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Runemark A, Moore EC, Larson EL. Hybridization and gene expression: Beyond differentially expressed genes. Mol Ecol 2024:e17303. [PMID: 38411307 DOI: 10.1111/mec.17303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
| | - Emily C Moore
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
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2
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Akiyama R, Goto T, Tameshige T, Sugisaka J, Kuroki K, Sun J, Akita J, Hatakeyama M, Kudoh H, Kenta T, Tonouchi A, Shimahara Y, Sese J, Kutsuna N, Shimizu-Inatsugi R, Shimizu KK. Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation. Nat Commun 2023; 14:5792. [PMID: 37737204 PMCID: PMC10517152 DOI: 10.1038/s41467-023-41260-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/29/2023] [Indexed: 09/23/2023] Open
Abstract
Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color. We processed >4 million images of small individuals of four Arabidopsis species in the field, where the plant shape, color, and background vary over months. Past radiation, coldness, and precipitation significantly affected the anthocyanin content. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation facilitates the study of plant responses to complex environments termed "in natura".
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Affiliation(s)
- Reiko Akiyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Takao Goto
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192, Japan
| | - Jiro Sugisaka
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Ken Kuroki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jianqiang Sun
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8517, Japan
| | - Junichi Akita
- Department of Electric and Computer Engineering, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, 520-2113, Japan
| | - Tanaka Kenta
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-kogen, Ueda, 386-2204, Japan
| | - Aya Tonouchi
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yuki Shimahara
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Humanome Lab, Inc., L-HUB 3F, 1-4, Shumomiyabi-cho, Shinjuku, Tokyo, 162-0822, Japan
- AIST-Tokyo Tech RWBC-OIL, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Natsumaro Kutsuna
- Research and Development Division, LPIXEL Inc., Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- Kihara Institute for Biological Research (KIBR), Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan.
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Oruganti V, Toegelová H, Pečinka A, Madlung A, Schneeberger K. Rapid large-scale genomic introgression in Arabidopsis suecica via an autoallohexaploid bridge. Genetics 2023; 223:iyac132. [PMID: 36124968 PMCID: PMC9910397 DOI: 10.1093/genetics/iyac132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/24/2022] [Indexed: 11/14/2022] Open
Abstract
Gene flow between species in the genus Arabidopsis occurs in significant amounts, but how exactly gene flow is achieved is not well understood. Polyploidization may be one avenue to explain gene flow between species. One problem, however, with polyploidization as a satisfying explanation is the occurrence of lethal genomic instabilities in neopolyploids as a result of genomic exchange, erratic meiotic behavior, and genomic shock. We have created an autoallohexaploid by pollinating naturally co-occurring diploid Arabidopsis thaliana with allotetraploid Arabidopsis suecica (an allotetraploid composed of A. thaliana and Arabidopsis arenosa). Its triploid offspring underwent spontaneous genome duplication and was used to generate a multigenerational pedigree. Using genome resequencing, we show that 2 major mechanisms promote stable genomic exchange in this population. Legitimate meiotic recombination and chromosome segregation between the autopolyploid chromosomes of the 2 A. thaliana genomes occur without any obvious bias for the parental origin and combine the A. thaliana haplotypes from the A. thaliana parent with the A. thaliana haplotypes from A. suecica similar to purely autopolyploid plants. In addition, we repeatedly observed that occasional exchanges between regions of the homoeologous chromosomes are tolerated. The combination of these mechanisms may result in gene flow leading to stable introgression in natural populations. Unlike the previously reported resynthesized neoallotetraploid A. suecica, this population of autoallohexaploids contains mostly vigorous, and genetically, cytotypically, and phenotypically variable individuals. We propose that naturally formed autoallohexaploid populations might serve as an intermediate bridge between diploid and polyploid species, which can facilitate gene flow rapidly and efficiently.
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Affiliation(s)
- Vidya Oruganti
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Helena Toegelová
- Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic
| | - Aleš Pečinka
- Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic
| | - Andreas Madlung
- Department of Biology, University of Puget Sound, Tacoma, WA 98416, USA
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Department of Genetics, Faculty of Biology, Ludwig Maximilian Universität München, 82152 Planegg-Martinsried, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany
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4
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Hao Y, Su X, Li W, Li L, Zhang Y, Mumtaz MA, Shu H, Cheng S, Zhu G, Wang Z. The creation of autotetraploid provides insights into critical features of DNA methylome changes after genome doubling in water spinach ( Ipomoea aquatica Forsk). FRONTIERS IN PLANT SCIENCE 2023; 14:1155531. [PMID: 37123819 PMCID: PMC10140364 DOI: 10.3389/fpls.2023.1155531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Water spinach (Ipomoea aquatica Forsk) is an essential green leafy vegetable in Asia. In this study, we induced autotetraploid water spinach by colchicine. Furthermore, DNA methylation and transcriptome of tetraploid and diploid were compared using Whole Genome Bisulfite Sequencing (WGBS) and RNA-sequencing techniques. Autotetraploid water spinach was created for the first time. Compared with the diploid parent, autotetraploid water spinach had wider leaves, thicker petioles and stems, thicker and shorter adventitious roots, longer stomas, and larger parenchyma cells. The whole genome methylation level of the autotetraploid was slightly higher than that of the diploid. Compared with the diploid, 12281 Differentially Methylated Regions (DMRs)were found in the autotetraploid, including 2356 hypermethylated and 1310 hypomethylated genes, mainly enriched in 'Arginine and Proline metabolism', 'beta - Alanine metabolism', 'Plant homone signal translation', 'Ribome', and 'Plant - pathgen interaction' pathways. Correlation analysis of transcriptome and DNA methylation data showed that 121 differentially expressed genes undergone differential methylation, related to four pathways 'Other types of O-glycan biosynthesis', 'Terpenoid backbone biosynthesis', 'Biosynthesis of secondary metabolites', and 'Metabolic paths'. This work obtained important autotetraploid resources of water spinach and revealed the genomic DNA methylation changes after genome doubling, being helpful for further studying the molecular mechanism of variations caused by polyploids of the Ipomoea genus.
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Affiliation(s)
- Yuanyuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiao Su
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Wen Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Lin Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Yu Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Muhammad Ali Mumtaz
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Guopeng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Zhiwei Wang,
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Zheng M, Li J, Zeng C, Liu X, Chu W, Lin J, Wang F, Wang W, Guo W, Xin M, Yao Y, Peng H, Ni Z, Sun Q, Hu Z. Subgenome-biased expression and functional diversification of a Na +/H + antiporter homoeologs in salt tolerance of polyploid wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1072009. [PMID: 36570929 PMCID: PMC9768589 DOI: 10.3389/fpls.2022.1072009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Common wheat (Triticum aestivum, BBAADD) is an allohexaploid species combines the D genome from Ae. tauschii and with the AB genomes from tetraploid wheat (Triticum turgidum). Compared with tetraploid wheat, hexaploid wheat has wide-ranging adaptability to environmental adversity such as salt stress. However, little is known about the molecular basis underlying this trait. The plasma membrane Na+/H+ transporter Salt Overly Sensitive 1 (SOS1) is a key determinant of salt tolerance in plants. Here we show that the upregulation of TaSOS1 expression is positively correlated with salt tolerance variation in polyploid wheat. Furthermore, both transcriptional analysis and GUS staining on transgenic plants indicated TaSOS1-A and TaSOS1-B exhibited higher basal expression in roots and leaves in normal conditions and further up-regulated under salt stress; while TaSOS1-D showed markedly lower expression in roots and leaves under normal conditions, but significant up-regulated in roots but not leaves under salt stress. Moreover, transgenic studies in Arabidopsis demonstrate that three TaSOS1 homoeologs display different contribution to salt tolerance and TaSOS1-D plays the prominent role in salt stress. Our findings provide insights into the subgenomic homoeologs variation potential to broad adaptability of natural polyploidy wheat, which might effective for genetic improvement of salinity tolerance in wheat and other crops.
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Affiliation(s)
- Mei Zheng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jinpeng Li
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Chaowu Zeng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Xinjiang Academy of Agricultural Sciences, Urumuqi, China
| | - Xingbei Liu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Wei Chu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jingchen Lin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Fengzhi Wang
- Hebei Key Laboratory of Crop Salt-alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou Academy of Agriculture and Forestry Science, Cangzhou, China
| | - Weiwei Wang
- Hebei Key Laboratory of Crop Salt-alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou Academy of Agriculture and Forestry Science, Cangzhou, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (Ministry of Education), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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6
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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Clo J. Polyploidization: Consequences of genome doubling on the evolutionary potential of populations. AMERICAN JOURNAL OF BOTANY 2022; 109:1213-1220. [PMID: 35862788 DOI: 10.1002/ajb2.16029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Whole-genome duplication is common in plants and is considered to have a broad range of effects on individuals' phenotypes and genomes and to be an important driver of plant adaptation and speciation. Despite their increased capacity to cope with challenging environments, polyploid lineages are generally as prone to extinction, and sometimes more prone, than their diploid progenitors. Although several explanations have been proposed to explain the short- and long-term disadvantages of polyploidy on the survival probability of populations, the consequences of whole-genome doubling on the heritable variance remain poorly studied. Whole-genome doubling can have major effects not only on the genetics, but also on the ecology and life history of the populations. Modifications of other properties of populations can reverse the effects of polyploidization per se on heritable variance. In this synthesis, I summarize the empirical and theoretical knowledge about the multifarious consequences of genome doubling on the heritable variance of quantitative traits and on the evolutionary potential of polyploid populations compared to their diploid progenitors. I propose several ways to decipher the consequences of whole-genome doubling on survival probability and to study the further consequences of shifting the ecological niche and life-history traits of a population. I also highlight some practical considerations for comparing the heritable variance of a trait among different cytotypes. Such investigations appear to be timely and necessary to understand more about the paradoxical aspects of polyploidization and to understand the evolutionary potential of polyploid lineages in a global warming context.
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Affiliation(s)
- Josselin Clo
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01, Prague, Czech Republic
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Wen Y, Liu H, Meng H, Qiao L, Zhang G, Cheng Z. In vitro Induction and Phenotypic Variations of Autotetraploid Garlic ( Allium sativum L.) With Dwarfism. FRONTIERS IN PLANT SCIENCE 2022; 13:917910. [PMID: 35812906 PMCID: PMC9258943 DOI: 10.3389/fpls.2022.917910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 05/16/2023]
Abstract
Garlic (Allium sativum L.) is a compelling horticultural crop with high culinary and therapeutic values. Commercial garlic varieties are male-sterile and propagated asexually from individual cloves or bulbils. Consequently, its main breeding strategy has been confined to the time-consuming and inefficient selection approach from the existing germplasm. Polyploidy, meanwhile, plays a prominent role in conferring plants various changes in morphological, physiological, and ecological properties. Artificial polyploidy induction has gained pivotal attention to generate new genotype for further crop improvement as a mutational breeding method. In our study, efficient and reliable in vitro induction protocols of autotetraploid garlic were established by applying different antimitotic agents based on high-frequency direct shoot organogenesis initiated from inflorescence explant. The explants were cultured on solid medium containing various concentrations of colchicine or oryzalin for different duration days. Afterward, the ploidy levels of regenerated plantlets with stable and distinguished characters were confirmed by flow cytometry and chromosome counting. The colchicine concentration at 0.2% (w/v) combined with culture duration for 20 days was most efficient (the autotetraploid induction rate was 21.8%) compared to the induction rate of 4.3% using oryzalin at 60 μmol L-1 for 20 days. No polymorphic bands were detected by simple sequence repeat analysis between tetraploid and diploid plantlets. The tetraploids exhibited a stable and remarkable dwarfness effect rarely reported in artificial polyploidization among wide range of phenotypic variations. There are both morphological and cytological changes including extremely reduced plant height, thickening and broadening of leaves, disappearance of pseudostem, density reduction, and augmented width of stomatal. Furthermore, the level of phytohormones, including, indole propionic acid, gibberellin, brassinolide, zeatin, dihydrozeatin, and methyl jasmonate, was significantly lower in tetraploids than those in diploid controls, except indole acetic acid and abscisic acid, which could partly explain the dwarfness in hormonal regulation aspect. Moreover, as the typical secondary metabolites of garlic, organosulfur compounds including allicin, diallyl disulfide, and diallyl trisulfide accumulated a higher content significantly in tetraploids. The obtained dwarf genotype of autotetraploid garlic could bring new perspectives for the artificial polyploids breeding and be implemented as a new germplasm to facilitate investigation into whole-genome doubling consequences.
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Affiliation(s)
- Yanbin Wen
- College of Horticulture, Northwest A&F University, Xianyang, China
- Development Center of Fruit Vegetable and Herbal Tea, Datong, China
| | - Hongjiu Liu
- College of Horticulture, Northwest A&F University, Xianyang, China
| | - Huanwen Meng
- College of Horticulture, Northwest A&F University, Xianyang, China
| | - Lijun Qiao
- College of Horticulture, Northwest A&F University, Xianyang, China
| | - Guoqing Zhang
- Business School, Shanxi Datong University, Datong, China
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Xianyang, China
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9
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Cheng A, Mohd Hanafiah N, Harikrishna JA, Eem LP, Baisakh N, Mispan MS. A Reappraisal of Polyploidy Events in Grasses (Poaceae) in a Rapidly Changing World. BIOLOGY 2022; 11:biology11050636. [PMID: 35625365 PMCID: PMC9138248 DOI: 10.3390/biology11050636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Around 80% of megaflora species became extinct at the Cretaceous–Paleogene (K–Pg) boundary. Subsequent polyploidy events drove the survival of thousands of plant species and played a significant historical role in the development of the most successful modern cereal crops. However, current and rapid global temperature change poses an urgent threat to food crops worldwide, including the world’s big three cereals: rice, wheat, and maize, which are members of the grass family, Poaceae. Some minor cereals from the same family (such as teff) have grown in popularity in recent years, but there are important knowledge gaps regarding the similarities and differences between major and minor crops, including how polyploidy affects their biological processes under natural and (a)biotic stress conditions and thus the potential to harness polyploidization attributes for improving crop climate resilience. This review focuses on the impact of polyploidy events on the Poaceae family, which includes the world’s most important food sources, and discusses the past, present, and future of polyploidy research for major and minor crops. The increasing accessibility to genomes of grasses and their wild progenitors together with new tools and interdisciplinary research on polyploidy can support crop improvement for global food security in the face of climate change.
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Affiliation(s)
- Acga Cheng
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Noraikim Mohd Hanafiah
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Jennifer Ann Harikrishna
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Lim Phaik Eem
- Institute of Ocean and Earth Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- Correspondence: (N.B.); (M.S.M.)
| | - Muhamad Shakirin Mispan
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (N.B.); (M.S.M.)
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10
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Bomblies K. The quiet evolutionary response to cellular challenges. AMERICAN JOURNAL OF BOTANY 2022; 109:189-192. [PMID: 35170018 PMCID: PMC9304244 DOI: 10.1002/ajb2.1822] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Kirsten Bomblies
- Institute of Plant Molecular Biology, Department of Biology, ETH ZürichSwitzerland
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11
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Tossi VE, Martínez Tosar LJ, Laino LE, Iannicelli J, Regalado JJ, Escandón AS, Baroli I, Causin HF, Pitta-Álvarez SI. Impact of polyploidy on plant tolerance to abiotic and biotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:869423. [PMID: 36072313 PMCID: PMC9441891 DOI: 10.3389/fpls.2022.869423] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/25/2022] [Indexed: 05/04/2023]
Abstract
Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism's cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.
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Affiliation(s)
- Vanesa E. Tossi
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Leandro J. Martínez Tosar
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biotecnología, Alimentos, Agro y Ambiental (DEBAL), Facultad de Ingeniería y Ciencias Exactas, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Leandro E. Laino
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Jesica Iannicelli
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - José Javier Regalado
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Alejandro Salvio Escandón
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
| | - Irene Baroli
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Irene Baroli,
| | - Humberto Fabio Causin
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Humberto Fabio Causin,
| | - Sandra Irene Pitta-Álvarez
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- *Correspondence: Sandra Irene Pitta-Álvarez, ;
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12
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Reis AC, Chester M, de Sousa SM, Campos VR, de Queiroz Nascimento LS, Pacheco Júnior S, Franco AL, Viccini LF. Chromosomal view of Lippia alba, a tropical polyploid complex under genome stabilization process. PROTOPLASMA 2022; 259:33-46. [PMID: 33760982 DOI: 10.1007/s00709-021-01636-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Lippia alba is a phenotypically variable tropical shrub thought to comprise a young autopolyploid complex. Chromosome numbers in L. alba include 2n = 30, 38, 45, 60, and 90. High levels of chemical and phenotypic variation associated with economic and medicinal importance were reported. However, the genetic background including chromosome composition remains under-explored. Furthermore, the occurrence of at least four ploidal levels in L. alba and the lack of data for polyploid plants in tropical areas also merit further study of L. alba. Here we assessed the chromosome composition using two new satellite repeats (CL98 and CL66) applied as FISH probes to mitotic chromosomes, and we proposed to calculate the degree of homozygosis for CL66 satDNA (named as index h) and to associate it to meiotic instability. The CL98 mapping showed few variations in both number of signals and position. However, the levels of structural homozygosity for a satellite repeat CL66 were very variable. The numbers of CL66-bearing-chromosomes were under-represented in tetraploids relative to diploids implying that CL66 arrays have been lost in tetraploid lineages as a result of increased meiotic instability. High percentage of irregularities was observed in meiotic cells, especially in polyploids. L. alba complex comprised a mixture of homomorphic and heteromorphic chromosomes. Overall, the polyploid complex presents features typical of both young and older stable polyploids. It seems that L. alba genome is still in the process of stabilization.
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Affiliation(s)
- Aryane Campos Reis
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | - Saulo Marçal de Sousa
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Victória Rabelo Campos
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | | | | | - Ana Luiza Franco
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-900, Brazil.
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13
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Ferreira RCU, da Costa Lima Moraes A, Chiari L, Simeão RM, Vigna BBZ, de Souza AP. An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures. FRONTIERS IN PLANT SCIENCE 2021; 12:770461. [PMID: 34966402 PMCID: PMC8710810 DOI: 10.3389/fpls.2021.770461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
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Affiliation(s)
| | - Aline da Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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Zhao C, Zhang Y, Qin H, Wang C, Huang X, Yang L, Yu T, Xu X, Luo X, Qin Q, Liu S. Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus. BMC Ecol Evol 2021; 21:201. [PMID: 34740327 PMCID: PMC8569995 DOI: 10.1186/s12862-021-01918-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Background Autotetraploid Carassius auratus (4n = 200, RRRR) (abbreviated as 4nRR) is derived from whole genome duplication of Carassius auratus red var. (2n = 100, RR) (abbreviated as RCC). Ribosome DNA (rDNA) is often used to study molecular evolution of repeated sequences because it has high copy number and special conserved coding regions in genomes. In this study, we analysed the sequences (5S, ITS1-5.8S-ITS2 region), structure, methylation level (NTS and IGS), and expression level (5S and 18S) of 5S and 45S ribosomal RNA (rRNA) genes in 4nRR and RCC in order to elucidate the effects of autotetraploidization on rDNA in fish. Results Results showed that there was high sequence similarity of 5S, 5.8S and ITS1 region between 4nRR and RCC. This study also identified two different types of ITS2 region in 4nRR and predicted the secondary structure of ITS2. It turns out that both secondary structures are functional. Compared with RCC, there was no significant difference in NTS (5S rRNA) methylation level, but the expression level of 5S rRNA was lower in 4nRR, indicating that methylation had little effect on the expression level in 4nRR. IGS (45S rRNA) was hypermethylated in 4nRR compared to RCC, but the expression of 18S rRNA gene was no significantly different from that in RCC, indicating that methylation regulation affected gene expression in 4nRR. Conclusion The above studies initially revealed the effects of autotetraploidization on the structure and function of 5S and 45S rRNA in Carassius auratus, and provided a theoretical support for the systematic study of the evolution pattern and characteristics of rDNA in vertebrates.
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Affiliation(s)
- 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
| | - Yuxin Zhang
- 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
| | - 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
| | - Xu Huang
- 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
| | - Xidan Xu
- 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
| | - Xiang Luo
- 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
| | - 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.
| | - 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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15
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Yu X, Wang P, Li J, Zhao Q, Ji C, Zhu Z, Zhai Y, Qin X, Zhou J, Yu H, Cheng X, Isshiki S, Jahn M, Doyle JJ, Ottosen C, Bai Y, Cai Q, Cheng C, Lou Q, Huang S, Chen J. Whole-Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004222. [PMID: 33977063 PMCID: PMC8097326 DOI: 10.1002/advs.202004222] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/14/2021] [Indexed: 05/16/2023]
Abstract
The importance of allopolyploidy in plant evolution has been widely recognized. The genetic changes triggered by allopolyploidy, however, are not yet fully understood due to inconsistent phenomena reported across diverse species. The construction of synthetic polyploids offers a controlled approach to systematically reveal genomic changes that occur during the process of polyploidy. This study reports the first fully sequenced synthetic allopolyploid constructed from a cross between Cucumis sativus and C. hystrix, with high-quality assembly. The two subgenomes are confidently partitioned and the C. sativus-originated subgenome predominates over the C. hystrix-originated subgenome, retaining more sequences and showing higher homeologous gene expression. Most of the genomic changes emerge immediately after interspecific hybridization. Analysis of a series of genome sequences from several generations (S0, S4-S13) of C. ×hytivus confirms that genomic changes occurred in the very first generations, subsequently slowing down as the process of diploidization is initiated. The duplicated genome of the allopolyploid with double genes from both parents broadens the genetic base of C. ×hytivus, resulting in enhanced phenotypic plasticity. This study provides novel insights into plant polyploid genome evolution and demonstrates a promising strategy for the development of a wide array of novel plant species and varieties through artificial polyploidization.
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Affiliation(s)
- Xiaqing Yu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Panqiao Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Ji Li
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Qinzheng Zhao
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Changmian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou571101China
- Biomarker TechnologiesBeijing101300China
| | - Zaobing Zhu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Yufei Zhai
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Xiaodong Qin
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Junguo Zhou
- College of Horticulture and LandscapeHenan Institute of Science and TechnologyXinxiang453000China
| | - Haiyan Yu
- Biomarker TechnologiesBeijing101300China
| | | | - Shiro Isshiki
- Faculty of AgricultureSaga UniversitySaga840‐8502Japan
| | - Molly Jahn
- Jahn Research GroupUSDA/FPLMadisonWI53726USA
| | - Jeff J. Doyle
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell UniversityIthacaNY14853USA
| | | | - Yuling Bai
- Department of Plant SciencesWageningen University and ResearchWageningen6700 AJNetherlands
| | - Qinsheng Cai
- College of Life ScienceNanjing Agricultural UniversityNanjing210095China
| | - Chunyan Cheng
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Qunfeng Lou
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
| | - Sanwen Huang
- Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Jinfeng Chen
- National Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing210095China
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16
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Bomblies K. When everything changes at once: finding a new normal after genome duplication. Proc Biol Sci 2020; 287:20202154. [PMID: 33203329 PMCID: PMC7739491 DOI: 10.1098/rspb.2020.2154] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
Whole-genome duplication (WGD), which leads to polyploidy, is implicated in adaptation and speciation. But what are the immediate effects of WGD and how do newly polyploid lineages adapt to them? With many studies of new and evolved polyploids now available, along with studies of genes under selection in polyploids, we are in an increasingly good position to understand how polyploidy generates novelty. Here, I will review consistent effects of WGD on the biology of plants, such as an increase in cell size, increased stress tolerance and more. I will discuss how a change in something as fundamental as cell size can challenge the function of some cell types in particular. I will also discuss what we have learned about the short- to medium-term evolutionary response to WGD. It is now clear that some of this evolutionary response may 'lock in' traits that happen to be beneficial, while in other cases, it might be more of an 'emergency response' to work around physiological changes that are either deleterious, or cannot be undone in the polyploid context. Yet, other traits may return rapidly to a diploid-like state. Polyploids may, by re-jigging many inter-related processes, find a new, conditionally adaptive, normal.
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Affiliation(s)
- Kirsten Bomblies
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
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17
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Meeus S, Šemberová K, De Storme N, Geelen D, Vallejo-Marín M. Effect of Whole-Genome Duplication on the Evolutionary Rescue of Sterile Hybrid Monkeyflowers. PLANT COMMUNICATIONS 2020; 1:100093. [PMID: 33367262 PMCID: PMC7747968 DOI: 10.1016/j.xplc.2020.100093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/08/2020] [Accepted: 07/01/2020] [Indexed: 05/15/2023]
Abstract
Hybridization is a creative evolutionary force, increasing genomic diversity and facilitating adaptation and even speciation. Hybrids often face significant challenges to establishment, including reduced fertility that arises from genomic incompatibilities between their parents. Whole-genome duplication in hybrids (allopolyploidy) can restore fertility, cause immediate phenotypic changes, and generate reproductive isolation. Yet the survival of polyploid lineages is uncertain, and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions. Here, we use natural and synthetically produced hybrid and polyploid monkeyflowers (Mimulus spp.) to study how polyploidy contributes to the fertility, reproductive isolation, phenotype, and performance of hybrids in the field. We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents. The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication, in which plants have larger organs and are slower to flower. Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents, whereas natural hybrids have higher survival than all other taxa. We conclude that hybridization and polyploidy can act as sources of genomic novelty, but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.
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Affiliation(s)
- Sofie Meeus
- Department of Biological and Environmental Sciences. University of Stirling, Stirling FK9 4LA, UK
| | - Kristýna Šemberová
- Department of Botany, Charles University, 128 43 Prague 2, Czech Republic
| | - Nico De Storme
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Mario Vallejo-Marín
- Department of Biological and Environmental Sciences. University of Stirling, Stirling FK9 4LA, UK
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Walter GM, Abbott RJ, Brennan AC, Bridle JR, Chapman M, Clark J, Filatov D, Nevado B, Ortiz-Barrientos D, Hiscock SJ. Senecio as a model system for integrating studies of genotype, phenotype and fitness. THE NEW PHYTOLOGIST 2020; 226:326-344. [PMID: 31951018 DOI: 10.1111/nph.16434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically diverse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized diverse environments, often through rapid phenotypic divergence and adaptive radiation. These diverse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Adrian C Brennan
- School of Biological and Biomedical Sciences, University of Durham, Durham, DH1 3LE, UK
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Mark Chapman
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - James Clark
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | | | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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Julião SA, Ribeiro CDV, Lopes JML, de Matos EM, Reis AC, Peixoto PHP, Machado MA, Azevedo ALS, Grazul RM, de Campos JMS, Viccini LF. Induction of Synthetic Polyploids and Assessment of Genomic Stability in Lippia alba. FRONTIERS IN PLANT SCIENCE 2020; 11:292. [PMID: 32273876 PMCID: PMC7113378 DOI: 10.3389/fpls.2020.00292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Polyploidy is widely recognized as a major evolutionary force in plants and has been reported in the genus Lippia (Verbenaceae). Lippia alba, the most studied species, has been documented as a polyploid complex involving at least four ploidal levels. L. alba presents remarkable chemical and genetic variation and represents a model for understanding genome organization. Although the economic and medicinal importance of the species has been widely described, no established polyploid induction protocol has been reported so far. Here, we describe the production of synthetic polyploid plants of L. alba using colchicine. The ploidal levels were estimated by flow cytometry and chromosome counting. In addition, FISH and molecular markers approaches were used to confirm the stability of the synthetic polyploids. The major component of the essential oils was estimated by GCMS to compare with the natural individuals. Tetraploids and triploids were produced providing new opportunities for investigating medicinal, pharmacological, and economic applications as well as addressing intrinsic questions involved in the polyploidization process in tropical plants.
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Affiliation(s)
| | | | | | | | - Aryane Campos Reis
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Brazil
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20
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Levin DA. Plant speciation in the age of climate change. ANNALS OF BOTANY 2019; 124:769-775. [PMID: 31250895 PMCID: PMC6868396 DOI: 10.1093/aob/mcz108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/25/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Species diversity is likely to undergo a sharp decline in the next century. Perhaps as many as 33 % of all plant species may expire as a result of climate change. All parts of the globe will be impacted, and all groups of organisms will be affected. Hundreds of species throughout the world have already experienced local extinction. PERSPECTIVES While thousands of species may become extinct in the next century and beyond, species formation will still occur. I consider which modes of plant species formation are likely to prevail in the next 500 years. I argue that speciation primarily will involve mechanisms that produce reproductively isolated lineages within less (often much less) than 100 generations. I will not especially consider the human element in promoting species formation, because it will continue and because the conclusions presented here are unaffected by it. The impact of climate change may be much more severe and widespread. CONCLUSIONS The most common modes of speciation likely to be operative in the next 500 years ostensibly will be auto- and allopolyploidy. Polyploid species or the antecedents thereof can arise within two generations. Moreover, polyploids often have broader ecological tolerances, and are likely to be more invasive than are their diploid relatives. Polyploid species may themselves spawn additional higher level polyploids either through crosses with diploid species or between pre-existing polyploids. The percentage of polyploid species is likely to exceed 50 % within the next 500 years vs. 35 % today. The stabilized hybrid derivatives (homoploid hybrid speciation) could emerge within a hundred generations after species contact, as could speciation involving chromosomal rearrangements (and perhaps number), but the number of such events is likely to be low. Speciation involving lineage splitting will be infrequent because the formation of substantive pre- and post-zygotic barriers typically takes many thousands of years.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, USA
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21
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Oberprieler C, Talianova M, Griesenbeck J. Effects of polyploidy on the coordination of gene expression between organellar and nuclear genomes in Leucanthemum Mill. (Compositae, Anthemideae). Ecol Evol 2019; 9:9100-9110. [PMID: 31463007 PMCID: PMC6706232 DOI: 10.1002/ece3.5455] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/04/2019] [Accepted: 06/15/2019] [Indexed: 11/30/2022] Open
Abstract
Whole-genome duplications (WGD) through polyploid speciation are associated with disruptions of well-tuned relationships among the three plant cell genomes. Key metabolic processes comprising multi-subunit enzyme complexes, for which partner proteins are both nuclear- and plastid-encoded, are dependent on maintenance of stoichiometric ratios among the subunits to avoid cytonuclear imbalances after WGDs. By using qPCR for gene copy and transcript number quantification, we have studied the relationship of subunit expression in the two gene pairs rbcL/rbcS (the two subunits of RuBisCO) and psbA/psbO (two members of photosystem II) in closely related members of Leucanthemum (Compositae, Anthemideae), comprising a diploid, a tetraploid, and a hexaploid species. While gene copy numbers exhibit the expected pattern of an increase in the nuclear-encoded partner gene relative to the plastid-encoded one, we find that the two partner gene systems behave differently after WGD: While in the psbA/psbO partner gene system, shifts in the gene copy balance caused by polyploidization are not accommodated for through changes in transcription intensities of the two partner genes, the rbcL/rbcS system even shows an unexpected reversed dosage effect with up-regulated transcription intensities on both the nuclear and the plastidal side. We interpret the behavior of the psbA/psbO partner gene system as being due to the stoichiometrically relaxed relationship between the two gene products caused by a fast, damage-provoked combustion of the psbA gene product (the D1 core protein of PSII). Conversely, the finely tuned expression dependencies of the rbcL/rbcS system may be the reason for the observed positive feedback runaway signal as reaction to gene copy imbalances caused by a polyploidization shock.
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Affiliation(s)
- Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Martina Talianova
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
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22
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Mhiri C, Parisod C, Daniel J, Petit M, Lim KY, Dorlhac de Borne F, Kovarik A, Leitch AR, Grandbastien MA. Parental transposable element loads influence their dynamics in young Nicotiana hybrids and allotetraploids. THE NEW PHYTOLOGIST 2019; 221:1619-1633. [PMID: 30220091 DOI: 10.1111/nph.15484] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/06/2018] [Indexed: 05/29/2023]
Abstract
The genomic shock hypothesis suggests that allopolyploidy is associated with genome changes driven by transposable elements, as a response to imbalances between parental insertion loads. To explore this hypothesis, we compared three allotetraploids, Nicotiana arentsii, N. rustica and N. tabacum, which arose over comparable time frames from hybridisation between increasingly divergent diploid species. We used sequence-specific amplification polymorphism (SSAP) to compare the dynamics of six transposable elements in these allopolyploids, their diploid progenitors and in corresponding synthetic hybrids. We show that element-specific dynamics in young Nicotiana allopolyploids reflect their dynamics in diploid progenitors. Transposable element mobilisation is not concomitant with immediate genome merger, but occurs within the first generations of allopolyploid formation. In natural allopolyploids, such mobilisations correlate with imbalances in the repeat profile of the parental species, which increases with their genetic divergence. Other restructuring leading to locus loss is immediate, nonrandom and targeted at specific subgenomes, independently of cross orientation. The correlation between transposable element mobilisation in allopolyploids and quantitative imbalances in parental transposable element loads supports the genome shock hypothesis proposed by McClintock.
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Affiliation(s)
- Corinne Mhiri
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Christian Parisod
- Ecological Genomics, Institute of Plant Sciences, University of Bern, Bern, CH-3013, Switzerland
| | - Julien Daniel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Maud Petit
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - K Yoong Lim
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | | | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Marie-Angèle Grandbastien
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
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23
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Amah D, van Biljon A, Maziya-Dixon B, Labuschagne M, Swennen R. Effects of In Vitro Polyploidization on Agronomic Characteristics and Fruit Carotenoid Content; Implications for Banana Genetic Improvement. FRONTIERS IN PLANT SCIENCE 2019; 10:1450. [PMID: 31781149 PMCID: PMC6861373 DOI: 10.3389/fpls.2019.01450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 10/17/2019] [Indexed: 05/08/2023]
Abstract
Bananas (Musa spp.), native to South East Asia, have spread worldwide and are integrated into the diets of millions of people in tropical regions. Carotenoid content varies dramatically between different banana genotypes, providing an opportunity for vitamin A biofortification. Polyploidization is a useful tool for crop improvement with potential to generate new diversity, especially in a polyploid crop like bananas. Ten induced tetraploids generated from six diploid banana genotypes were evaluated for their agronomic attributes and fruit carotenoid content in comparison to their diploid progenitors. Tetraploids had distinct plant morphology, but generally displayed inferior vegetative and yield characteristics with 20% lower bunch weights than their original diploids. Similarly, a 50% decrease in fruit provitamin A carotenoids (α-carotene, 13-cis β-carotene, 9-cis β-carotene, trans-β-carotene) accompanied by a corresponding increase in lutein was recorded in induced tetraploids in comparison to their original diploids. Additionally, all lines were subjected to pollen viability tests to assess their fertility. Pollen viability tests indicated over 70% viability for induced tetraploids and diploid controls, suggesting their possible use in crosses. These findings provide a basis for the application of induced polyploidization in bananas to generate useful genetic material for integration in hybridization programmes aiming to produce vitamin A enriched triploids valuable to malnourished populations.
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Affiliation(s)
- Delphine Amah
- Plantain and Banana Improvement Program, International Institute of Tropical Agriculture, Ibadan, Nigeria
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
- *Correspondence: Delphine Amah,
| | - Angeline van Biljon
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
| | - Bussie Maziya-Dixon
- Food and Nutrition Sciences Laboratory, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Maryke Labuschagne
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
| | - Rony Swennen
- International Institute of Tropical Agriculture, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- Laboratory of Tropical Crop Improvement, Bioversity International, Heverlee, Belgium
- Department of Biosystems, KU Leuven, Heverlee, Belgium
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24
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Čertner M, Sudová R, Weiser M, Suda J, Kolář F. Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in Knautia serpentinicola (Caprifoliaceae). THE NEW PHYTOLOGIST 2019; 221:1117-1127. [PMID: 30221362 DOI: 10.1111/nph.15426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
Whole genome duplication is a key process in plant evolution and has direct phenotypic consequences. However, it remains unclear whether ploidy-related phenotypic changes can significantly alter the fitness of polyploids in nature and thus contribute to establishment of new polyploid mutants in diploid populations. We addressed this question using a unique natural system encompassing a diploid and its sympatric locally established autotetraploid derivative. By setting a common garden experiment with two manipulated environmental factors (presence/absence of serpentine substrate and competition), we tested whether these two locally important factors differently shape the phenotypic response of the two ploidy levels. Tetraploids attained significantly higher values of both above- and below-ground biomass, and root : shoot ratio compared to their diploid progenitors. Tetraploid superiority in vegetative fitness indicators was most prominent when they were cultivated together with a competitor in nutrient-rich nonserpentine substrate. We show that even genetically very closely related diploids and tetraploids can respond differently to key environmental factors. Provided there are sufficient nutrients, tetraploids can be more successful in tolerating interspecific competition than their diploid progenitors. Such superior performance might have provided an adaptive advantage for the newly established tetraploid promoting colonisation of new (micro-)habitats, which was indeed observed at the natural site.
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Affiliation(s)
- Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Radka Sudová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Martin Weiser
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43, Průhonice, Czech Republic
- Institute of Botany, University of Innsbruck, AT-6020, Innsbruck, Austria
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25
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Zhao L, Han L, Xiao C, Lin X, Xu C, Yang C. Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids. BMC Genomics 2018; 19:756. [PMID: 30340512 PMCID: PMC6194744 DOI: 10.1186/s12864-018-5150-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partitioning of duplicated genes among different tissues. Many studies of the tissue-specific homeolog expression partitioning have focused on allopolyploids that have very different parental genomes, while few studies have focused on autopolyploids or allopolyploids that have similar parental genomes. Results In this study, we used a set of reciprocal F1 hybrids and synthetic tetraploids constructed from subspecies (japonica and indica) of Asian rice (Oryza sativa L.) as a model to gain insights into the expression partitioning of homeologs among tissues in a developmental context. We assayed the tissue-specific silencing (TSS) of the parental homeologs of 30 key genes in the hybrids and tetraploids relative to the in vitro “hybrids” (parental mixes) using Sequenom MassARRAY. We found that the parental mix and synthetic tetraploids had higher frequencies of homeolog TSS than the F1, revealing an instantaneous role of WGD on homeolog expression partitioning. Conclusions Our observations contradicted those of previous studies in which newly formed allopolyploids had a low TSS frequency, similar to that of F1 hybrids, suggesting that the impact of WGD on homeolog expression requires a longer time to manifest. In addition, we found that the TSS frequency in the tetraploids varied at different growth stages and that roots had a much higher frequency of TSS than leaves, which indicated that developmental and metabolic traits may influence the expression states of duplicated genes in newly formed plant polyploids. Electronic supplementary material The online version of this article (10.1186/s12864-018-5150-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Long Zhao
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Han
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chaoxia Xiao
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunwu Yang
- Key laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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26
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Hojsgaard D. Transient Activation of Apomixis in Sexual Neotriploids May Retain Genomically Altered States and Enhance Polyploid Establishment. FRONTIERS IN PLANT SCIENCE 2018; 9:230. [PMID: 29535745 PMCID: PMC5834478 DOI: 10.3389/fpls.2018.00230] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/09/2018] [Indexed: 05/19/2023]
Abstract
Polyploid genomes evolve and follow a series of dynamic transfigurations along with adaptation and speciation. The initial formation of a new polyploid individual within a diploid population usually involves a triploid bridge, a two-step mechanism of cell fusions between ubiquitous (reduced) and rare (unreduced) gametes. The primary fusion event creates an intermediate triploid individual with unbalanced genome sets, a situation of genomic-shock characterized by gene expression dysregulation, high dosage sensitivity, disturbed cell divisions, and physiological and reproductive attributes drastically altered. This near-sterile neotriploid must produce (even) eupolyploids through secondary fusion events to restore genome steadiness, meiotic balance, and fertility required for the demographic establishment of a nascent lineage. Natural conditions locate several difficulties to polyploid establishment, including the production of highly unbalanced and rarely unreduced (euploid) gametes, frequency-dependent disadvantages (minority cytotype exclusion), severe fitness loss, and ecological competition with diploid parents. Persistence and adaptation of neopolyploids depend upon genetic and phenotypic novelty coupled to joint selective forces that preserve shock-induced genomic changes (subgenome homeolog partitioning) and drive meiotic (reproductive) stabilization and ecological diversification. Thus, polyploid establishment through the triploid bridge is a feasible but not ubiquitous process that requires a number of low-probability events and singular circumstances. Yet, frequencies of polyploids suggest that polyploid establishment is a pervasive process. To explain this disparity, and supported in experimental evidence, I propose that situations like hybridization and ploidy-state transitions associated to genomic shock and substantial developmental alterations can transiently activate apomixis as a mechanism to halt genomic instability and cancel factors restraining neopolyploid's sexual fertility, particularly in triploids. Apomixis -as a temporal alternative to sex- skip meiosis and syngamy, and thus can freeze genomic attributes, avoid unbalanced chromosomal segregation and increase the formation of unreduced euploid gametes, elude frequency-dependent reproductive disadvantages by parthenogenetic development of the embryo and permissive development of endosperm during seed formation, and increase the effective population size of the neopolyploid lineage favoring the formation rate of eupolyploids compared to aneuploids. The subsequent action of genome resilience mechanisms that alleviate transcriptomic shock and selection upon gene interactions might restore a stable meiosis and sexual fertility within few generations, as observed in synthetic polyploids. Alternatively, provided that resilience mechanisms fail, the neopolyploid might retain apomixis and hold genomically and transcriptionally altered states for many generations.
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Affiliation(s)
- Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, Georg August University of Göttingen, Göttingen, Germany
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27
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Powell AF, Doyle JJ. Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors. Genes (Basel) 2017; 8:E357. [PMID: 29189710 PMCID: PMC5748675 DOI: 10.3390/genes8120357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/29/2022] Open
Abstract
Root nodule symbioses (nodulation) and whole genome duplication (WGD, polyploidy) are both important phenomena in the legume family (Leguminosae). Recently, it has been proposed that polyploidy may have played a critical role in the origin or refinement of nodulation. However, while nodulation and polyploidy have been studied independently, there have been no direct studies of mechanisms affecting the interactions between these phenomena in symbiotic, nodule-forming species. Here, we examined the transcriptome-level responses to inoculation in the young allopolyploid Glycine dolichocarpa (T2) and its diploid progenitor species to identify underlying processes leading to the enhanced nodulation responses previously identified in T2. We assessed the differential expression of genes and, using weighted gene co-expression network analysis (WGCNA), identified modules associated with nodulation and compared their expression between species. These transcriptomic analyses revealed patterns of non-additive expression in T2, with evidence of transcriptional responses to inoculation that were distinct from one or both progenitors. These differential responses elucidate mechanisms underlying the nodulation-related differences observed between T2 and the diploid progenitors. Our results indicate that T2 has reduced stress-related transcription, coupled with enhanced transcription of modules and genes implicated in hormonal signaling, both of which are important for nodulation.
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Affiliation(s)
- Adrian F Powell
- Section of Plant Biology, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
- Boyce Thompson Institute, Ithaca, NY 14853, USA.
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853, USA.
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28
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Abstract
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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29
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Čertner M, Fenclová E, Kúr P, Kolář F, Koutecký P, Krahulcová A, Suda J. Evolutionary dynamics of mixed-ploidy populations in an annual herb: dispersal, local persistence and recurrent origins of polyploids. ANNALS OF BOTANY 2017; 120:303-315. [PMID: 28398545 PMCID: PMC5737363 DOI: 10.1093/aob/mcx032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/08/2017] [Indexed: 05/18/2023]
Abstract
Background and Aims Despite the recent wealth of studies targeted at contact zones of cytotypes in various species, some aspects of polyploid evolution are still poorly understood. This is especially the case for the frequency and success rate of spontaneous neopolyploidization or the temporal dynamics of ploidy coexistence, requiring massive ploidy screening and repeated observations, respectively. To fill this gap, an extensive study of spatio-temporal patterns of ploidy coexistence was initiated in the widespread annual weed Tripleurospermum inodorum (Asteraceae). Methods DNA flow cytometry along with confirmatory chromosome counts was employed to assess ploidy levels of 11 018 adult individuals and 1263 ex situ germinated seedlings from 1209 Central European populations. The ploidy screening was conducted across three spatial scales and supplemented with observations of temporal development of 37 mixed-ploidy populations. Key Results The contact zone between the diploid and tetraploid cytotypes has a diffuse, mosaic-like structure enabling common cytotype coexistence from the within-population to the landscape level. A marked difference in monoploid genome size between the two cytotypes enabled the easy distinction of neotetraploid mutants from long-established tetraploids. Neotetraploids were extremely rare (0·03 %) and occurred solitarily. Altogether five ploidy levels (2 x -6 x ) and several aneuploids were discovered; the diversity in nuclear DNA content was highest in early ontogenetic stages (seedlings) and among individuals from mixed-ploidy populations. In spite of profound temporal oscillations in cytotype frequencies in mixed-ploidy populations, both diploids and tetraploids usually persisted up to the last census. Conclusions Diploids and tetraploids commonly coexist at all spatial scales and exhibit considerable temporal stability in local ploidy mixtures. Mixed-ploidy populations containing fertile triploid hybrids probaby act as effective generators of cytogenetic novelty and may facilitate inter-ploidy gene flow. Neopolyploid mutants were incapable of local establishment.
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Affiliation(s)
- Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00 Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Eliška Fenclová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00 Prague, Czech Republic
| | - Pavel Kúr
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00 Prague, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00 Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
- National Centre for Biosystematics, Natural History Museum, University of Oslo, NO-0318 Oslo, Norway
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic
| | - Anna Krahulcová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00 Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
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Münzbergová Z. Colchicine application significantly affects plant performance in the second generation of synthetic polyploids and its effects vary between populations. ANNALS OF BOTANY 2017; 120:329-339. [PMID: 28633349 PMCID: PMC5737759 DOI: 10.1093/aob/mcx070] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/12/2017] [Indexed: 05/05/2023]
Abstract
Background and Aims Understanding the direct consequences of polyploidization is necessary for assessing the evolutionary significance of this mode of speciation. Previous studies have not studied the degree of between-population variation that occurs due to these effects. Although it is assumed that the effects of the substances that create synthetic polyploids disappear in second-generation synthetic polyploids, this has not been tested. Methods The direct consequences of polyploidization were assessed and separated from the effects of subsequent evolution in Vicia cracca , a naturally occurring species with diploid and autotetraploid cytotypes. Synthetic tetraploids were created from diploids of four mixed-ploidy populations. Performance of natural diploids and tetraploids was compared with that of synthetic tetraploids. Diploid offspring of the synthetic tetraploid mothers were also included in the comparison. In this way, the effects of colchicine application in the maternal generation on offspring performance could be compared independently of the effects of polyploidization. Key Results The sizes of seeds and stomata were primarily affected by cytotype, while plant performance differed between natural and synthetic polyploids. Most performance traits were also determined by colchicine application to the mothers, and most of these results were largely population specific. Conclusions Because the consequences of colchicine application are still apparent in the second generation of the plants, at least the third-generation polyploids should be considered in future comparisons. The specificities of the colchicine-treated plants may also be caused by strong selection pressures during the creation of synthetic polyploids. This could be tested by comparing the initial sizes of plants that survived the colchicine treatments with those of plants that did not. High variation between populations also suggests that different polyploids follow different evolutionary trajectories, and this should be considered when studying the effects of polyploidization.
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Affiliation(s)
- Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
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Chen ECH, Morin A, Chauchat JH, Sankoff D. Statistical analysis of fractionation resistance by functional category and expression. BMC Genomics 2017; 18:366. [PMID: 28589858 PMCID: PMC5461532 DOI: 10.1186/s12864-017-3736-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background The current literature establishes the importance of gene functional category and expression in promoting or suppressing duplicate gene loss after whole genome doubling in plants, a process known as fractionation. Inspired by studies that have reported gene expression to be the dominating factor in preventing duplicate gene loss, we analyzed the relative effect of functional category and expression. Methods We use multivariate methods to study data sets on gene retention, function and expression in rosids and asterids to estimate effects and assess their interaction. Results Our results suggest that the effect on duplicate gene retention fractionation by functional category and expression are independent and have no statistical interaction. Conclusion In plants, functional category is the more dominant factor in explaining duplicate gene loss.
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Affiliation(s)
- Eric C H Chen
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, K1N 6N5, Canada
| | - Annie Morin
- Department of Computer Science, Université de Rennes 1, Rennes Cedex, 69676, France
| | | | - David Sankoff
- Department of Mathematics and Statistics, 585 King Edward, Ottawa, K1N 6N5, Canada.
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32
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Blaine Marchant D, Soltis DE, Soltis PS. Patterns of abiotic niche shifts in allopolyploids relative to their progenitors. THE NEW PHYTOLOGIST 2016; 212:708-718. [PMID: 27399976 DOI: 10.1111/nph.14069] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/23/2016] [Indexed: 05/05/2023]
Abstract
Polyploidy has extensive genetic, physiological, morphological, and ecological ramifications. While the patterns underlying the genetic and morphological consequences of polyploidy are being rapidly elucidated, the effects on ecological niche are still largely unknown. This study investigated 13 allopolyploid systems in North America (10 ferns and three angiosperms) using digitized natural history museum specimens. The abiotic niches of the allopolyploids were compared with those of their diploid progenitors using ecological niche modeling, niche analyses, and multivariate analyses. We identified four patterns of niche shifts through our analyses: niche expansion, niche contraction, niche intermediacy, and niche novelty. The classification of these shifts depended on the amount of niche overlap and breadth between the polyploid and progenitors. The most common niche shift was niche intermediacy in which the polyploid inhabited a geographic range between that of the progenitors and had a high degree of niche overlap. Each polyploid had at least partial geographic sympatry and abiotic niche overlap with one of its progenitors, suggesting that biotic and/or microclimate factors may play a larger role in polyploid establishment than previously hypothesized. This study provides a baseline for future comparisons of the diverse outcomes of genome merger and duplication on abiotic niche preference.
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Affiliation(s)
- D Blaine Marchant
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Florida Museum of Natural History, Gainesville, FL, 32611, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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33
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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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Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat. Sci Rep 2016; 6:26363. [PMID: 27198893 PMCID: PMC4873831 DOI: 10.1038/srep26363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/27/2016] [Indexed: 11/08/2022] Open
Abstract
Allopolyploidy often triggers phenotypic novelty and gene expression remolding in the resulting polyploids. In this study, we employed multiple phenotypic and genetic approaches to investigate the nature and consequences of allotetraploidization between A- and S-subgenome of tetraploid wheat. Results showed that karyotype of the nascent allopolyploid plants (AT2) is stable but they showed clear novelty in multiple morphological traits which might have positively contributed to the initial establishment of the tetraploids. Further microarray-based transcriptome profiling and gene-specific cDNA-pyrosequencing have documented that transcriptome shock was exceptionally strong in AT2, but a substantial proportion of the induced expression changes was rapidly stabilized in early generations. Meanwhile, both additive and nonadditive expression genes showed extensive homeolog expression remodeling and which have led to the subgenome expression dominance in leaf and young inflorescence of AT2. Through comparing the homeolog-expressing patterns between synthetic and natural tetraploid wheats, it appears that the shock-induced expression changes at both the total expression level and subgenome homeolog partitioning are evolutionarily persistent. Together, our study shed new light on how gene expression changes have rapidly occurred at the initial stage following allotetraploidization, as well as their evolutionary relevance, which may have implications for wheat improvements.
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35
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Yant L, Bomblies K. Genome management and mismanagement--cell-level opportunities and challenges of whole-genome duplication. Genes Dev 2016; 29:2405-19. [PMID: 26637526 PMCID: PMC4691946 DOI: 10.1101/gad.271072.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Whole-genome duplication (WGD) doubles the DNA content in the nucleus and leads to polyploidy. In this review, Yant and Bomblies discuss both the adaptive potential and problems associated with WGD, focusing primarily on cellular effects. Whole-genome duplication (WGD) doubles the DNA content in the nucleus and leads to polyploidy. In whole-organism polyploids, WGD has been implicated in adaptability and the evolution of increased genome complexity, but polyploidy can also arise in somatic cells of otherwise diploid plants and animals, where it plays important roles in development and likely environmental responses. As with whole organisms, WGD can also promote adaptability and diversity in proliferating cell lineages, although whether WGD is beneficial is clearly context-dependent. WGD is also sometimes associated with aging and disease and may be a facilitator of dangerous genetic and karyotypic diversity in tumorigenesis. Scaling changes can affect cell physiology, but problems associated with WGD in large part seem to arise from problems with chromosome segregation in polyploid cells. Here we discuss both the adaptive potential and problems associated with WGD, focusing primarily on cellular effects. We see value in recognizing polyploidy as a key player in generating diversity in development and cell lineage evolution, with intriguing parallels across kingdoms.
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Affiliation(s)
- Levi Yant
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
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36
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Lazebnik Y. The shock of being united and symphiliosis. Another lesson from plants? Cell Cycle 2015; 13:2323-9. [PMID: 25483182 DOI: 10.4161/cc.29704] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Yuri Lazebnik
- a Yale Cardiovascular Research Center; New Haven, CT USA
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37
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Vallejo-Marín M, Buggs RJA, Cooley AM, Puzey JR. Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus. Evolution 2015; 69:1487-1500. [PMID: 25929999 PMCID: PMC5033005 DOI: 10.1111/evo.12678] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Abstract
Whole genome duplication (polyploidization) is a mechanism of “instantaneous” species formation that has played a major role in the evolutionary history of plants. Much of what we know about the early evolution of polyploids is based upon studies of a handful of recently formed species. A new polyploid hybrid (allopolyploid) species Mimulus peregrinus, formed within the last 140 years, was recently discovered on the Scottish mainland and corroborated by chromosome counts. Here, using targeted, high‐depth sequencing of 1200 genic regions, we confirm the parental origins of this new species from M. x robertsii, a sterile triploid hybrid between the two introduced species M. guttatus and M. luteus that are naturalized and widespread in the United Kingdom. We also report a new population of M. peregrinus on the Orkney Islands and demonstrate that populations on the Scottish mainland and Orkney Islands arose independently via genome duplication from local populations of M. x robertsii. Our data raise the possibility that some alleles are already being lost in the evolving M. peregrinus genomes. The recent origins of a new species of the ecological model genus Mimulus via allopolyploidization provide a powerful opportunity to explore the early stages of hybridization and genome duplication in naturally evolved lineages.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington, 99362
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, 23185
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38
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Asbe A, Matsushita SC, Gordon S, Kirkpatrick HE, Madlung A. Floral Reversion in Arabidopsis suecica Is Correlated with the Onset of Flowering and Meristem Transitioning. PLoS One 2015; 10:e0127897. [PMID: 26011630 PMCID: PMC4444321 DOI: 10.1371/journal.pone.0127897] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/20/2015] [Indexed: 12/13/2022] Open
Abstract
Angiosperm flowers are usually determinate structures that may produce seeds. In some species, flowers can revert from committed flower development back to an earlier developmental phase in a process called floral reversion. The allopolyploid Arabidopsis suecica displays photoperiod-dependent floral reversion in a subset of its flowers, yet little is known about the environmental conditions enhancing this phenotype, or the morphological processes leading to reversion. We have used light and electron microscopy to further describe this phenomenon. Additionally, we have further studied the phenology of flowering and floral reversion in A. suecica. In this study we confirm and expand upon our previous findings that floral reversion in the allopolyploid A. suecica is photoperiod-dependent, and show that its frequency is correlated with the timing for the onset of flowering. Our results also suggest that floral reversion in A. suecica displays natural variation in its penetrance between geographic populations of A. suecica.
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Affiliation(s)
- Amelia Asbe
- Department of Biology, University of Puget Sound, Tacoma, Washington, United States of America
| | - Starr C. Matsushita
- Department of Biology, University of Puget Sound, Tacoma, Washington, United States of America
| | - Spencer Gordon
- Department of Biology, University of Puget Sound, Tacoma, Washington, United States of America
| | - H. E. Kirkpatrick
- Department of Biology, University of Puget Sound, Tacoma, Washington, United States of America
| | - Andreas Madlung
- Department of Biology, University of Puget Sound, Tacoma, Washington, United States of America
- * E-mail:
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39
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Li Y, Sarkar FH. Targeting Epigenetically Deregulated miRNA by Nutraceuticals: Focusing on Cancer Prevention and Treatment. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40495-015-0016-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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Variation in transcriptome size: are we getting the message? Chromosoma 2014; 124:27-43. [DOI: 10.1007/s00412-014-0496-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/30/2022]
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41
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Abstract
Hexaploid bread wheat (Triticum aestivum L., genome BBAADD) is generally more salt tolerant than its tetraploid wheat progenitor (Triticum turgidum L.). However, little is known about the physiological basis of this trait or about the relative contributions of allohexaploidization and subsequent evolutionary genetic changes on the trait development. Here, we compared the salt tolerance of a synthetic allohexaploid wheat (neo-6x) with its tetraploid (T. turgidum; BBAA) and diploid (Aegilops tauschii; DD) parents, as well as a natural hexaploid bread wheat (nat-6x). We studied 92 morphophysiological traits and analyzed homeologous gene expression of a major salt-tolerance gene High-Affinity K(+) Transporter 1;5 (HKT1;5). We observed that under salt stress, neo-6x exhibited higher fitness than both of its parental genotypes due to inheritance of favorable traits like higher germination rate from the 4x parent and the stronger root Na(+) retention capacity from the 2x parent. Moreover, expression of the D-subgenome HKT1;5 homeolog, which is responsible for Na(+) removal from the xylem vessels, showed an immediate transcriptional reprogramming following allohexaploidization, i.e., from constitutive high basal expression in Ae. tauschii (2x) to salt-induced expression in neo-6x. This phenomenon was also witnessed in the nat-6x. An integrated analysis of 92 traits showed that, under salt-stress conditions, neo-6x resembled more closely the 2x than the 4x parent, suggesting that the salt stress induces enhanced expressivity of the D-subgenome homeologs in the synthetic hexaploid wheat. Collectively, the results suggest that condition-dependent functionalization of the subgenomes might have contributed to the wide-ranging adaptability of natural hexaploid wheat.
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42
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Zerulla K, Soppa J. Polyploidy in haloarchaea: advantages for growth and survival. Front Microbiol 2014; 5:274. [PMID: 24982654 PMCID: PMC4056108 DOI: 10.3389/fmicb.2014.00274] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 05/19/2014] [Indexed: 02/02/2023] Open
Abstract
The investigated haloarchaeal species, Halobacterium salinarum, Haloferax mediterranei, and H. volcanii, have all been shown to be polyploid. They contain several replicons that have independent copy number regulation, and most have a higher copy number during exponential growth phase than in stationary phase. The possible evolutionary advantages of polyploidy for haloarchaea, most of which have experimental support for at least one species, are discussed. These advantages include a low mutation rate and high resistance toward X-ray irradiation and desiccation, which depend on homologous recombination. For H. volcanii, it has been shown that gene conversion operates in the absence of selection, which leads to the equalization of genome copies. On the other hand, selective forces might lead to heterozygous cells, which have been verified in the laboratory. Additional advantages of polyploidy are survival over geological times in halite deposits as well as at extreme conditions on earth and at simulated Mars conditions. Recently, it was found that H. volcanii uses genomic DNA as genetic material and as a storage polymer for phosphate. In the absence of phosphate, H. volcanii dramatically decreases its genome copy number, thereby enabling cell multiplication, but diminishing the genetic advantages of polyploidy. Stable storage of phosphate is proposed as an alternative driving force for the emergence of DNA in early evolution. Several additional potential advantages of polyploidy are discussed that have not been addressed experimentally for haloarchaea. An outlook summarizes selected current trends and possible future developments.
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Affiliation(s)
- Karolin Zerulla
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
| | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
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43
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Moghe GD, Shiu SH. The causes and molecular consequences of polyploidy in flowering plants. Ann N Y Acad Sci 2014; 1320:16-34. [PMID: 24903334 DOI: 10.1111/nyas.12466] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polyploidy is an important force shaping plant genomes. All flowering plants are descendants of an ancestral polyploid species, and up to 70% of extant vascular plant species are believed to be recent polyploids. Over the past century, a significant body of knowledge has accumulated regarding the prevalence and ecology of polyploid plants. In this review, we summarize our current understanding of the causes and molecular consequences of polyploidization in angiosperms. We also provide a discussion on the relationships between polyploidy and adaptation and suggest areas where further research may provide a better understanding of polyploidy.
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44
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Bombarely A, Coate JE, Doyle JJ. Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ 2014; 2:e391. [PMID: 24883252 PMCID: PMC4034613 DOI: 10.7717/peerj.391] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/01/2014] [Indexed: 12/18/2022] Open
Abstract
Allopolyploidy combines two progenitor genomes in the same nucleus. It is a common speciation process, especially in plants. Deciphering the origins of polyploid species is a complex problem due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. Among the perennial species of Glycine, the plant genus that includes the cultivated soybean (G. max), are eight allopolyploid species, three of which are studied here. Previous crossing studies and molecular systematic results from two nuclear gene sequences led to hypotheses of origin for these species from among extant diploid species. We use several phylogenetic and population genomics approaches to clarify the origins of the genomes of three of these allopolyploid species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that all three polyploid species are fixed hybrids combining the genomes of the two putative parents hypothesized on the basis of previous work. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also are consistent with multiple origins for these allopolyploid species, and suggest that origins occurred within the last several hundred thousand years.
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Affiliation(s)
| | - Jeremy E Coate
- Department of Biology, Reed College , Portland, OR , USA
| | - Jeff J Doyle
- Department of Plant Biology, Cornell University , Ithaca, NY , USA
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45
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Noyes RD, Wagner JD. Dihaploidy yields diploid apomicts and parthenogens in Erigeron (Asteraceae). AMERICAN JOURNAL OF BOTANY 2014; 101:865-74. [PMID: 24752887 DOI: 10.3732/ajb.1400008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 03/27/2014] [Indexed: 05/23/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Dihaploids result when tetraploids produce reduced eggs that develop without fertilization into diploid progeny. This process is useful for reducing genome complexity and studying trait expression at different ploidal levels. In this study we evaluated genetic inheritance and expression of diplospory (D) and parthenogenesis (P) in a population of dihaploids produced by tetraploid apomictic Erigeron• METHODS From 400 mostly maternal (tetraploid) progeny, we identified 64 (16%) dihaploids with 2n = 18 (53 plants) or 2n = 19 (11 plants). Differential interference contrast (DIC) imaging of ovules was used to evaluate megasporogenesis (meiosis vs. diplospory) and capacity for parthenogenetic embryo development. Seed production was estimated as the proportion of filled seeds.• KEY RESULTS For 60 analyzed dihaploids, diplospory vs. meiosis segregated approximately 1: 1 (P = 0.44) while all exhibited parthenogenetic embryo development. Parthenogenesis for meiotic progeny (n = 27) was observed in approximately 50% of ovules. Apomictic dihaploids (combining D and P; n = 33) produced seeds with mean 24.8% (range 1.3-74.4%) of total flowers.• CONCLUSIONS The dihaploid population consisted of half apomicts (D + P) and half parthenogens (P only). We infer that formation of dihaploid seeds requires the parthenogenesis locus. The highest seed values obtained for diploid apomicts are comparable to those recorded for wild type polyploid apomicts. This is one of the first reports of diploid apomixis in the Asteraceae and it demonstrates that both diplospory and parthenogenesis can be transmitted and expressed at a high level in the diploid condition.
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Affiliation(s)
- Richard D Noyes
- Department of Biology, University of Central Arkansas, Conway, Arkansas 72035 USA
| | - Jennifer D Wagner
- Department of Biology, University of Central Arkansas, Conway, Arkansas 72035 USA
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47
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet 2014; 5:87. [PMID: 24795749 PMCID: PMC4007016 DOI: 10.3389/fgene.2014.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 12/29/2022] Open
Abstract
Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of ChicagoChicago, IL, USA
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48
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Rusin LY, Lyubetskaya EV, Gorbunov KY, Lyubetsky VA. Reconciliation of gene and species trees. BIOMED RESEARCH INTERNATIONAL 2014; 2014:642089. [PMID: 24800245 PMCID: PMC3985182 DOI: 10.1155/2014/642089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 11/27/2013] [Indexed: 11/18/2022]
Abstract
The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.
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Affiliation(s)
- L. Y. Rusin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia
- Faculty of Biology, Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia
| | - E. V. Lyubetskaya
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia
| | - K. Y. Gorbunov
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia
| | - V. A. Lyubetsky
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia
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