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Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava. BMC Genomics 2019; 20:514. [PMID: 31226927 PMCID: PMC6588902 DOI: 10.1186/s12864-019-5895-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/10/2019] [Indexed: 01/21/2023] Open
Abstract
Background Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are involved in drought tolerance in various crops. Results Herein, we demonstrate that tetraploidy potentiates tolerance to drought stress in cassava (Manihot esculenta Crantz). Autotetraploidy reduces transpiration by lesser extent increasing of stomatal density, smaller stomatal aperture size, or greater stomatal closure, and reducing accumulation of H2O2 under drought stress. Transcriptome analysis of autotetraploid samples revealed down-regulation of genes involved in photosynthesis under drought stress, and less down-regulation of subtilisin-like proteases involved in increasing stomatal density. UDP-glucosyltransferases were increased more or reduced less in dehydrated leaves of autotetraploids compared with controls. Strand-specific RNA-seq data (validated by quantitative real time PCR) identified 2372 lncRNAs, and 86 autotetraploid-specific lncRNAs were differentially expressed in stressed leaves. The co-expressed network analysis indicated that LNC_001148 and LNC_000160 in autotetraploid dehydrated leaves regulated six genes encoding subtilisin-like protease above mentioned, thereby result in increasing the stomatal density to a lesser extent in autotetraploid cassava. Trans-regulatory network analysis suggested that autotetraploid-specific differentially expressed lncRNAs were associated with galactose metabolism, pentose phosphate pathway and brassinosteroid biosynthesis, etc. Conclusion Tetraploidy potentiates tolerance to drought stress in cassava, and LNC_001148 and LNC_000160 mediate drought tolerance by regulating stomatal density in autotetraploid cassava. Electronic supplementary material The online version of this article (10.1186/s12864-019-5895-7) contains supplementary material, which is available to authorized users.
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Ciska M, Hikida R, Masuda K, Moreno Díaz de la Espina S. Evolutionary history and structure of nuclear matrix constituent proteins, the plant analogues of lamins. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2651-2664. [PMID: 30828723 PMCID: PMC6506774 DOI: 10.1093/jxb/erz102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/20/2019] [Indexed: 05/09/2023]
Abstract
Nuclear matrix constituent proteins (NMCPs), the structural components of the plant lamina, are considered to be the analogues of lamins in plants based on numerous structural and functional similarities. Current phylogenetic knowledge suggests that, in contrast to lamins, which are widely distributed in eukaryotes, NMCPs are taxonomically restricted to Streptophyta. At present, most information about NMCPs comes from angiosperms, and virtually no data are available from more ancestral groups. In angiosperms, the NMCP family comprises two phylogenetic groups, NMCP1 and NMCP2, which evolved from the NMCP1 and NMCP2 progenitor genes. Based on sequence conservation and the presence of NMCP-specific domains, we determined the structure and number of NMCP genes present in different Streptophyta clades. We analysed 91 species of embryophytes and report additional NMCP sequences from mosses, liverworts, clubmosses, horsetail, ferns, gymnosperms, and Charophyta algae. Our results confirm an origin of NMCPs in Charophyta (the earliest diverging group of Streptophyta), resolve the number and structure of NMCPs in the different clades, and propose the emergence of additional NMCP homologues by whole-genome duplication events. Immunofluorescence microscopy demonstrated localization of a basal NMCP from the moss Physcomitrella patens at the nuclear envelope, suggesting a functional conservation for basal and more evolved NMCPs.
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Affiliation(s)
- Malgorzata Ciska
- Cell and Molecular Biology Department, Centre of Biological Researches, CSIC, Ramiro de Maeztu, Madrid, Spain
| | - Riku Hikida
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo Japan
| | - Kiyoshi Masuda
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Sapporo Japan
| | - Susana Moreno Díaz de la Espina
- Cell and Molecular Biology Department, Centre of Biological Researches, CSIC, Ramiro de Maeztu, Madrid, Spain
- Correspondence:
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Long YL, Qiao F, Jiang XF, Cong HQ, Sun ML, Xu ZJ. Screening and analysis on the differentially expression genes between diploid and autotetraploid watermelon by using of digital gene expression profile. BRAZ J BIOL 2019; 79:180-190. [DOI: 10.1590/1519-6984.174475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 12/27/2017] [Indexed: 11/22/2022] Open
Abstract
Abstract Synthetic polyploids are key breeding materials for watermelon. Compared with diploid watermelon, the tetraploid watermelon often exhibit wide phenotypic differences and differential gene expression. Digital gene expression (DGE) profile technique was performed in this study to present gene expression patterns in an autotetraploid and its progenitor diploid watermelon, and deferentially expressed genes (DEGs) related to the abiotic and biotic stress were also addressed. Altogether, 4,985 DEGs were obtained in the autotetraploid against its progenitor diploid, and 66.02% DEGs is up-regulated. GO analysis shows that these DEGs mainly distributed in ‘metabolic process’, ‘cell’ and ‘catalytic activity’. KEGG analysis revealed that these DEGs mainly cover ‘metabolic pathways’, ‘secondary metabolites’ and ‘ribosome’. Moreover, 134 tolerance related DEGs were identified which cover osmotic adjustment substance, protective enzymes/protein, signaling proteins and pathogenesis-related proteins. This study present the differential expression of stress related genes and global gene expression patterns at background level in autotetraploid watermelons. These new evidences could supplement the molecular theoretical basis for the better resistance after the genome doubling in the gourd family.
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Affiliation(s)
- Y. L. Long
- Hainan University, China; Chinese Academy of Tropical Agricultural Sciences, China
| | - F. Qiao
- Chinese Academy of Tropical Agricultural Sciences, China
| | | | - H. Q. Cong
- Chinese Academy of Tropical Agricultural Sciences, China
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Liu Y, Yu Y, Sun J, Cao Q, Tang Z, Liu M, Xu T, Ma D, Li Z, Sun J. Root-zone-specific sensitivity of K+-and Ca2+-permeable channels to H2O2 determines ion homeostasis in salinized diploid and hexaploid Ipomoea trifida. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1389-1405. [PMID: 30689932 PMCID: PMC6382330 DOI: 10.1093/jxb/ery461] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/11/2018] [Accepted: 12/19/2018] [Indexed: 05/13/2023]
Abstract
Polyploids generally possess superior K+/Na+ homeostasis under saline conditions compared with their diploid progenitors. In this study, we identified the physiological mechanisms involved in the ploidy-related mediation of K+/Na+ homeostasis in the roots of diploid (2x) and hexaploid (6x; autohexaploid) Ipomoea trifida, which is the closest relative of cultivated sweet potato. Results showed that 6x I. trifida retained more K+ and accumulated less Na+ in the root and leaf tissues under salt stress than 2x I. trifida. Compared with its 2x ancestor, 6x I. trifida efficiently prevents K+ efflux from the meristem root zone under salt stress through its plasma membrane (PM) K+-permeable channels, which have low sensitivity to H2O2. Moreover, 6x I. trifida efficiently excludes Na+ from the elongation and mature root zones under salt stress because of the high sensitivity of PM Ca2+-permeable channels to H2O2. Our results suggest the root-zone-specific sensitivity to H2O2 of PM K+- and Ca2+-permeable channels in the co-ordinated control of K+/Na+ homeostasis in salinized 2x and 6x I. trifida. This work provides new insights into the improved maintenance of K+/Na+ homeostasis of polyploids under salt stress.
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Affiliation(s)
- Yang Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Yicheng Yu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jianying Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Qinghe Cao
- Sweet Potato Research Institute (CAAS), Jiangsu Xuzhou Sweet Potato Research Institute, MOA Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Xuzhou, Jiangsu, China
| | - Zhonghou Tang
- Sweet Potato Research Institute (CAAS), Jiangsu Xuzhou Sweet Potato Research Institute, MOA Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Xuzhou, Jiangsu, China
| | - Meiyan Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Daifu Ma
- Sweet Potato Research Institute (CAAS), Jiangsu Xuzhou Sweet Potato Research Institute, MOA Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Xuzhou, Jiangsu, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- Correspondence: or
| | - Jian Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- Correspondence: or
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Visger CJ, Wong GKS, Zhang Y, Soltis PS, Soltis DE. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. AMERICAN JOURNAL OF BOTANY 2019; 106:280-291. [PMID: 30779448 DOI: 10.1002/ajb2.1239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance. METHODS We use RNA spike-in standards in concert with cell size and density to identify and correct for differences in transcriptome size and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass. KEY RESULTS In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size. CONCLUSIONS While each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.
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Affiliation(s)
- Clayton J Visger
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, 95819, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yong Zhang
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Shenzhen Hua Han Gene Co. Ltd., 7F Jian An Shan Hai Building, No. 8000, Shennan Road, Futian District, Shenzhen, 518040, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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Baduel P, Bray S, Vallejo-Marin M, Kolář F, Yant L. The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00117] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Martínez LM, Fernández-Ocaña A, Rey PJ, Salido T, Amil-Ruiz F, Manzaneda AJ. Variation in functional responses to water stress and differentiation between natural allopolyploid populations in the Brachypodium distachyon species complex. ANNALS OF BOTANY 2018; 121:1369-1382. [PMID: 29893879 PMCID: PMC6007385 DOI: 10.1093/aob/mcy037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/26/2018] [Indexed: 05/21/2023]
Abstract
Background and Aims Some polyploid species show enhanced physiological tolerance to drought compared with their progenitors. However, very few studies have examined the consistency of physiological drought response between genetically differentiated natural polyploid populations, which is key to evaluation of the importance of adaptive evolution after polyploidization in those systems where drought exerts a selective pressure. Methods A comparative functional approach was used to investigate differentiation of drought-tolerance-related traits in the Brachypodium species complex, a model system for grass polyploid adaptive speciation and functional genomics that comprises three closely related annual species: the two diploid parents, B. distachyon and B. stacei, and the allotetraploid derived from them, B. hybridum. Differentiation of drought-tolerance-related traits between ten genetically distinct B. hybridum populations and its ecological correlates was further analysed. Key Results The functional drought response is overall well differentiated between Brachypodium species. Brachypodium hybridum allotetraploids showed a transgressive expression pattern in leaf phytohormone content in response to drought. In contrast, other B. hybridum physiological traits correlated to B. stacei ones. Particularly, proline and water content were the traits that best discriminated these species from B. distachyon under drought. Conclusions After polyploid formation and/or colonization, B. hybridum populations have adaptively diverged physiologically and genetically in response to variations in aridity.
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Affiliation(s)
- Luisa M Martínez
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Ana Fernández-Ocaña
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Pedro J Rey
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Teresa Salido
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Francisco Amil-Ruiz
- Bioinformatics Unit, Central Service for Research Support (SCAI), University of Córdoba, Córdoba, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
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Li M, Xu G, Xia X, Wang M, Yin X, Zhang B, Zhang X, Cui Y. Deciphering the physiological and molecular mechanisms for copper tolerance in autotetraploid Arabidopsis. PLANT CELL REPORTS 2017; 36:1585-1597. [PMID: 28685360 DOI: 10.1007/s00299-017-2176-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/29/2017] [Indexed: 05/21/2023]
Abstract
Autotetraploid Arabidopsis line esd and 4COL exhibit enhanced tolerance to Cu stress by enhancing activation of antioxidative defenses, altering expression of genes related to Cu transport, chelation, and ABA-responsive. Autopolyploidy is ubiquitous among angiosperms and often results in better adaptation to stress conditions. Although copper (Cu) is an essential trace element, excess amounts can inhibit plant growth and even result in death. Here, we report that autotetraploid Arabidopsis thaliana esd and 4COL exhibit higher tolerance to Cu stress. Under such conditions, tetraploid plants had lower Cu contents and significantly more biomass compared with diploid plants. When exposed to excess Cu for 24 h, levels of superoxide anions, hydrogen peroxide, and malondialdehyde were lower in tetraploids than in diploids. Moreover, activities of the antioxidant enzymes superoxide dismutase and peroxidase were stimulated and glutathione content was maintained at a relative higher level in the tetraploids. The expression of genes related to Cu transport and chelation was altered in autotetraploid Arabidopsis under Cu stress, and several key genes involved in the response to abscisic acid (ABA) were significantly up-regulated. Our results indicate that tetraploid Arabidopsis esd and 4COL acquire improved tolerance to Cu stress through enhanced activation of antioxidative defense mechanisms, altered expression of genes related to Cu transport and chelation, and positive regulation of expression for ABA-responsive genes.
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Affiliation(s)
- Mingjuan Li
- Key Laboratory for Agro-ecological Process in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoyun Xu
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, 450001, China
| | - Xinjie Xia
- Key Laboratory for Agro-ecological Process in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Manling Wang
- Key Laboratory for Agro-ecological Process in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Xuming Yin
- Key Laboratory for Agro-ecological Process in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
| | - Bin Zhang
- Key Laboratory for Agro-ecological Process in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhang
- Key Laboratory for Agro-ecological Process in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanchun Cui
- Key Laboratory for Agro-ecological Process in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, Hunan, China.
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Liu B, Sun G. microRNAs contribute to enhanced salt adaptation of the autopolyploid Hordeum bulbosum compared with its diploid ancestor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:57-69. [PMID: 28370696 DOI: 10.1111/tpj.13546] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/14/2017] [Accepted: 03/20/2017] [Indexed: 05/21/2023]
Abstract
Several studies have shown that autopolyploid can tolerate abiotic stresses better than its diploid ancestor. However, the underlying molecular mechanism is poorly known. microRNAs (miRNAs) are small RNAs that regulate the target gene expression post-transcriptionally and play a critical role in the response to abiotic stresses. Duplication of the whole genome can result in the expansion of miRNA families, and the innovative miRNA-target interaction is important for adaptive responses to various environments. We identified new microRNAs induced by genome duplication, that are also associated with stress response and the distinctive microRNA networks in tetraploid and diploid Hordeum bulbosum using high-throughput sequencing. Physiological results showed that autotetraploid Hordeum bulbosum tolerated salt stress better than its diploid. Comparison of miRNAs expression between diploid and tetraploid check (CK) and salt stress revealed that five miRNAs affected by genome doubling were also involved in salt stress response. Of these, miR528b-3p was only detected in the tetraploid, and downregulated under salt stress relative to that in tetraploid CK. Moreover, through target prediction, it was found that miR528b-3p was not only involved in DNA replication and repair but also participated in salt stress response. Finally, by analyzing all the differentially expressed microRNAs and their targets, we also discovered distinguished microRNAs-target regulatory networks in diploid and tetraploid, respectively. Overall, the results demonstrated the critical role of microRNAs in autopolyploid to have better tolerance salt stress.
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Affiliation(s)
- Beibei Liu
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
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Hias N, Leus L, Davey MW, Vanderzande S, Van Huylenbroeck J, Keulemans J. Effect of polyploidization on morphology in two apple (Malus × domestica) genotypes. HORTICULTURAL SCIENCE 2017; 44:55-63. [PMID: 0 DOI: 10.17221/7/2016-hortsci] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Autopolyploidy leads to rapid genomic changes in Arabidopsis thaliana. Theory Biosci 2017; 136:199-206. [PMID: 28612184 DOI: 10.1007/s12064-017-0252-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/09/2017] [Indexed: 10/19/2022]
Abstract
Polyploidy is a widespread feature of plant genomes. As a typical model of polyploidy, autopolyploidy has been postulated evolutionary dead ends and received little attention compared with allopolyploidy. For the limited data available so far, the evolutionary outcome of genome diversity in autopolyploids remains controversial in comparison with its diploid ancestors. In the present study, the effects of autopolyploidy on genome diversity were revealed at a genome-wide scale by comparative analyses of polymorphism between Arabidopsis autopolyploids (autotetraploids and autotriploids) and related diploids within the first ten successive inbred generations using amplified fragment length polymorphism. The results showed that in contrast with diploids, the rapid genomic changes (including gain and loss of DNA sequences) in autopolyploids were definitely found within the first generations after autopolyploidization, but slow down and probably stabilized in the higher generations as a source of genetic diversity in the long term. The sequencing of these DNA fragments indicated that these changes occurred both on genic and inter-genic (or intronic) regions, and quantitative PCR showed that the expression of some corresponding genes in the genic regions was obviously affected (including upregulation, downregulation and silencing) in autopolyploids. Therefore, this study demonstrated that autopolyploidy could lead to rapid genomic changes and probably influence expression and function of certain genes within the first generations, giving rising to genetic diversification after polyploidization.
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Visger CJ, Germain-Aubrey CC, Patel M, Sessa EB, Soltis PS, Soltis DE. Niche divergence between diploid and autotetraploid Tolmiea. AMERICAN JOURNAL OF BOTANY 2016; 103:1396-1406. [PMID: 27507838 DOI: 10.3732/ajb.1600130] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF STUDY Polyploidy is common in eukaryotes and is of major evolutionary importance over both short and long time-scales. Compared to allopolyploids, autopolyploids remain understudied; they are often morphologically cryptic and frequently remain taxonomically unrecognized, although there is increasing recognition of the high frequency of autopolyploidy in angiosperms. While autopolyploidy can serve as an instant speciation mechanism, little is known about the ecological consequences of this process. We describe the ecological divergence of a diploid-autotetraploid species pair in Tolmiea. METHODS We investigated whether abiotic niche divergence has shaped the current allopatric distribution of diploid T. diplomenziesii and its autotetraploid derivative, T. menziesii, in the Pacific Northwest of North America. We employed field measures of light availability, as well as niche modeling and a principal component analysis of environmental space. Within a common garden, we also investigated physiological responses to changes in soil moisture. KEY RESULTS Diploid and autotetraploid Tolmiea inhabit significantly different climatic niche spaces. The climatic niche divergence between these two species is best explained by a shift in precipitation availability, and we found evidence of differing physiological response to water availability between these species. CONCLUSIONS We found that spatial segregation of T. diplomenziesii and T. menziesii was accompanied by adaptation to changes in climatic regime. Tolmiea menziesii is not a nascent autotetraploid, having persisted long enough to be established throughout the Pacific Northwest, and therefore both polyploidization and subsequent evolution have contributed to the observed differences between T. menziesii and T. diplomenziesii.
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Affiliation(s)
- Clayton J Visger
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | | | - Maya Patel
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA Genetics Institute, University of Florida, Gainesville, Florida 32608 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
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA 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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Zhang J, Tian Y, Yan L, Zhang G, Wang X, Zeng Y, Zhang J, Ma X, Tan Y, Long N, Wang Y, Ma Y, He Y, Xue Y, Hao S, Yang S, Wang W, Zhang L, Dong Y, Chen W, Sheng J. Genome of Plant Maca (Lepidium meyenii) Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes. MOLECULAR PLANT 2016; 9:1066-77. [PMID: 27174404 DOI: 10.1016/j.molp.2016.04.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/01/2016] [Accepted: 04/26/2016] [Indexed: 05/20/2023]
Abstract
Maca (Lepidium meyenii Walp, 2n = 8x = 64), belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru (4000-4500 m). Considering that the rapid uplift of the central Andes occurred 5-10 million years ago (Ma), an evolutionary question arises regarding how plants such as maca acquire high-altitude adaptation within a short geological period. Here, we report the high-quality genome assembly of maca, in which two closely spaced maca-specific whole-genome duplications (WGDs; ∼6.7 Ma) were identified. Comparative genomic analysis between maca and closely related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway, and secondary metabolite biosynthesis via WGDs. The retention and subsequent functional divergence of many duplicated genes may account for the morphological and physiological changes (i.e., small leaf shape and self-fertility) in maca in a high-altitude environment. In addition, some duplicated maca genes were identified with functions in morphological adaptation (i.e., LEAF CURLING RESPONSIVENESS) and abiotic stress response (i.e., GLYCINE-RICH RNA-BINDING PROTEINS and DNA-DAMAGE-REPAIR/TOLERATION 2) under positive selection. Collectively, the maca genome provides useful information to understand the important roles of WGDs in the high-altitude adaptation of plants in the Andes.
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Affiliation(s)
- Jing Zhang
- College of Life Science, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yang Tian
- College of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Liang Yan
- Pu'er Institute of Pu-erh Tea, Pu'er 665000, China
| | - Guanghui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming 650201, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajin Zhang
- School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China
| | - Xiao Ma
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yuntao Tan
- College of Life Science, Kunming University of Science and Technology, Kunming 650504, China
| | - Ni Long
- College of Life Science, Kunming University of Science and Technology, Kunming 650504, China
| | - Yangzi Wang
- College of Life Science, Kunming University of Science and Technology, Kunming 650504, China
| | - Yujin Ma
- College of Life Science, Kunming University of Science and Technology, Kunming 650504, China
| | - Yuqi He
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yu Xue
- College of Life Science, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shumei Hao
- Yunnan University, Kunming 650091, China
| | - Shengchao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming 650201, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yang Dong
- College of Life Science, Kunming University of Science and Technology, Kunming 650504, China; Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China.
| | - Wei Chen
- Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China.
| | - Jun Sheng
- College of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory of Pu-erh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; Pu'er Institute of Pu-erh Tea, Pu'er 665000, China.
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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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Fasano C, Diretto G, Aversano R, D'Agostino N, Di Matteo A, Frusciante L, Giuliano G, Carputo D. Transcriptome and metabolome of synthetic Solanum autotetraploids reveal key genomic stress events following polyploidization. THE NEW PHYTOLOGIST 2016; 210:1382-94. [PMID: 26915816 DOI: 10.1111/nph.13878] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/06/2015] [Indexed: 05/19/2023]
Abstract
Polyploids are generally classified as autopolyploids, derived from a single species, and allopolyploids, arising from interspecific hybridization. The former represent ideal materials with which to study the consequences of genome doubling and ascertain whether there are molecular and functional rules operating following polyploidization events. To investigate whether the effects of autopolyploidization are common to different species, or if species-specific or stochastic events are prevalent, we performed a comprehensive transcriptomic and metabolomic characterization of diploids and autotetraploids of Solanum commersonii and Solanum bulbocastanum. Autopolyploidization remodelled the transcriptome and the metabolome of both species. In S. commersonii, differentially expressed genes (DEGs) were highly enriched in pericentromeric regions. Most changes were stochastic, suggesting a strong genotypic response. However, a set of robustly regulated transcripts and metabolites was also detected, including purine bases and nucleosides, which are likely to underlie a common response to polyploidization. We hypothesize that autopolyploidization results in nucleotide pool imbalance, which in turn triggers a genomic shock responsible for the stochastic events observed. The more extensive genomic stress and the higher number of stochastic events observed in S. commersonii with respect to S. bulbocastanum could be the result of the higher nucleoside depletion observed in this species.
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Affiliation(s)
- Carlo Fasano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, Rome, 00123, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Nunzio D'Agostino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca per l'orticoltura (CRA-ORT), via dei Cavalleggeri 25, Pontecagnano, Salerno, 84098, Italy
| | - Antonio Di Matteo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, Rome, 00123, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055, Italy
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Monda K, Araki H, Kuhara S, Ishigaki G, Akashi R, Negi J, Kojima M, Sakakibara H, Takahashi S, Hashimoto-Sugimoto M, Goto N, Iba K. Enhanced Stomatal Conductance by a Spontaneous Arabidopsis Tetraploid, Me-0, Results from Increased Stomatal Size and Greater Stomatal Aperture. PLANT PHYSIOLOGY 2016; 170:1435-44. [PMID: 26754665 PMCID: PMC4775119 DOI: 10.1104/pp.15.01450] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/08/2016] [Indexed: 05/03/2023]
Abstract
The rate of gas exchange in plants is regulated mainly by stomatal size and density. Generally, higher densities of smaller stomata are advantageous for gas exchange; however, it is unclear what the effect of an extraordinary change in stomatal size might have on a plant's gas-exchange capacity. We investigated the stomatal responses to CO2 concentration changes among 374 Arabidopsis (Arabidopsis thaliana) ecotypes and discovered that Mechtshausen (Me-0), a natural tetraploid ecotype, has significantly larger stomata and can achieve a high stomatal conductance. We surmised that the cause of the increased stomatal conductance is tetraploidization; however, the stomatal conductance of another tetraploid accession, tetraploid Columbia (Col), was not as high as that in Me-0. One difference between these two accessions was the size of their stomatal apertures. Analyses of abscisic acid sensitivity, ion balance, and gene expression profiles suggested that physiological or genetic factors restrict the stomatal opening in tetraploid Col but not in Me-0. Our results show that Me-0 overcomes the handicap of stomatal opening that is typical for tetraploids and achieves higher stomatal conductance compared with the closely related tetraploid Col on account of larger stomatal apertures. This study provides evidence for whether larger stomatal size in tetraploids of higher plants can improve stomatal conductance.
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Affiliation(s)
- Keina Monda
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Hiromitsu Araki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Satoru Kuhara
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Genki Ishigaki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Ryo Akashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Juntaro Negi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Mikiko Kojima
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Hitoshi Sakakibara
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Sho Takahashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Mimi Hashimoto-Sugimoto
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Nobuharu Goto
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Koh Iba
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
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Narukawa H, Yokoyama R, Nishitani K. Possible pathways linking ploidy level to cell elongation and cuticular function in hypocotyls of dark-grown Arabidopsis seedlings. PLANT SIGNALING & BEHAVIOR 2016; 11:e1118597. [PMID: 26618780 PMCID: PMC4883887 DOI: 10.1080/15592324.2015.1118597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The mechanisms underlying correlations between ploidy level and cell size in eukaryotes remain unclear. Recently, we showed that cell length was higher in tetraploid than in diploid dark-grown Arabidopsis hypocotyls. Cuticular function was aberrant, and expression of genes of cuticle formation was reduced. Here, the links between cell elongation, cuticular function, and ploidy level in the etiolated hypocotyl were examined. Seedlings defective in cuticle formation exhibited shorter hypocotyls. This was due to inhibition of cell elongation rather than cell proliferation, indicating that the reduced cuticular function was a consequence of tetraploidy-induced cell elongation rather than its cause. Inhibition of hypocotyl elongation by impaired cuticles was lower in tetraploid than diploid, indicating that tetraploid hypocotyls were less sensitive to cuticular damage.
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Affiliation(s)
- Hideki Narukawa
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryusuke Yokoyama
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kazuhiko Nishitani
- Laboratory of Plant Cell Wall Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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del Pozo JC, Ramirez-Parra E. Whole genome duplications in plants: an overview from Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6991-7003. [PMID: 26417017 DOI: 10.1093/jxb/erv432] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Polyploidy is a common event in plants that involves the acquisition of more than two complete sets of chromosomes. Allopolyploidy originates from interspecies hybrids while autopolyploidy originates from intraspecies whole genome duplication (WGD) events. In spite of inconveniences derived from chromosomic rearrangement during polyploidization, natural plant polyploids species often exhibit improved growth vigour and adaptation to adverse environments, conferring evolutionary advantages. These advantages have also been incorporated into crop breeding programmes. Many tetraploid crops show increased stress tolerance, although the molecular mechanisms underlying these different adaptation abilities are poorly known. Understanding the physiological, cellular, and molecular mechanisms coupled to WGD, in both allo- and autopolyploidy, is a major challenge. Over the last few years, several studies, many of them in Arabidopsis, are shedding light on the basis of genetic, genomic, and epigenomic changes linked to WGD. In this review we summarize and discuss the latest advances made in Arabidopsis polyploidy, but also in other agronomic plant species.
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Affiliation(s)
- Juan Carlos del Pozo
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Elena Ramirez-Parra
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
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Liu Z, Xin M, Qin J, Peng H, Ni Z, Yao Y, Sun Q. Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2015; 15:152. [PMID: 26092253 PMCID: PMC4474349 DOI: 10.1186/s12870-015-0511-8] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/28/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Hexaploid wheat (Triticum aestivum) is a globally important crop. Heat, drought and their combination dramatically reduce wheat yield and quality, but the molecular mechanisms underlying wheat tolerance to extreme environments, especially stress combination, are largely unknown. As an allohexaploid, wheat consists of three closely related subgenomes (A, B, and D), and was reported to show improved tolerance to stress conditions compared to tetraploid. But so far very little is known about how wheat coordinates the expression of homeologous genes to cope with various environmental constraints on the whole-genome level. RESULTS To explore the transcriptional response of wheat to the individual and combined stress, we performed high-throughput transcriptome sequencing of seedlings under normal condition and subjected to drought stress (DS), heat stress (HS) and their combination (HD) for 1 h and 6 h, and presented global gene expression reprograms in response to these three stresses. Gene Ontology (GO) enrichment analysis of DS, HS and HD responsive genes revealed an overlap and complexity of functional pathways between each other. Moreover, 4,375 wheat transcription factors were identified on a whole-genome scale based on the released scaffold information by IWGSC, and 1,328 were responsive to stress treatments. Then, the regulatory network analysis of HSFs and DREBs implicated they were both involved in the regulation of DS, HS and HD response and indicated a cross-talk between heat and drought stress. Finally, approximately 68.4 % of homeologous genes were found to exhibit expression partitioning in response to DS, HS or HD, which was further confirmed by using quantitative RT-PCR and Nullisomic-Tetrasomic lines. CONCLUSIONS A large proportion of wheat homeologs exhibited expression partitioning under normal and abiotic stresses, which possibly contributes to the wide adaptability and distribution of hexaploid wheat in response to various environmental constraints.
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Affiliation(s)
- Zhenshan Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Jinxia Qin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, NO.2 Yuanmingyuan Xi Road, Beijing, Haidian District, 100193, China.
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Tan FQ, Tu H, Liang WJ, Long JM, Wu XM, Zhang HY, Guo WW. Comparative metabolic and transcriptional analysis of a doubled diploid and its diploid citrus rootstock (C. junos cv. Ziyang xiangcheng) suggests its potential value for stress resistance improvement. BMC PLANT BIOLOGY 2015; 15:89. [PMID: 25848687 PMCID: PMC4374211 DOI: 10.1186/s12870-015-0450-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/05/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Polyploidy has often been considered to confer plants a better adaptation to environmental stresses. Tetraploid citrus rootstocks are expected to have stronger stress tolerance than diploid. Plenty of doubled diploid citrus plants were exploited from diploid species for citrus rootstock improvement. However, limited metabolic and molecular information related to tetraploidization is currently available at a systemic biological level. This study aimed to evaluate the occurrence and extent of metabolic and transcriptional changes induced by tetraploidization in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka), which is a special citrus germplasm native to China and widely used as an iron deficiency tolerant citrus rootstock. RESULTS Doubled diploid Ziyang xiangcheng has typical morphological and anatomical features such as shorter plant height, larger and thicker leaves, bigger stomata and lower stomatal density, compared to its diploid parent. GC-MS (Gas chromatography coupled to mass spectrometry) analysis revealed that tetraploidization has an activation effect on the accumulation of primary metabolites in leaves; many stress-related metabolites such as sucrose, proline and γ-aminobutyric acid (GABA) was remarkably up-regulated in doubled diploid. However, LC-QTOF-MS (Liquid chromatography quadrupole time-of-flight mass spectrometry) analysis demonstrated that tetraploidization has an inhibition effect on the accumulation of secondary metabolites in leaves; all the 33 flavones were down-regulated while all the 6 flavanones were up-regulated in 4x. By RNA-seq analysis, only 212 genes (0.8% of detected genes) are found significantly differentially expressed between 2x and 4x leaves. Notably, those genes were highly related to stress-response functions, including responses to salt stress, water and abscisic acid. Interestingly, the transcriptional divergence could not explain the metabolic changes, probably due to post-transcriptional regulation. CONCLUSION Taken together, tetraploidization induced considerable changes in leaf primary and secondary metabolite accumulation in Ziyang xiangcheng. However, the effect of tetraploidization on transcriptome is limited. Compared to diploid, higher expression level of stress related genes and higher content of stress related metabolites in doubled diploid could be beneficial for its stress tolerance.
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Affiliation(s)
- Feng-Quan Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hong Tu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wu-Jun Liang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jian-Mei Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hong-Yan Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region) (Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
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Fan G, Wang L, Deng M, Niu S, Zhao Z, Xu E, Cao X, Zhang X. Transcriptome analysis of the variations between autotetraploid Paulownia tomentosa and its diploid using high-throughput sequencing. Mol Genet Genomics 2015; 290:1627-38. [PMID: 25773315 DOI: 10.1007/s00438-015-1023-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/01/2015] [Indexed: 11/30/2022]
Abstract
Timber properties of autotetraploid Paulownia tomentosa are heritable with whole genome duplication, but the molecular mechanisms for the predominant characteristics remain unclear. To illuminate the genetic basis, high-throughput sequencing technology was used to identify the related unigenes. 2677 unigenes were found to be significantly differentially expressed in autotetraploid P. tomentosa. In total, 30 photosynthesis-related, 21 transcription factor-related, and 22 lignin-related differentially expressed unigenes were detected, and the roles of the peroxidase in lignin biosynthesis, MYB DNA-binding proteins, and WRKY proteins associated with the regulation of relevant hormones are extensively discussed. The results provide transcriptome data that may bring a new perspective to explain the polyploidy mechanism in the long growth cycle of plants and offer some help to the future Paulownia breeding.
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Affiliation(s)
- Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan, China,
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