788048 PMCID: PMC6007786 DOI: 10.1093/gbe/evy095] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/23/2022] Open
Abstract
The merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. Although our study did not examine TE transposition activity in hybrids, the examination of the transcriptome shows that TE expression is globally robust to hybridization. The term “genomic shock” is perhaps not appropriate to describe transcriptional modification in a viable hybrid merging divergent genomes.
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Affiliation(s)
- Ulrike Göbel
- Botanical Institute, University of Cologne, Germany
| | - Agustin L Arce
- Laboratorio de Biología del ARN, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), 3000 Santa Fe, Argentina
| | - Fei He
- Botanical Institute, University of Cologne, Germany
| | - Alain Rico
- Thermo Fisher Scientific, Villebon-sur-Yvette, France
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Shan S, Mavrodiev EV, Li R, Zhang Z, Hauser BA, Soltis PS, Soltis DE, Yang B. Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy. Mol Ecol Resour 2018; 18:1427-1443. [PMID: 30086204 DOI: 10.1111/1755-0998.12935] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/23/2018] [Accepted: 07/28/2018] [Indexed: 01/21/2023]
Abstract
Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing site-specific mutations in Tragopogon protoplasts. Agrobacterium-mediated transformation with Cas9-sgRNA constructs targeting the phytoene desaturase gene (TraPDS) was implemented in this model polyploid system. Sequencing of PCR amplicons from the target regions indicated simultaneous mutations of two alleles and four alleles of TraPDS in albino shoots from Tragopogon porrifolius (2x) and Tragopogon mirus (4x), respectively. The average proportions of successfully transformed calli with the albino phenotype were 87% and 78% in the diploid and polyploid, respectively. This appears to be the first demonstration of CRISPR/Cas9-based genome editing in any naturally formed neopolyploid system. Although a more efficient tissue culture system should be developed in Tragopogon, application of a robust CRISPR/Cas9 system will permit unique studies of biased fractionation, the gene-balance hypothesis and cytonuclear interactions in polyploids. In addition, the CRISPR/Cas9 platform enables investigations of those genes involved in phenotypic changes in polyploids and will also facilitate novel functional biology studies in Asteraceae. Our workflow provides a guide for applying CRISPR/Cas9 to other nongenetic model plant systems.
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Affiliation(s)
- Shengchen Shan
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida.,Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa.,Florida Museum of Natural History, University of Florida, Gainesville, Florida
| | - Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, Florida
| | - Riqing Li
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa
| | - Zhengzhi Zhang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa
| | - Bernard A Hauser
- Department of Biology, University of Florida, Gainesville, Florida
| | - Pamela S Soltis
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida.,Florida Museum of Natural History, University of Florida, Gainesville, Florida.,Biodiversity Institute, University of Florida, Gainesville, Florida
| | - Douglas E Soltis
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida.,Florida Museum of Natural History, University of Florida, Gainesville, Florida.,Department of Biology, University of Florida, Gainesville, Florida.,Biodiversity Institute, University of Florida, Gainesville, Florida
| | - Bing Yang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa
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