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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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2
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Hajrudinović-Bogunić A, Frajman B, Schönswetter P, Siljak-Yakovlev S, Bogunić F. Apomictic Mountain Whitebeam (Sorbus austriaca, Rosaceae) Comprises Several Genetically and Morphologically Divergent Lineages. BIOLOGY 2023; 12:biology12030380. [PMID: 36979072 PMCID: PMC10045669 DOI: 10.3390/biology12030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
The interplay of polyploidisation, hybridization, and apomixis contributed to the exceptional diversity of Sorbus (Rosaceae), giving rise to a mosaic of genetic and morphological entities. The Sorbus austriaca species complex from the mountains of Central and South-eastern Europe represents an allopolyploid apomictic system of populations that originated following hybridisation between S. aria and S. aucuparia. However, the mode and frequency of such allopolyploidisations and the relationships among different, morphologically more or less similar populations that have often been described as different taxa remain largely unexplored. We used amplified fragment length polymorphism (AFLP) fingerprinting, plastid DNA sequencing, and analyses of nuclear microsatellites, along with multivariate morphometrics and ploidy data, to disentangle the relationships among populations within this intricate complex. Our results revealed a mosaic of genetic lineages—many of which have not been taxonomically recognised—that originated via multiple allopolyploidisations. The clonal structure within and among populations was then maintained via apomixis. Our results thus support previous findings that hybridisation, polyploidization, and apomixis are the main drivers of Sorbus diversification in Europe.
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Affiliation(s)
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria
- Correspondence: (B.F.); (F.B.)
| | - Peter Schönswetter
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Faruk Bogunić
- Faculty of Forestry, University of Sarajevo, Zagrebačka 20, 71000 Sarajevo, Bosnia and Herzegovina
- Correspondence: (B.F.); (F.B.)
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3
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Berbel-Filho WM, Pacheco G, Lira MG, Garcia de Leaniz C, Lima SMQ, Rodríguez-López CM, Zhou J, Consuegra S. Additive and non-additive epigenetic signatures of natural hybridisation between fish species with different mating systems. Epigenetics 2022; 17:2356-2365. [PMID: 36082413 PMCID: PMC9665120 DOI: 10.1080/15592294.2022.2123014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hybridization is a major source of evolutionary innovation. In plants, epigenetic mechanisms can help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the relationship between genetic background and methylation patterns in natural hybrids of two genetically divergent fish species with different mating systems, Kryptolebias hermaphroditus (self-fertilizing) and K. ocellatus (outcrossing). Co-existing parental species displayed highly distinct genetic (SNPs) and methylation patterns (37,000 differentially methylated cytosines). Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridization between genetically distant species. The large number of differentially methylated cytosines between hybrids and parental species (n = 5,800) suggests that hybridization may play a role in increasing genetic and epigenetic variation. Although most of the observed epigenetic variation was additive and had a strong genetic component, we also found a small percentage of non-additive, potentially stochastic, methylation differences that might act as an evolutionary bet-hedging strategy and increase fitness under environmental instability.
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Affiliation(s)
- Waldir M Berbel-Filho
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - George Pacheco
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Mateus G Lira
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Carlos Garcia de Leaniz
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Sergio M Q Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Carlos M Rodríguez-López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Jia Zhou
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sofia Consuegra
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
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4
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Sun D, Yu H, Li Q. Genome-Wide Differential DNA Methylomes Provide Insights into the Infertility of Triploid Oysters. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:18-31. [PMID: 35041105 DOI: 10.1007/s10126-021-10083-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
Chromosomal incompatibility and gene expression changes would affect the development of polyploid gonad and gamete formation. The role of epigenetics like DNA methylation in reproductive development is fully demonstrated in diploid animals. The lack of polyploid species and the infertility of polyploid animals, especially the odd ploidy, limit the study of epigenetic regulation mechanism of polyploid reproduction. Fertile and infertile individuals exist in triploid Pacific oyster Crassostrea gigas, which provide an interesting model for studies on the effect of epigenetic regulation on gonadal development. The whole genome single base resolution DNA methylomes in gonads of triploid females α (F-3nα), triploid females β (F-3nβ), triploid males α (M-3nα), triploid hermaphrodite predominantly males (HPM-3n), diploid females (F-2n), and diploid males (M-2n) were generated by using bisulfite-sequencing. The overall DNA methylation profiles in gene regions and transposable regions of fertile and infertile triploid oysters were consistent with those of diploid oysters. The DNA methylation level of CG context decreased in infertile triploid oysters, with more hypomethylated than hypermethylated regions, and the opposite is true in fertile triploid oysters. Genes harbored with differentially methylated regions (DMRs) in infertile triploids were mainly related to the metabolism pathways and the signal pathways. Correlation analysis indicated that the expression of gene transcriptions was generally positively associated with DNA methylation in gene body regions, and DMRs in infertile triploid oysters played significant roles in gonadal development as a possible critical epigenetic regulator of gonadal development gene transcriptional activity. These findings indicate a potential relationship between DNA methylation variability and gene expression plasticity in newly formed polyploidy. As far as we know, this is the first study revealing the epigenetic regulation of gonadal development in invertebrates based on fertile and infertile models, meanwhile providing a new mentality to explore the regulatory mechanisms of infertility in triploids.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China), Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China), Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China), Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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5
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Wong ELY, Hiscock SJ, Filatov DA. The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio. FRONTIERS IN PLANT SCIENCE 2022; 13:907363. [PMID: 35812981 PMCID: PMC9260247 DOI: 10.3389/fpls.2022.907363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/03/2022] [Indexed: 05/08/2023]
Abstract
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Edgar L. Y. Wong,
| | - Simon J. Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Botanic Garden and Arboretum, Oxford, United Kingdom
| | - Dmitry A. Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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7
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Janko K, Bartoš O, Kočí J, Roslein J, Drdová EJ, Kotusz J, Eisner J, Mokrejš M, Štefková-Kašparová E. Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. Mol Biol Evol 2021; 38:5255-5274. [PMID: 34410426 PMCID: PMC8662595 DOI: 10.1093/molbev/msab249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.
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Affiliation(s)
- Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Roslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Eisner
- Department of Mathematics, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Martin Mokrejš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- IT4Innovations, VŠB—Technical University of Ostrava, Ostrava-Poruba, Czech Republic
| | - Eva Štefková-Kašparová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Czech Republic
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8
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Syngelaki E, Paetzold C, Hörandl E. Gene Expression Profiles Suggest a Better Cold Acclimation of Polyploids in the Alpine Species Ranunculus kuepferi (Ranunculaceae). Genes (Basel) 2021; 12:1818. [PMID: 34828424 PMCID: PMC8625111 DOI: 10.3390/genes12111818] [Citation(s) in RCA: 6] [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] [Received: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022] Open
Abstract
Alpine habitats are shaped by harsh abiotic conditions and cold climates. Temperature stress can affect phenotypic plasticity, reproduction, and epigenetic profiles, which may affect acclimation and adaptation. Distribution patterns suggest that polyploidy seems to be advantageous under cold conditions. Nevertheless, whether temperature stress can induce gene expression changes in different cytotypes, and how the response is initialized through gene set pathways and epigenetic control remain vague for non-model plants. The perennial alpine plant Ranunculus kuepferi was used to investigate the effect of cold stress on gene expression profiles. Diploid and autotetraploid individuals were exposed to cold and warm conditions in climate growth chambers and analyzed via transcriptome sequencing and qRT-PCR. Overall, cold stress changed gene expression profiles of both cytotypes and induced cold acclimation. Diploids changed more gene set pathways than tetraploids, and suppressed pathways involved in ion/cation homeostasis. Tetraploids mostly activated gene set pathways related to cell wall and plasma membrane. An epigenetic background for gene regulation in response to temperature conditions is indicated. Results suggest that perennial alpine plants can respond to temperature extremes via altered gene expression. Tetraploids are better acclimated to cold conditions, enabling them to colonize colder climatic areas in the Alps.
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Affiliation(s)
- Eleni Syngelaki
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
| | - Claudia Paetzold
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany;
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
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9
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Qin J, Mo R, Li H, Ni Z, Sun Q, Liu Z. The Transcriptional and Splicing Changes Caused by Hybridization Can Be Globally Recovered by Genome Doubling during Allopolyploidization. Mol Biol Evol 2021; 38:2513-2519. [PMID: 33585937 PMCID: PMC8136492 DOI: 10.1093/molbev/msab045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Polyploidization is a major driving force in plant evolution. Allopolyploidization, involving hybridization and genome doubling, can cause extensive transcriptome reprogramming which confers allopolyploids higher evolutionary potential than their diploid progenitors. To date, little is known about the interplay between hybridization and genome doubling in transcriptome reprogramming. Here, we performed genome-wide analyses of transcriptome reprogramming during allopolyploidization in wheat and brassica lineages. Our results indicated that hybridization-induced transcriptional and splicing changes of genes can be largely recovered to parental levels by genome doubling in allopolyploids. As transcriptome reprogramming is an important contributor to heterosis, our finding updates a longstanding theory that heterosis in interspecific hybrids can be permanently fixed through genome doubling. Our results also indicated that much of the transcriptome reprogramming in interspecific hybrids was not caused by the merging of two parental genomes, providing novel insights into the mechanisms underlying both heterosis and hybrid speciation.
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Affiliation(s)
- Jinxia Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruirui Mo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongxia Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhenshan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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10
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Qiu T, Liu Z, Liu B. The effects of hybridization and genome doubling in plant evolution via allopolyploidy. Mol Biol Rep 2020; 47:5549-5558. [PMID: 32572735 DOI: 10.1007/s11033-020-05597-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022]
Abstract
Polyploidy is a pervasive and recurring phenomenon across the tree of life, which occurred at variable time scales, ecological amplitudes and cell types, and is especially prominent in the evolutionary histories of plants. Importantly, many of the world's most important crops and noxious invasive weeds are recent polyploids. Polyploidy includes two major types, autopolyploidy, referring to doubling of a single species genome, and allopolyploidy referring to doubling of two or more merged genomes via biological hybridization of distinct but related species. The prevalence of both types of polyploidy implies that both genome doubling alone and doubling coupled with hybridization confer selective advantages over their diploid progenitors under specific circumstances. In cases of allopolyploidy, the two events, genome doubling and hybridization, have both advantages and disadvantages. Accumulated studies have established that, in allopolyploidy, some advantage(s) of doubling may compensate for the disadvantage(s) of hybridity and vice versa, although further study is required to validate generality of this trend. Some studies have also revealed a variety of non-Mendelian genetic and genomic consequences induced by doubling and hybridization separately or concertedly in nascent allopolyploidy; however, the significance of which to the immediate establishment and longer-term evolutionary success of allopolyploid species remain to be empirically demonstrated and ecologically investigated. This review aims to summarize recent advances in our understanding of the roles of hybridization and genome doubling, in separation and combination, in the evolution of allopolyploid genomes, as well as fruitful future research directions that are emerging from these studies.
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Affiliation(s)
- Tian Qiu
- School of Life Sciences, Changchun Normal University, Changchun, 130032, China.,Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Zhiyuan Liu
- College of Computer Science and Technology, Changchun University, Changchun, 130022, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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11
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Qin Q, Wang C, Zhou Y, Qin H, Zhao C, Yang L, Yu T, Liu S. Rapid Genomic and Epigenetic Alterations in Gynogenetic Carassius auratus Red Var. Derived from Distant Hybridization. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:433-442. [PMID: 32249338 DOI: 10.1007/s10126-020-09963-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
Gynogenesis is an important reproductive mode in fish and is used fairly widely in genetic breeding. Gynogenetic offspring (2n = 100, abbreviated as GRCC) were generated through the distant hybridization of Carassius auratus red var. (2n = 100, RCC) (♀) × Megalobrama amblycephala (2n = 48, BSB) (♂), in which male and female individual both had normal gonadal development. To better understand genomic and epigenetic consequences of GRCC, fluorescence in situ hybridization, amplified fragment length polymorphism, and methylation-sensitive amplification polymorphism analysis were performed on GRCC and RCC. GRCC possess two sets of RCC-derived chromosomes and one to three microchromosomes, in which 30.44% of bands inherit these patterns from red crucian carp and blunt snout bream, and 24.12% of novel bands were found by amplified fragment length polymorphism analysis. In terms of methylation, the DNA methylation level of GRCC was lower than that of their parents, and 45.29% of methylation patterns in GRCC were altered compared with their parents. GRCC show a special genetic composition in the genome, in which genome-wide changes and the adjustment of DNA methylation levels and patterns occurred. The result revealed that genetic and epigenetic changes were rapidly triggered in gynogenetic fish that were derived from distant hybridization, showing a special genetic composition in the genome. This study provides new insights into fish genetic breeding and the evolutionary patterns of the vertebrate genome.
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Affiliation(s)
- Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yuwei Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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12
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Syngelaki E, Schinkel CCF, Klatt S, Hörandl E. Effects of Temperature Treatments on Cytosine-Methylation Profiles of Diploid and Autotetraploid Plants of the Alpine Species Ranunculus kuepferi (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:435. [PMID: 32322263 PMCID: PMC7158262 DOI: 10.3389/fpls.2020.00435] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/25/2020] [Indexed: 05/23/2023]
Abstract
The exposure to environmental stress can trigger epigenetic variation, which may have several evolutionary consequences. Polyploidy seems to affect the DNA methylation profiles. Nevertheless, it abides unclear whether temperature stress can induce methylations changes in different cytotypes and to what extent a treatment shift is translated to an epigenetic response. A suitable model system for studying these questions is Ranunculus kuepferi, an alpine perennial herb. Diploid and autotetraploid individuals of R. kuepferi were exposed to cold (+7°C day/+2°C night; frost treatment -1°C cold shocks for 3 nights per week) and warm (+15° day/+10°C night) conditions in climate growth chambers for two consecutive flowering periods and shifted from one condition to the other after the first flowering period. Methylation-sensitive amplified fragment-length polymorphism markers were applied for both years, to track down possible alterations induced by the stress treatments. Patterns of methylation suggested that cytotypes differed significantly in their profiles, independent from year of treatment. Likewise, the treatment shift had an impact on both cytotypes, resulting in significantly less epiloci, regardless the shift's direction. The AMOVAs revealed higher variation within than among treatments in diploids. In tetraploids, internally-methylated loci had a higher variation among than within treatments, as a response to temperature's change in both directions, and support the hypothesis of temperature stress affecting the epigenetic variation. Results suggest that the temperature-sensitivity of DNA methylation patterns shows a highly dynamic phenotypic plasticity in R. kuepferi, as both cytotypes responded to temperature shifts. Furthermore, ploidy level, even without effects of hybridization, has an important effect on epigenetic background variation, which may be correlated with the DNA methylation dynamics during cold acclimation.
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Affiliation(s)
- Eleni Syngelaki
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Christoph C. F. Schinkel
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Simone Klatt
- Section Safety and Environmental Protection, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
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13
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Meng WL, Zhao MJ, Yang XB, Zhang AX, Wang NN, Xu ZS, Ma J. Examination of Genomic and Transcriptomic Alterations in a Morphologically Stable Line, MU1, Generated by Intergeneric Pollination. Genes (Basel) 2020; 11:genes11020199. [PMID: 32075264 PMCID: PMC7073617 DOI: 10.3390/genes11020199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
Interspecific hybridization creates genetic variation useful for crop improvement. However, whether pollen from a different genus affects the genomic stability and/or transcriptome of the recipient species during intergeneric pollination has not been investigated. Here, we crossed japonica rice cv. Z12 with the maize accession B73 (pollen donor) and obtained a morphologically stable line, MU1, exhibiting moderate dwarfism, higher tiller number, and increased grain weight compared with Z12. To reveal the genetic basis of these morphological changes in MU1, we performed whole-genome resequencing of MU1 and Z12. Compared with Z12, MU1 showed 107,250 single nucleotide polymorphisms (SNPs) and 23,278 insertion/deletions (InDels). Additionally, 5'-upstream regulatory regions (5'UTRs) of 429 and 309 differentially expressed genes (DEGs) in MU1 contained SNPs and InDels, respectively, suggesting that a subset of these DEGs account for the variation in 5'UTRs. Transcriptome analysis revealed 2190 DEGs in MU1 compared with Z12. Genes up-regulated in MU1 were mainly involved in photosynthesis, generation of precursor metabolites, and energy and cellular biosynthetic processes; whereas those down-regulated in MU1 were involved in plant hormone signal transduction pathway and response to stimuli and stress processes. Quantitative PCR (qPCR) further identified the expression levels of the up- or down-regulated gene in plant hormone signal transduction pathway. The expression level changes of plant hormone signal transduction pathway may be significant for plant growth and development. These findings suggest that mutations caused by intergeneric pollination could be the important reason for changes of MU1 in agronomic traits.
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Affiliation(s)
- Wei-Long Meng
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Meng-Jie Zhao
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China;
| | - Xiang-Bo Yang
- College of Agronomy, Jilin Agricultural Science and Technology University, Jilin 132101, China;
| | - An-Xing Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Ning-Ning Wang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Zhao-Shi Xu
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China;
- Correspondence: (Z.-S.X.); (J.M.)
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
- Correspondence: (Z.-S.X.); (J.M.)
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14
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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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15
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Martinez Palacios P, Jacquemot MP, Tapie M, Rousselet A, Diop M, Remoué C, Falque M, Lloyd A, Jenczewski E, Lassalle G, Chévre AM, Lelandais C, Crespi M, Brabant P, Joets J, Alix K. Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids. Mol Biol Evol 2019; 36:709-726. [PMID: 30657939 PMCID: PMC6445299 DOI: 10.1093/molbev/msz007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target noncoding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation.
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Affiliation(s)
- Paulina Martinez Palacios
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Marie-Pierre Jacquemot
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.,Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Marion Tapie
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Agnès Rousselet
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mamoudou Diop
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Carine Remoué
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Matthieu Falque
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Andrew Lloyd
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Eric Jenczewski
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Gilles Lassalle
- IGEPP, INRA, Agrocampus Ouest, Univ. Rennes I, Le Rheu, France.,ESE, INRA, Agrocampus Ouest, Rennes, France
| | | | - Christine Lelandais
- IPS2, Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris Sud and Evry, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martin Crespi
- IPS2, Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris Sud and Evry, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Brabant
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Karine Alix
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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16
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Cara N, Ferrer MS, Masuelli RW, Camadro EL, Marfil CF. Epigenetic consequences of interploidal hybridisation in synthetic and natural interspecific potato hybrids. THE NEW PHYTOLOGIST 2019; 222:1981-1993. [PMID: 30681145 DOI: 10.1111/nph.15706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Interploidal hybridisation can generate changes in plant chromosome numbers, which might exert effects additional to the expected due to genome merger per se (that is genetic, epigenetic and phenotypic novelties). Wild potatoes are suitable to address this question in an evolutionary context. To this end, we performed genetic (AFLP and single sequence repeart (SSR)), epigenetic (MSAP), and cytological comparisons in: (1) natural populations of the diploid cytotype of the hybrid taxonomic species Solanum × rechei (2n = 2×, 3×) and its parental species, the triploid cytotype of Solanum microdontum (2n = 2×, 3×) and Solanum kurtzianum (2n = 2×); and (2) newly synthesised intraploidal (2× × 2×) and interploidal (3× × 2×) S. microdontum × S. kurtzianum hybrids. Aneuploidy was detected in S. × rechei and the synthetic interploidal progeny; this phenomenon might have originated the significantly higher number of methylation changes observed in the interploidal vs the intraploidal hybrids. The wide epigenetic variability induced by interploidal hybridisation is consistent with the novel epigenetic pattern established in S. × rechei compared to its parental species in nature. These results suggest that aneuploid potato lineages can persist throughout the short term, and possibly medium term, and that differences in parental ploidy resulting in aneuploidy are an additional source of epigenetic variation.
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Affiliation(s)
- Nicolás Cara
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - María Soledad Ferrer
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - Ricardo Williams Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - Elsa Lucila Camadro
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Carlos Federico Marfil
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
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17
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Shao GM, Li XY, Wang Y, Wang ZW, Li Z, Zhang XJ, Zhou L, Gui JF. Whole Genome Incorporation and Epigenetic Stability in a Newly Synthetic Allopolyploid of Gynogenetic Gibel Carp. Genome Biol Evol 2018; 10:2394-2407. [PMID: 30085110 PMCID: PMC6143163 DOI: 10.1093/gbe/evy165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/23/2022] Open
Abstract
Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid animals is scarce. In this study, the genome constitution and DNA methylation inheritance in a newly synthetic allopolyploid of gynogenetic gibel carp were analyzed. The incorporation of a whole genome of paternal common carp sperm in the allopolyploid was confirmed by genomic in situ hybridization, chromosome localization of 45S rDNAs, and sequence comparison. Pooled sample-based methylation sensitive amplified polymorphism (MSAP) revealed that an overwhelming majority (98.82%) of cytosine methylation patterns in the allopolyploid were inherited from its parents of hexaploid gibel carp clone D and common carp. Compared to its parents, 11 DNA fragments in the allopolyploid were proved to be caused by interindividual variation, recombination, deletion, and mutation through individual sample-based MSAP and sequencing. Contrast to the rapid and remarkable epigenetic changes in most of analyzed neopolyploids, no cytosine methylation variation was detected in the gynogenetic allopolyploid. Therefore, the newly synthetic allopolyploid of gynogenetic gibel carp combined genomes from its parents and maintained genetic and epigenetic stability after its formation and subsequently seven successive gynogenetic generations. Our current results provide a paradigm for recurrent polyploidy consequences in the gynogenetic allopolyploid animals.
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Affiliation(s)
- Guang-Ming Shao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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18
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Hao DC, Xiao PG. Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants. CHINESE HERBAL MEDICINES 2018. [DOI: 10.1016/j.chmed.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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19
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Wang T, Huang D, Chen B, Mao N, Qiao Y, Ji M. Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp. Genes Genomics 2018; 40:321-331. [DOI: 10.1007/s13258-018-0647-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/04/2018] [Indexed: 12/26/2022]
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20
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Qi X, Wang H, Song A, Jiang J, Chen S, Chen F. Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in the Chrysanthemum nankingense× Tanacetum vulgare hybrid and allopolyploid (Asteraceae). HORTICULTURE RESEARCH 2018; 5:5. [PMID: 29423235 PMCID: PMC5802763 DOI: 10.1038/s41438-017-0003-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/22/2017] [Accepted: 11/26/2017] [Indexed: 05/05/2023]
Abstract
Allopolyploid formation involves two major events: interspecific hybridization and polyploidization. A number of species in the Asteraceae family are polyploids because of frequent hybridization. The effects of hybridization on genomics and transcriptomics in Chrysanthemum nankingense×Tanacetum vulgare hybrids have been reported. In this study, we obtained allopolyploids by applying a colchicine treatment to a synthesized C. nankingense×T. vulgare hybrid. Sequence-related amplified polymorphism (SRAP), methylation-sensitive amplification polymorphism (MSAP), and high-throughput RNA sequencing (RNA-Seq) technologies were used to investigate the genomic, epigenetic, and transcriptomic alterations in both the hybrid and allopolyploids. The genomic alterations in the hybrid and allopolyploids mainly involved the loss of parental fragments and the gain of novel fragments. The DNA methylation level of the hybrid was reduced by hybridization but was restored somewhat after polyploidization. There were more significant differences in gene expression between the hybrid/allopolyploid and the paternal parent than between the hybrid/allopolyploid and the maternal parent. Most differentially expressed genes (DEGs) showed down-regulation in the hybrid/allopolyploid relative to the parents. Among the non-additive genes, transgressive patterns appeared to be dominant, especially repression patterns. Maternal expression dominance was observed specifically for down-regulated genes. Many methylase and methyltransferase genes showed differential expression between the hybrid and parents and between the allopolyploid and parents. Our data indicate that hybridization may be a major factor affecting genomic and transcriptomic changes in newly formed allopolyploids. The formation of allopolyploids may not simply be the sum of hybridization and polyploidization changes but also may be influenced by the interaction between these processes.
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Affiliation(s)
- Xiangyu Qi
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Haibin Wang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Aiping Song
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Jiafu Jiang
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Sumei Chen
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, College of Horticulture, Nanjing Agricultural University, Ministry of Agriculture, Nanjing, 210095 China
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21
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Anastasiadi D, Díaz N, Piferrer F. Small ocean temperature increases elicit stage-dependent changes in DNA methylation and gene expression in a fish, the European sea bass. Sci Rep 2017; 7:12401. [PMID: 28963513 PMCID: PMC5622125 DOI: 10.1038/s41598-017-10861-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/16/2017] [Indexed: 01/24/2023] Open
Abstract
In natural fish populations, temperature increases can result in shifts in important phenotypic traits. DNA methylation is an epigenetic mechanism mediating phenotypic changes. However, whether temperature increases of the magnitude predicted by the latest global warming models can affect DNA methylation is unknown. Here, we exposed European sea bass to moderate temperature increases in different periods within the first two months of age. We show that increases of even 2 °C in larvae significantly changed global DNA methylation and the expression of ecologically-relevant genes related to DNA methylation, stress response, muscle and organ formation, while 4 °C had no effect on juveniles. Furthermore, DNA methylation changes were more marked in larvae previously acclimated to a different temperature. The expression of most genes was also affected by temperature in the larvae but not in juveniles. In conclusion, this work constitutes the first study of DNA methylation in fish showing that temperature increases of the magnitude predicted by the latest global warming models result in stage-dependent alterations in global DNA methylation and gene expression levels. This study, therefore, provides insights on the possible consequences of climate change in fish mediated by genome-wide epigenetic modifications.
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Affiliation(s)
- Dafni Anastasiadi
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim, 37-49, 08003, Barcelona, Spain
| | - Noelia Díaz
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim, 37-49, 08003, Barcelona, Spain.,Max Planck Institute for Molecular Biomedicine, Regulatory Genomics Lab, Röntgenstraße 20, 48149, Münster, Germany
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim, 37-49, 08003, Barcelona, Spain.
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22
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Sun Y, Wu Y, Yang C, Sun S, Lin X, Liu L, Xu C, Wendel JF, Gong L, Liu B. Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice. Mol Ecol 2017; 26:5451-5466. [PMID: 28802080 DOI: 10.1111/mec.14297] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/04/2017] [Accepted: 07/24/2017] [Indexed: 02/03/2023]
Abstract
Allopolyploidization, that is, concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genomewide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock." However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain underinvestigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic and homoeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed generation (S5). We show that hybridization and whole genome duplication (WGD) have opposing effects on allelic and homoeologous expression in the F1 hybrids and tetraploids, respectively. Whereas hybridization exerts strong attenuating effects on allelic expression differences in diploid hybrids, WGD augments the intrinsic parental differences and generates extensive and variable homoeolog content which triggers diversification in expression patterning among the tetraploid plants. Coupled with the vast phenotypic diversity observed among the tetraploid individuals, our results provide experimental evidence in support of the notion that allopolyploidy catalyses rapid phenotypic diversification in higher plants. Our data further suggest that largely stochastic homoeolog content reshuffling rather than alteration in total expression level may be an important feature of evolution in young segmental allopolyploids, which underlies rapid expression diversity at the population level.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Shuai Sun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Jilin Academy of Agriculture, Changchun, China
| | - Lixia Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Uhrinová V, Zozomová-Lihová J, Bernátová D, Paule J, Paule L, Gömöry D. Origin and genetic differentiation of pink-flowered Sorbus hybrids in the Western Carpathians. ANNALS OF BOTANY 2017; 120:271-284. [PMID: 28334280 PMCID: PMC5737586 DOI: 10.1093/aob/mcx013] [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: 11/08/2016] [Accepted: 01/09/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Diversity of the genus Sorbus has been affected by interspecific hybridizations. Pink-flowered hybrid species have been insufficiently studied so far. They comprise bigenomic hybrid species derived from crosses S. aria s.l. × S. chamaemespilus and trigenomic ones, where S. aucuparia was involved as well. The main objective of the present study was to reconstruct their hybrid origins as well as to assess genetic distinction among several morphologically recognized hybrid species. METHODS Samples from putative maternal species and eight pink-flowered and two white-flowered hybrid species were collected in the Western Carpathians and the Sudetes. In total, 370 specimens were analysed. Six chloroplast microsatellites were used to infer parentage, whereas nuclear amplified fragment length polymorphism (AFLP) markers were employed for the identification of clones and patterns of genetic variation. Ploidy levels were estimated by flow cytometry on a subset of 140 individuals. KEY RESULTS Genetic data supported their hybrid origins proposed based on flower and leaf morphology, and chloroplast DNA (cpDNA) revealed recurrent origins ( S. caeruleomontana , S. haljamovae ), even from bidirectional hybridization events ( S. zuzanae ). All bigenomic and trigenomic hybrid species (except triploid S. zuzanae ) were found to be tetraploid. In addition to polyploidy, low genetic variation and the presence of clones within and among populations were observed, suggesting predominantly apomictic reproduction of the hybrid species. Most of the described hybrid species appeared also genetically distinct. CONCLUSIONS The data suggest that multiple hybridization events in the Western Carpathian Sorbus have led to the formation of separate, partially reproductively isolated genetic lineages, which may or may not be discriminated morphologically. Even bidirectional hybridization can produce individuals classified to the same taxon based on phenotype. For some hybrid taxa, hybridization pathways were proposed based on their genetic proximity to parental species and differences in genome sizes.
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Affiliation(s)
- Veronika Uhrinová
- Technical University in Zvolen, Faculty of Forestry, TG Masaryka 24, 96053 Zvolen, Slovakia
| | - Judita Zozomová-Lihová
- Slovak Academy of Sciences, Institute of Botany, Plant Science and Biodiversity Centre, Dúbravská cesta 9, 84523 Bratislava, Slovakia
| | - Dana Bernátová
- Comenius University, Botanical Garden, Detached Unit, 03815 Blatnica 315, Slovakia
| | - Juraj Paule
- Senckenberg Research Institute and Natural History Museum, Department of Botany and Molecular Evolution, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Ladislav Paule
- Technical University in Zvolen, Faculty of Forestry, TG Masaryka 24, 96053 Zvolen, Slovakia
| | - Dušan Gömöry
- Technical University in Zvolen, Faculty of Forestry, TG Masaryka 24, 96053 Zvolen, Slovakia
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Guevara MÁ, de María N, Sáez-Laguna E, Vélez MD, Cervera MT, Cabezas JA. Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP). Methods Mol Biol 2017; 1456:99-112. [PMID: 27770361 DOI: 10.1007/978-1-4899-7708-3_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.
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Affiliation(s)
- María Ángeles Guevara
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Nuria de María
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Enrique Sáez-Laguna
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Dolores Vélez
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Teresa Cervera
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
| | - José Antonio Cabezas
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
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Correlation analysis of the mRNA and miRNA expression profiles in the nascent synthetic allotetraploid Raphanobrassica. Sci Rep 2016; 6:37416. [PMID: 27874043 PMCID: PMC5118723 DOI: 10.1038/srep37416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/27/2016] [Indexed: 11/08/2022] Open
Abstract
Raphanobrassica is an allopolyploid species derived from inter-generic hybridization that combines the R genome from R. sativus and the C genome from B. oleracea var. alboglabra. In the present study, we used a high-throughput sequencing method to identify the mRNA and miRNA profiles in Raphanobrassica and its parents. A total of 33,561 mRNAs and 283 miRNAs were detected, 9,209 mRNAs and 134 miRNAs were differentially expressed respectively, 7,633 mRNAs and 39 miRNAs showed ELD expression, 5,219 mRNAs and 57 miRNAs were non-additively expressed in Raphanobrassica. Remarkably, differentially expressed genes (DEGs) were up-regulated and maternal bias was detected in Raphanobrassica. In addition, a miRNA-mRNA interaction network was constructed based on reverse regulated miRNA-mRNAs, which included 75 miRNAs and 178 mRNAs, 31 miRNAs were non-additively expressed target by 13 miRNAs. The related target genes were significantly enriched in the GO term 'metabolic processes'. Non-additive related target genes regulation is involved in a range of biological pathways, like providing a driving force for variation and adaption in this allopolyploid. The integrative analysis of mRNA and miRNA profiling provides more information to elucidate gene expression mechanism and may supply a comprehensive and corresponding method to study genetic and transcription variation of allopolyploid.
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26
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Alonso C, Balao F, Bazaga P, Pérez R. Epigenetic contribution to successful polyploidizations: variation in global cytosine methylation along an extensive ploidy series in Dianthus broteri (Caryophyllaceae). THE NEW PHYTOLOGIST 2016; 212:571-576. [PMID: 27483440 DOI: 10.1111/nph.14138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/11/2016] [Indexed: 05/27/2023]
Abstract
Polyploidization is a significant evolutionary force in plants which involves major genomic and genetic changes, frequently regulated by epigenetic factors. We explored whether natural polyploidization in Dianthus broteri complex resulted in substantial changes in global DNA cytosine methylation associated to ploidy. Global cytosine methylation was estimated by high-performance liquid chromatography (HPLC) in 12 monocytotypic populations with different ploidies (2×, 4×, 6×, 12×) broadly distributed within D. broteri distribution range. The effects of ploidy level and local variation on methylation were assessed by generalized linear mixed models (GLMMs). Dianthus broteri exhibited a higher methylation percent (˜33%) than expected by its monoploid genome size and a large variation among study populations (range: 29.3-35.3%). Global methylation tended to increase with ploidy but did not significantly differ across levels due to increased variation within the highest-order polyploidy categories. Methylation varied more among hexaploid and dodecaploid populations, despite such cytotypes showing more restricted geographic location and increased genetic relatedness than diploids and tetraploids. In this study, we demonstrate the usefulness of an HPLC method in providing precise and genome reference-free global measure of DNA cytosine methylation, suitable to advance current knowledge of the roles of this epigenetic mechanism in polyploidization processes.
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Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, 41092, Sevilla, Spain.
| | - Francisco Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Apdo. 1095, 41080, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, CSIC, Avenida Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Ricardo Pérez
- Centro de Investigaciones Científicas Isla de La Cartuja, Instituto de Investigaciones Químicas, CSIC-US, Avenida Américo Vespucio 49, 41092, Sevilla, Spain
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27
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Schinkel CCF, Kirchheimer B, Dellinger AS, Klatt S, Winkler M, Dullinger S, Hörandl E. Correlations of polyploidy and apomixis with elevation and associated environmental gradients in an alpine plant. AOB PLANTS 2016; 8:plw064. [PMID: 27594702 PMCID: PMC5091893 DOI: 10.1093/aobpla/plw064] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/29/2016] [Indexed: 05/20/2023]
Abstract
Apomictic plants expand their geographical distributions more to higher elevations compared to their sexual progenitors. It was so far unclear whether this tendency is related to mode of reproduction itself or represents a side effect of polyploidy. Apomixis is advantageous for range expansions as no mating partners and pollinators are needed (Baker's rule). Polyploidy is thought to infer fitness advantages and a higher vigour that would enable plants to adjust better to more extreme climatic conditions. However, little is known about actual performance of plants at higher elevations. We analyzed 81 populations of Ranunculus kuepferi from the whole distribution area in the European Alps to quantify apomictic versus sexual seed formation via flow cytometric seed screening. Seed set and vegetative growth were measured as fitness parameters. All parameters were correlated to geographical distribution, elevation, temperature and precipitation. Flow cytometric seed screening revealed predominantly obligate sexuality (88.9 %) and facultative apomixis in diploid populations, while tetraploid populations are predominantly facultative (65.4 %) to obligate apomictic. Apomictic seed formation correlated significantly to higher elevations, which explains also the observed niche shift to lower temperatures. However, within the tetraploid range, there is no apparent correlation of degree of facultative apomixis to geographical distance. Apomixis appeared in diploids three times independently in separated, otherwise sexual populations in the southwestern refugial areas of the Alps. Diploid apomixis was not successful in range expansions, and obligate sexual polyploids were not observed. Polyploidy may relate to cold tolerance as an adaptation to conditions at high elevations, where diploid sexuals have no fitness advantage. Instead, facultative apomixis may have aided colonization of higher elevations and range expansions in the Alps without mate and pollinator limitation, but did not necessarily involve long-distance dispersal. A direct influence of low temperatures on unreduced gamete formation cannot be ruled out.
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Affiliation(s)
- Christoph C F Schinkel
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), Georg-August-University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Bernhard Kirchheimer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Agnes S Dellinger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Simone Klatt
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), Georg-August-University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Manuela Winkler
- GLORIA co-ordination, University of Natural Resources and Life Sciences Vienna, Centre for Global Change and Sustainability, Vienna, Austria
| | - Stefan Dullinger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), Georg-August-University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
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Vallejo-Marín M, Hiscock SJ. Hybridization and hybrid speciation under global change. THE NEW PHYTOLOGIST 2016; 211:1170-87. [PMID: 27214560 DOI: 10.1111/nph.14004] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/07/2016] [Indexed: 05/24/2023]
Abstract
Contents 1170 I. 1170 II. 1172 III. 1175 IV. 1180 V. 1183 1184 References 1184 SUMMARY: An unintended consequence of global change is an increase in opportunities for hybridization among previously isolated lineages. Here we illustrate how global change can facilitate the breakdown of reproductive barriers and the formation of hybrids, drawing on the flora of the British Isles for insight. Although global change may ameliorate some of the barriers preventing hybrid establishment, for example by providing new ecological niches for hybrids, it will have limited effects on environment-independent post-zygotic barriers. For example, genic incompatibilities and differences in chromosome numbers and structure within hybrid genomes are unlikely to be affected by global change. We thus speculate that global change will have a larger effect on eroding pre-zygotic barriers (eco-geographical isolation and phenology) than post-zygotic barriers, shifting the relative importance of these two classes of reproductive barriers from what is usually seen in naturally produced hybrids where pre-zygotic barriers are the largest contributors to reproductive isolation. Although the long-term fate of neo-hybrids is still to be determined, the massive impact of global change on the dynamics and distribution of biodiversity generates an unprecedented opportunity to study large numbers of unpredicted, and often replicated, hybridization 'experiments', allowing us to peer into the birth and death of evolutionary lineages.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Simon J Hiscock
- University of Oxford Botanic Garden, Rose Lane, Oxford, OX1 4AZ, UK
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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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Sexual Polyploidization in Medicago sativa L.: Impact on the Phenotype, Gene Transcription, and Genome Methylation. G3-GENES GENOMES GENETICS 2016; 6:925-38. [PMID: 26858330 PMCID: PMC4825662 DOI: 10.1534/g3.115.026021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome, and on genome expression, has both basic and applied interest. We crossed two diploid (2n = 2x = 16) Medicago sativa plants, a subsp. falcata seed parent, and a coerulea × falcata pollen parent that form a mixture of n and 2n eggs and pollen, respectively. Such a cross produced full-sib diploid and tetraploid (2n = 4x = 32) hybrids, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and to separate the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. Simple sequence repeat marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, and larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x, but not in 4x, hybrids. Our results indicate that sexual polyploidization induces significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that could underpin improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture.
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Cheng S, Huang Z, Li Y, Liao T, Suo Y, Zhang P, Wang J, Kang X. Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:1031-1045. [PMID: 25557321 DOI: 10.1111/jipb.12328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution.
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Affiliation(s)
- Shiping Cheng
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Huang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ting Liao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yujing Suo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jun Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangyang Kang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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Covelo-Soto L, Leunda PM, Pérez-Figueroa A, Morán P. Genome-wide methylation study of diploid and triploid brown trout (Salmo trutta L.). Anim Genet 2015; 46:280-8. [PMID: 25917300 DOI: 10.1111/age.12287] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2015] [Indexed: 12/15/2022]
Abstract
The induction of triploidization in fish is a very common practice in aquaculture. Although triploidization has been applied successfully in many salmonid species, little is known about the epigenetic mechanisms implicated in the maintenance of the normal functions of the new polyploid genome. By means of methylation-sensitive amplified polymorphism (MSAP) techniques, genome-wide methylation changes associated with triploidization were assessed in DNA samples obtained from diploid and triploid siblings of brown trout (Salmo trutta). Simple comparative body measurements showed that the triploid trout used in the study were statistically bigger, however, not heavier than their diploid counterparts. The statistical analysis of the MSAP data showed no significant differences between diploid and triploid brown trout in respect to brain, gill, heart, liver, kidney or muscle samples. Nonetheless, local analysis pointed to the possibility of differences in connection with concrete loci. This is the first study that has investigated DNA methylation alterations associated with triploidization in brown trout. Our results set the basis for new studies to be undertaken and provide a new approach concerning triploidization effects of the salmonid genome while also contributing to the better understanding of the genome-wide methylation processes.
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Affiliation(s)
- L Covelo-Soto
- Dpto Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, Vigo, 36210, Spain
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Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza). PLoS One 2015. [PMID: 26208215 PMCID: PMC4514751 DOI: 10.1371/journal.pone.0132911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica) and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown. Methodology/Principal Findings We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH) and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs) and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i) all three triploid hybrids are stable in both chromosome number and gross structure; (ii) stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii) alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv) transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner. Conclusions/Significance Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might provide a rich resource of genetic and epigenetic diversities for potential utilization in rice genetic improvements.
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Inheritance and variation of Cytosine methylation in three populus allotriploid populations with different heterozygosity. PLoS One 2015; 10:e0126491. [PMID: 25901359 PMCID: PMC4406749 DOI: 10.1371/journal.pone.0126491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is an epigenetic mechanism with the potential to regulate gene expression and affect plant phenotypes. Both hybridization and genome doubling may affect the DNA methylation status of newly formed allopolyploid plants. Previous studies demonstrated that changes in cytosine methylation levels and patterns were different among individual hybrid plant, therefore, studies investigating the characteristics of variation in cytosine methylation status must be conducted at the population level to avoid sampling error. In the present study, an F1 hybrid diploid population and three allotriploid populations with different heterozygosity [originating from first-division restitution (FDR), second-division restitution (SDR), and post-meiotic restitution (PMR) 2n eggs of the same female parent] were used to investigate cytosine methylation inheritance and variation relative to their common parents using methylation-sensitive amplification polymorphism (MSAP). The variation in cytosine methylation in individuals in each population exhibited substantial differences, confirming the necessity of population epigenetics. The total methylation levels of the diploid population were significantly higher than in the parents, but those of the three allotriploid populations were significantly lower than in the parents, indicating that both hybridization and polyploidization contributed to cytosine methylation variation. The vast majority of methylated status could be inherited from the parents, and the average percentages of non-additive variation were 6.29, 3.27, 5.49 and 5.07% in the diploid, FDR, SDR and PMR progeny populations, respectively. This study lays a foundation for further research on population epigenetics in allopolyploids.
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Stapley J, Santure AW, Dennis SR. Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol Ecol 2015; 24:2241-52. [PMID: 25611725 DOI: 10.1111/mec.13089] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 12/11/2022]
Abstract
Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies.
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Affiliation(s)
- Jessica Stapley
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
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Bock DG, Caseys C, Cousens RD, Hahn MA, Heredia SM, Hübner S, Turner KG, Whitney KD, Rieseberg LH. What we still don't know about invasion genetics. Mol Ecol 2015; 24:2277-97. [PMID: 25474505 DOI: 10.1111/mec.13032] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/27/2014] [Accepted: 11/28/2014] [Indexed: 12/12/2022]
Abstract
Publication of The Genetics of Colonizing Species in 1965 launched the field of invasion genetics and highlighted the value of biological invasions as natural ecological and evolutionary experiments. Here, we review the past 50 years of invasion genetics to assess what we have learned and what we still don't know, focusing on the genetic changes associated with invasive lineages and the evolutionary processes driving these changes. We also suggest potential studies to address still-unanswered questions. We now know, for example, that rapid adaptation of invaders is common and generally not limited by genetic variation. On the other hand, and contrary to prevailing opinion 50 years ago, the balance of evidence indicates that population bottlenecks and genetic drift typically have negative effects on invasion success, despite their potential to increase additive genetic variation and the frequency of peak shifts. Numerous unknowns remain, such as the sources of genetic variation, the role of so-called expansion load and the relative importance of propagule pressure vs. genetic diversity for successful establishment. While many such unknowns can be resolved by genomic studies, other questions may require manipulative experiments in model organisms. Such studies complement classical reciprocal transplant and field-based selection experiments, which are needed to link trait variation with components of fitness and population growth rates. We conclude by discussing the potential for studies of invasion genetics to reveal the limits to evolution and to stimulate the development of practical strategies to either minimize or maximize evolutionary responses to environmental change.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Room 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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Bocchini M, Bartucca ML, Ciancaleoni S, Mimmo T, Cesco S, Pii Y, Albertini E, Del Buono D. Iron deficiency in barley plants: phytosiderophore release, iron translocation, and DNA methylation. FRONTIERS IN PLANT SCIENCE 2015; 6:514. [PMID: 26217365 PMCID: PMC4496560 DOI: 10.3389/fpls.2015.00514] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
All living organisms require iron (Fe) to carry out many crucial metabolic pathways. Despite its high concentrations in the geosphere, Fe bio-availability to plant roots can be very scarce. To cope with Fe shortage, plants can activate different strategies. For these reasons, we investigated Fe deficient Hordeum vulgare L. plants by monitoring growth, phytosiderophores (PS) release, iron content, and translocation, and DNA methylation, with respect to Fe sufficient ones. Reductions of plant growth, roots to shoots Fe translocation, and increases in PS release were found. Experiments on DNA methylation highlighted significant differences between fully and hemy-methylated sequences in Fe deficient plants, with respect to Fe sufficient plants. Eleven DNA bands differently methylated were found in starved plants. Of these, five sequences showed significant alignment to barley genes encoding for a glucosyltransferase, a putative acyl carrier protein, a peroxidase, a β-glucosidase and a transcription factor containing a Homeodomin. A resupply experiment was carried out on starved barley re-fed at 13 days after sowing (DAS), and it showed that plants did not recover after Fe addition. In fact, Fe absorption and root to shoot translocation capacities were impaired. In addition, resupplied barley showed DNA methylation/demethylation patterns very similar to that of barley grown in Fe deprivation. This last finding is very encouraging because it indicates as these variations/modifications could be transmitted to progenies.
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Affiliation(s)
- Marika Bocchini
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Maria Luce Bartucca
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Simona Ciancaleoni
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Youry Pii
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
- *Correspondence: Emidio Albertini, Department of Agriculture, Food and Environmental Sciences, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Daniele Del Buono
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
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Zhang D, Pan Q, Cui C, Tan C, Ge X, Shao Y, Li Z. Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq. FRONTIERS IN PLANT SCIENCE 2015; 6:957. [PMID: 26583027 PMCID: PMC4631939 DOI: 10.3389/fpls.2015.00957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/20/2015] [Indexed: 05/18/2023]
Abstract
Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC) were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids.
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Affiliation(s)
- Dawei Zhang
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Qi Pan
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural SciencesChengdu, China
| | - Chen Tan
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xianhong Ge
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yujiao Shao
- College of Chemistry and Life Science, Hubei University of EducationWuhan, China
- *Correspondence: Yujiao Shao
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
- Zaiyun Li
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Wang H, Jiang J, Chen S, Qi X, Fang W, Guan Z, Teng N, Liao Y, Chen F. Rapid genetic and epigenetic alterations under intergeneric genomic shock in newly synthesized Chrysanthemum morifolium x Leucanthemum paludosum hybrids (Asteraceae). Genome Biol Evol 2014; 6:247-59. [PMID: 24407856 PMCID: PMC3914698 DOI: 10.1093/gbe/evu008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Asteraceae family is at the forefront of the evolution due to frequent hybridization. Hybridization is associated with the induction of widespread genetic and epigenetic changes and has played an important role in the evolution of many plant taxa. We attempted the intergeneric cross Chrysanthemum morifolium × Leucanthemum paludosum. To obtain the success in cross, we have to turn to ovule rescue. DNA profiling of the amphihaploid and amphidiploid was investigated using amplified fragment length polymorphism, sequence-related amplified polymorphism, start codon targeted polymorphism, and methylation-sensitive amplification polymorphism (MSAP). Hybridization induced rapid changes at the genetic and the epigenetic levels. The genetic changes mainly involved loss of parental fragments and gaining of novel fragments, and some eliminated sequences possibly from the noncoding region of L. paludosum. The MSAP analysis indicated that the level of DNA methylation was lower in the amphiploid (∼45%) than in the parental lines (51.5-50.6%), whereas it increased after amphidiploid formation. Events associated with intergeneric genomic shock were a feature of C. morifolium × L. paludosum hybrid, given that the genetic relationship between the parental species is relatively distant. Our results provide genetic and epigenetic evidence for understanding genomic shock in wide crosses between species in Asteraceae and suggest a need to expand our current evolutionary framework to encompass a genetic/epigenetic dimension when seeking to understand wide crosses.
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Affiliation(s)
- Haibin Wang
- College of Horticulture, Nanjing Agricultural University, China
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Cox MP, Dong T, Shen G, Dalvi Y, Scott DB, Ganley ARD. An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns. PLoS Genet 2014; 10:e1004180. [PMID: 24603805 PMCID: PMC3945203 DOI: 10.1371/journal.pgen.1004180] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/02/2014] [Indexed: 12/13/2022] Open
Abstract
Polyploidy, a state in which the chromosome complement has undergone an increase, is a major force in evolution. Understanding the consequences of polyploidy has received much attention, and allopolyploids, which result from the union of two different parental genomes, are of particular interest because they must overcome a suite of biological responses to this merger, known as “genome shock.” A key question is what happens to gene expression of the two gene copies following allopolyploidization, but until recently the tools to answer this question on a genome-wide basis were lacking. Here we utilize high throughput transcriptome sequencing to produce the first genome-wide picture of gene expression response to allopolyploidy in fungi. A novel pipeline for assigning sequence reads to the gene copies was used to quantify their expression in a fungal allopolyploid. We find that the transcriptional response to allopolyploidy is predominantly conservative: both copies of most genes are retained; over half the genes inherit parental gene expression patterns; and parental differential expression is often lost in the allopolyploid. Strikingly, the patterns of gene expression change are highly concordant with the genome-wide expression results of a cotton allopolyploid. The very different nature of these two allopolyploids implies a conserved, eukaryote-wide transcriptional response to genome merger. We provide evidence that the transcriptional responses we observe are mostly driven by intrinsic differences between the regulatory systems in the parent species, and from this propose a mechanistic model in which the cross-kingdom conservation in transcriptional response reflects conservation of the mutational processes underlying eukaryotic gene regulatory evolution. This work provides a platform to develop a universal understanding of gene expression response to allopolyploidy and suggests that allopolyploids are an exceptional system to investigate gene regulatory changes that have evolved in the parental species prior to allopolyploidization. Organisms are complex biological systems that must continue to function even as their genomes evolve. While evolution is usually gradual, the formation of new species by the hybridization of different parents—allopolyploidization—occurs nearly instantaneously. A key question is what happens to expression of the two parental gene copies following genome merger. To determine this, we focused on a fungal allopolyploid from a group that dominates many of the world's pastoral economies. To investigate the fate of gene expression in this system, we developed a novel pipeline to assign high throughput RNA sequence reads to the two parental gene copies, thus allowing quantification of expression. We found transcriptional responses to be predominantly conservative: most gene copies either inherit parental expression patterns, or if differentially expressed in the parents, that difference is lost in the hybrid. Moreover, we identified an extraordinary level of concordance in the fate of genome-wide allopolyploid gene expression with that seen in cotton. The very different nature of these two allopolyploids suggests that there is a set of universal rules for the transcriptional response to genome merger. We propose a mechanistic model whereby this conserved response reflects similarities in mutational processes that underlie gene regulatory evolution.
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Affiliation(s)
- Murray P. Cox
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail: (MPC); (ARDG)
| | - Ting Dong
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - GengGeng Shen
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Yogesh Dalvi
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - D. Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Austen R. D. Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- * E-mail: (MPC); (ARDG)
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Wang ZH, Zhang D, Bai Y, Zhang YH, Liu Y, Wu Y, Lin XY, Wen JW, Xu CM, Li LF, Liu B. Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing. PLoS One 2013; 8:e74479. [PMID: 24058573 PMCID: PMC3776793 DOI: 10.1371/journal.pone.0074479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp) paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs) and 17,839 homozygous insertions/deletions (indels) were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs) was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q) RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a sexually incompatible species may represent a potent means to generate novel genetic diversities, and which may have played relevant roles in plant evolution and can be manipulated for crop improvements.
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Affiliation(s)
- Zhen-Hui Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Di Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yun-Hong Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Ying Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiu-Yun Lin
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jia-Wei Wen
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chun-Ming Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- * E-mail: (LL); (BL)
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- * E-mail: (LL); (BL)
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Cara N, Marfil CF, Masuelli RW. Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum. Ecol Evol 2013; 3:3764-79. [PMID: 24198938 PMCID: PMC3810873 DOI: 10.1002/ece3.758] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/31/2013] [Accepted: 08/12/2013] [Indexed: 12/30/2022] Open
Abstract
Interspecific hybridization is known for triggering genetic and epigenetic changes, such as modifications on DNA methylation patterns and impact on phenotypic plasticity and ecological adaptation. Wild potatoes (Solanum, section Petota) are adapted to multiple habitats along the Andes, and natural hybridizations have proven to be a common feature among species of this group. Solanum× rechei, a recently formed hybrid that grows sympatrically with the parental species S. kurtzianum and S. microdontum, represents an ideal model for studying the ecologically and evolutionary importance of hybridization in generating of epigenetic variability. Genetic and epigenetic variability and their correlation with morphological variation were investigated in wild and ex situ conserved populations of these three wild potato species using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques. We observed that novel methylation patterns doubled the number of novel genetic patterns in the hybrid and that the morphological variability measured on 30 characters had a higher correlation with the epigenetic than with the genetic variability. Statistical comparison of methylation levels suggested that the interspecific hybridization induces genome demethylation in the hybrids. A Bayesian analysis of the genetic data reveled the hybrid nature of S. × rechei, with genotypes displaying high levels of admixture with the parental species, while the epigenetic information assigned S. × rechei to its own cluster with low admixture. These findings suggested that after the hybridization event, a novel epigenetic pattern was rapidly established, which might influence the phenotypic plasticity and adaptation of the hybrid to new environments.
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Affiliation(s)
- Nicolás Cara
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola Mendoza (IBAM), Universidad Nacional de Cuyo A. Brown 500 (M5528AHB), Chacras de Coria, Mendoza, Argentina
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Zhao Q, Zou J, Meng J, Mei S, Wang J. Tracing the transcriptomic changes in synthetic Trigenomic allohexaploids of Brassica using an RNA-Seq approach. PLoS One 2013; 8:e68883. [PMID: 23874799 PMCID: PMC3708896 DOI: 10.1371/journal.pone.0068883] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/02/2013] [Indexed: 01/07/2023] Open
Abstract
Polyploidization has played an important role in plant evolution and speciation, and newly formed allopolyploids have experienced rapid transcriptomic changes. Here, we compared the transcriptomic differences between a synthetic Brassica allohexaploid and its parents using a high-throughput RNA-Seq method. A total of 35,644,409 sequence reads were generated, and 32,642 genes were aligned from the data. Totals of 29,260, 29,060, and 29,697 genes were identified in Brassicarapa, Brassicacarinata, and Brassica allohexaploid, respectively. We compared 7,397 differentially expressed genes (DEGs) between Brassica hexaploid and its parents, as well as 2,545 nonadditive genes of Brassica hexaploid. We hypothesized that the higher ploidy level as well as secondary polyploidy might have influenced these changes. The majority of the 3,184 DEGs between Brassica hexaploid and its paternal parent, B. rapa, were involved in the biosynthesis of secondary metabolites, plant–pathogen interactions, photosynthesis, and circadian rhythm. Among the 2,233 DEGs between Brassica hexaploid and its maternal parent, B. carinata, several played roles in plant–pathogen interactions, plant hormone signal transduction, ribosomes, limonene and pinene degradation, photosynthesis, and biosynthesis of secondary metabolites. There were more significant differences in gene expression between the allohexaploid and its paternal parent than between it and its maternal parent, possibly partly because of cytoplasmic and maternal effects. Specific functional categories were enriched among the 2,545 nonadditive genes of Brassica hexaploid compared with the additive genes; the categories included response to stimulus, immune system process, cellular process, metabolic process, rhythmic process, and pigmentation. Many transcription factor genes, methyltransferases, and methylation genes showed differential expression between Brassica hexaploid and its parents. Our results demonstrate that the Brassica allohexaploid can generate extensive transcriptomic diversity compared with its parents. These changes may contribute to the normal growth and reproduction of allohexaploids.
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Affiliation(s)
- Qin Zhao
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shiyong Mei
- Hubei Academy of Agricultural Science, Wuhan, China
| | - Jianbo Wang
- National Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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Shapiro JA. How life changes itself: the Read-Write (RW) genome. Phys Life Rev 2013; 10:287-323. [PMID: 23876611 DOI: 10.1016/j.plrev.2013.07.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/02/2013] [Indexed: 01/06/2023]
Abstract
The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
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Affiliation(s)
- James A Shapiro
- Dept. of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA. http://www.huffingtonpost.com/james-a-shapiro
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46
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Hegarty M, Coate J, Sherman-Broyles S, Abbott R, Hiscock S, Doyle J. Lessons from natural and artificial polyploids in higher plants. Cytogenet Genome Res 2013; 140:204-25. [PMID: 23816545 DOI: 10.1159/000353361] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy in higher plants is a major source of genetic novelty upon which selection may act to drive evolution, as evidenced by the widespread success of polyploid species in the wild. However, research into the effects of polyploidy can be confounded by the entanglement of several processes: genome duplication, hybridisation (allopolyploidy is frequent in plants) and subsequent evolution. The discovery of the chemical agent colchicine, which can be used to produce artificial polyploids on demand, has enabled scientists to unravel these threads and understand the complex genomic changes involved in each. We present here an overview of lessons learnt from studies of natural and artificial polyploids, and from comparisons between the 2, covering basic cellular and metabolic consequences through to alterations in epigenetic gene regulation, together with 2 in-depth case studies in Senecio and Glycine. See also the sister article focusing on animals by Arai and Fujimoto in this themed issue.
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Affiliation(s)
- M Hegarty
- IBERS, Aberystwyth University, Aberystwyth, UK. ayh @ aber.ac.uk
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47
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Cui C, Ge X, Zhou Y, Li M, Li Z. Cytoplasmic and genomic effects on non-meiosis-driven genetic changes in Brassica hybrids and allotetraploids from pairwise crosses of three cultivated diploids. PLoS One 2013; 8:e65078. [PMID: 23741462 PMCID: PMC3669095 DOI: 10.1371/journal.pone.0065078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 04/22/2013] [Indexed: 12/27/2022] Open
Abstract
Nuclear-cytoplasmic interactions are predicted to be important in shaping the genetic changes in early stage of allopolyploidization. Our previous study shows the specific role of genome and cytoplasm affecting the chromosome pairing in Brassica hybrids and allotetraploids from pairwise crosses between three cultivated diploids with A, B and C genomes, respectively. Herein, to address how parental genomes and cytoplasm affects genomic, epigenetic and gene expression changes prior to meiosis in these hybrids and allopolyploids, their patterns of AFLP (Amplified fragment length polymorphism), mAFLP (Methylation AFLP) and cDNA-AFLP were compared with the progenitors, revealing the major absent bands within each genome. These changes varied under various cytoplasm backgrounds and genome combinations, following the significant order of AFLP> mAFLP> cDNA -AFLP. The frequencies of AFLP bands lost were positively correlated with the divergence degrees of parental genomes, but not obvious for those of mAFLP and cDNA-AFLP absent bands, and methylation change showed least variations among hybrids and within each genome. These changes within each genome followed the A>B>C hierarchy, except the highest rate of cDNA loss in B genome. Among three changes, only overall AFLP bands were significantly correlated with cDNA-AFLP, and their correlations varied within each genome. These changes in allotetraploids were mainly caused by genome merger rather than doubling. Parental genomes altered differently at three levels, responded to the types of cytoplasm and genome and their interaction or divergence. The result provides new clues for instant non-meiosis-driven genome restructuring following genome merger and duplication.
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Affiliation(s)
- Cheng Cui
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (GX); (ZL)
| | - Yingying Zhou
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Maoteng Li
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (GX); (ZL)
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48
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Schulz B, Eckstein RL, Durka W. Scoring and analysis of methylation-sensitive amplification polymorphisms for epigenetic population studies. Mol Ecol Resour 2013; 13:642-53. [PMID: 23617735 DOI: 10.1111/1755-0998.12100] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/05/2013] [Accepted: 03/06/2013] [Indexed: 12/12/2022]
Abstract
DNA methylation is an important, heritable epigenetic modification in most eukaryotic organisms that is connected with numerous biological processes. To study the impact of natural epigenetic variation in an ecological or evolutionary context, epigenetic studies are increasingly using methylation-sensitive amplification polymorphism (MSAP) for surveys at the population or species level. However, no consensus exists on how to interpret and score the multistate information obtained from the MSAP banding patterns. Here, we review the previously used scoring approaches for population epigenetic studies and develop new alternatives. To assess effects of the different approaches on parameters of epigenetic diversity and differentiation, we applied eight scoring schemes to a case study of three populations of the plant species Viola elatior. For a total number of 168 detected polymorphic MSAP fragments, the number of ultimately scored polymorphic epiloci ranged between 78 and 286 depending on the particular scoring scheme. Both, estimates of epigenetic diversity and differentiation varied strongly between scoring approaches. However, linear regression and PCoA revealed qualitatively similar patterns, suggesting that the scoring approaches are largely consistent. For single-locus analyses of MSAP data, for example the search for loci under selection, we advocate a new scoring approach that separately takes into account different methylation types and thus seems appropriate for drawing more detailed conclusions in ecological or evolutionary contexts. An R script (MSAP_score.r) for scoring and basic data analysis is provided.
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Affiliation(s)
- Benjamin Schulz
- Institute of Landscape Ecology and Resource Management, Research Centre for BioSystems, Land Use and Nutrition (IFZ), Justus Liebig University Giessen, Giessen, Germany.
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49
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Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
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50
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Sarilar V, Palacios PM, Rousselet A, Ridel C, Falque M, Eber F, Chèvre AM, Joets J, Brabant P, Alix K. Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids. THE NEW PHYTOLOGIST 2013; 198:593-604. [PMID: 23384044 DOI: 10.1111/nph.12156] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 12/19/2012] [Indexed: 05/02/2023]
Abstract
The role played by whole-genome duplication (WGD) in evolution and adaptation is particularly well illustrated in allopolyploids, where WGD is concomitant with interspecific hybridization. This 'Genome Shock', usually accompanied by structural and functional modifications, has been associated with the activation of transposable elements (TEs). However, the impact of allopolyploidy on TEs has been studied in only a few polyploid species, and not in Brassica, which has been marked by recurrent polyploidy events. Here, we developed sequence-specific amplification polymorphism (SSAP) markers for three contrasting TEs, and compared profiles between resynthesized Brassica napus allotetraploids and their diploid Brassica progenitors. To evaluate restructuring at TE insertion sites, we scored changes in SSAP profiles and analysed a large set of differentially amplified SSAP bands. No massive structural changes associated with the three TEs surveyed were detected. However, several transposition events, specific to the youngest TE originating from the B. oleracea genome, were identified. Our study supports the hypothesis that TE responses to allopolyploidy are highly specific. The changes observed in SSAP profiles lead us to hypothesize that they may partly result from changes in DNA methylation, questioning the role of epigenetics during the formation of a new allopolyploid genome.
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Affiliation(s)
- Véronique Sarilar
- AgroParisTech, 16 rue Claude Bernard, F-75231 Paris Cedex 05, France
- CNRS, UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | - Paulina Martinez Palacios
- Université Paris-Sud, UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | - Agnès Rousselet
- INRA, UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | - Céline Ridel
- INRA, UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- INRA, UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | - Frédérique Eber
- INRA, UMR 1349 IGEPP, BP 35327, F-35653 Le Rheu Cedex, France
| | | | - Johann Joets
- INRA, UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | - Philippe Brabant
- AgroParisTech, 16 rue Claude Bernard, F-75231 Paris Cedex 05, France
- UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
| | - Karine Alix
- AgroParisTech, 16 rue Claude Bernard, F-75231 Paris Cedex 05, France
- UMR 0320/8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France
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