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Li J, Yang X, Liu F, Liu X, Zhao T, Yan X, Pang Q. Redox Regulation of Salt Tolerance in Eutrema salsugineum by Proteomics. Int J Mol Sci 2023; 24:14518. [PMID: 37833966 PMCID: PMC10572166 DOI: 10.3390/ijms241914518] [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: 08/08/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Salt stress severely restricts plant growth and crop production, which is accompanied by accumulation of reactive oxygen species (ROS) that disturb cell redox homeostasis and oxidize redox-sensitive proteins. Eutrema salsugineum, a halophytic species closely related to Arabidopsis, shows a high level of tolerance to salinity and is increasingly used as a model plant in abiotic stress biology. To understand redox modifications and signaling pathways under salt stress, we used tandem mass tag (TMT)-based proteomics to quantify the salt-induced changes in protein redox modifications in E. salsugineum. Salt stress led to increased oxidative modification levels of 159 cysteine sites in 107 proteins, which play roles in carbohydrate and energy metabolism, transport, ROS homeostasis, cellular structure modulation, and folding and assembly. These lists of unknown redox reactive proteins in salt mustard lay the foundation for future research to understand the molecular mechanism of plant salt response. However, glutathione peroxidase (GPX) is one of the most important antioxidant enzymes in plants. Our research indicates that EsGPX may be involved in regulating ROS levels and that plants with overexpressed EsGPX have much improved salt tolerance.
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Affiliation(s)
- Jiawen Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Xiaomin Yang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Fuqing Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Xinxin Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Tong Zhao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
| | - Xiufeng Yan
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Qiuying Pang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China; (J.L.); (X.Y.); (F.L.); (X.L.); (T.Z.)
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2
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Xiao M, Hao G, Guo X, Feng L, Lin H, Yang W, Chen Y, Zhao K, Xiang L, Jiang X, Mei D, Hu Q. A high-quality chromosome-level Eutrema salsugineum genome, an extremophile plant model. BMC Genomics 2023; 24:174. [PMID: 37020189 PMCID: PMC10077641 DOI: 10.1186/s12864-023-09256-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Eutrema salsugineum (2n = 14), a halophyte in the family Brassicaceae, is an attractive model to study abiotic stress tolerance in plants. Two versions of E. salsugineum genomes that previously reported were based on relatively short reads; thus, the repetitive regions were difficult to characterize. RESULTS We report the sequencing and assembly of the E. salsugineum (Shandong accession) genome using long-read sequencing and chromosome conformation capture data. We generated Oxford Nanopore long reads at high depth (> 60X) of genome coverage with additional short reads for error correction. The new assembly has a total size of 295.5 Mb with 52.8% repetitive sequences, and the karyotype of E. salsugineum is consistent with the ancestral translocation Proto-Calepineae Karyotype structure in both order and orientation. Compared with previous assemblies, this assembly has higher contiguity, especially in the centromere region. Based on this new assembly, we predicted 25,399 protein-coding genes and identified the positively selected genes associated with salt and drought stress responses. CONCLUSION The new genome assembly will provide a valuable resource for future genomic studies and facilitate comparative genomic analysis with other plants.
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Grants
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
- 31700164, 32171606, 31700323 the National Natural Science Foundation of China
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Affiliation(s)
- Meng Xiao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Guoqian Hao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644007, Sichuan, China
| | - Xinyi Guo
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Landi Feng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Hao Lin
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Wenjie Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yanyu Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Kexin Zhao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Ling Xiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Xinyao Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Dong Mei
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Quanjun Hu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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Madhu, Sharma A, Kaur A, Tyagi S, Upadhyay SK. Glutathione Peroxidases in Plants: Innumerable Role in Abiotic Stress Tolerance and Plant Development. JOURNAL OF PLANT GROWTH REGULATION 2023; 42:598-613. [DOI: 10.1007/s00344-022-10601-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/02/2022] [Indexed: 10/09/2024]
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Yang X, Li J, Ji C, Wei Z, Zhao T, Pang Q. Overexpression of an aquaporin gene EsPIP1;4 enhances abiotic stress tolerance and promotes flowering in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 193:25-35. [PMID: 36323195 DOI: 10.1016/j.plaphy.2022.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/24/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Aquaporins are water channel proteins that play an essential role in plant growth and development. Despite extensive functional characterization of aquaporins in model plants such as Arabidopsis, their contributions to abiotic stress tolerance in non-model plants are still poorly understood. As a close relative of Arabidopsis thaliana, Eutrema salsugineum is an excellent model for studying salt tolerance. Here, we identified and functionally characterized EsPIP1;4, a gene encoding a plasma membrane intrinsic protein (PIP) aquaporin in E. salsugineum. Overexpression of EsPIP1;4 in Arabidopsis improved seed germination and root growth of transgenic plants under abiotic stress, which was accompanied by an increase in proline accumulation, reduction in MDA, and decrease in the rate of ion leakage. Under abiotic stress, transgenic plants overexpressing EsPIP1;4 also showed increased antioxidant enzyme activity, and enhanced K+/Na+ ratio compared to control plants. Furthermore, overexpression of EsPIP1;4 promoted flowering by regulating genes in multiple flowering pathways. Together, our results demonstrated that an aquaporin from E. salsugineum improves abiotic stress tolerance and promotes flowering.
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Affiliation(s)
- Xiaomin Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jiawen Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Chengcheng Ji
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Zhaoxin Wei
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Tong Zhao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Qiuying Pang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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5
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Li C, Duan C, Zhang H, Zhao Y, Meng Z, Zhao Y, Zhang Q. Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment. FRONTIERS IN PLANT SCIENCE 2022; 13:909527. [PMID: 35837468 PMCID: PMC9274170 DOI: 10.3389/fpls.2022.909527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.
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Affiliation(s)
- Chuanshun Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Chonghao Duan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Hengyang Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yaoyao Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Zhe Meng
- Research Team of Plant Pathogen Microbiology and Immunology, College of Life Science, Shandong Normal University, Jinan, China
| | - Yanxiu Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Quan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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Belloeil C, Jouannais P, Malfaisan C, Fernández RR, Lopez S, Gutierrez DMN, Maeder-Pras S, Villanueva P, Tisserand R, Gallopin M, Alfonso-Gonzalez D, Marrero IMF, Muller S, Invernon V, Pillon Y, Echevarria G, Iturralde RB, Merlot S. The X-ray fluorescence screening of multiple elements in herbarium specimens from the Neotropical region reveals new records of metal accumulation in plants. Metallomics 2021; 13:6329692. [PMID: 34320190 DOI: 10.1093/mtomcs/mfab045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/16/2021] [Indexed: 01/15/2023]
Abstract
Plants have developed a diversity of strategies to take up and store essential metals in order to colonize various types of soils including mineralized soils. Yet, our knowledge of the capacity of plant species to accumulate metals is still fragmentary across the plant kingdom. In this study, we have used the X-Ray Fluorescence technology to analyze metal concentration in a wide diversity of species of the Neotropical flora that was not extensively investigated so far. In total, we screened more than 11 000 specimens representing about 5000 species from herbaria in Paris and Cuba. Our study provides a large overview of the accumulation of metals such as manganese, zinc and nickel in the Neotropical flora. We report 30 new nickel hyperaccumulating species from Cuba, including the first records in the families Connaraceae, Melastomataceae, Polygonaceae, Santalaceae and Urticaceae. We also identified the first species from this region of the world that can be considered as manganese hyperaccumulators in the genera Lomatia (Proteaceae), Calycogonium (Melastomataceae), Ilex (Aquifoliaceae), Morella (Myricaceae) and Pimenta (Myrtaceae). Finally, we report the first zinc hyperaccumulator, Rinorea multivenosa (Violaceae), from the Amazonas region. The identification of species able to accumulate high amounts of metals will become instrumental to support the development of phytotechnologies in order to limit the impact of soil metal pollution in this region of the world.
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Affiliation(s)
- Célestine Belloeil
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pierre Jouannais
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Charles Malfaisan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Rolando Reyes Fernández
- Universidad Agraria de La Habana (UNAH), Facultad de Agronomía, Laboratorio Biotecnología Vegetal, Mayabeque, Cuba, CP: 32700
| | | | - Dulce Montserrat Navarrete Gutierrez
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement (LSE), 54000 Nancy, France.,Universidad Autónoma de Chapingo, Texcoco de Mora, State of México, México
| | - Swann Maeder-Pras
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Paola Villanueva
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Romane Tisserand
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement (LSE), 54000 Nancy, France
| | - Melina Gallopin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | | | - Ilsa M Fuentes Marrero
- Instituto de Ecología y Sistemática, Ministerio de Ciencia, Tecnología y Medio Ambiente, La Habana, Cuba, C.P : 11900
| | - Serge Muller
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Vanessa Invernon
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Yohan Pillon
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Guillaume Echevarria
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement (LSE), 54000 Nancy, France.,Centre for Mined Land Rehabilitation, SMI, University of Queensland, QLD 4072 St. Lucia, Australia
| | | | - Sylvain Merlot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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van der Ent A, Spiers KM, Brueckner D, Echevarria G, Aarts MGM, Montargès-Pelletier E. Spatially-resolved localization and chemical speciation of nickel and zinc in Noccaea tymphaea and Bornmuellera emarginata. Metallomics 2020; 11:2052-2065. [PMID: 31651002 DOI: 10.1039/c9mt00106a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Hyperaccumulator plants present the ideal model system for studying the physiological regulation of the essential (and potentially toxic) transition elements nickel and zinc. This study used synchrotron X-ray Fluorescence Microscopy (XFM) elemental imaging and spatially resolved X-ray Absorption Spectroscopy (XAS) to elucidate elemental localization and chemical speciation of nickel and zinc in the hyperaccumulators Noccaea tymphaea and Bornmuellera emarginata (synonym Leptoplax emarginata). The results show that in the leaves of N. tymphaea nickel and zinc have contrasting localization, and whereas nickel is present in vacuoles of epidermal cells, zinc occurs mainly in the mesophyll cells. In the seeds Ni and Zn are similarly localized and strongly enriched in the cotyledons in N. tymphaea. Nickel is strongly enriched in the tip of the radicle of B. emarginata. Noccaea tymphaea has an Fe-rich provascular strand network in the cotyledons of the seed. The chemical speciation of Ni in the seeds of N. tymphaea is unequivocally associated with carboxylic acids, whereas Zn is present as the phytate complex. The spatially resolved spectroscopy did not reveal any spatial variation in chemical speciation of Ni and Zn within the N. tymphaea seed. The dissimilar ecophysiological behaviour of Ni and Zn in N. tymphaea and B. emarginata raises questions about the evolution of hyperaccumulation in these species.
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Affiliation(s)
- Antony van der Ent
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Australia.
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8
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Cesarino I, Dello Ioio R, Kirschner GK, Ogden MS, Picard KL, Rast-Somssich MI, Somssich M. Plant science's next top models. ANNALS OF BOTANY 2020; 126:1-23. [PMID: 32271862 PMCID: PMC7304477 DOI: 10.1093/aob/mcaa063] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models. SCOPE Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers. CONCLUSIONS Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.
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Affiliation(s)
- Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão 277, Butantã, São Paulo, Brazil
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Gwendolyn K Kirschner
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Division of Crop Functional Genomics, Bonn, Germany
| | - Michael S Ogden
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Kelsey L Picard
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Madlen I Rast-Somssich
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, VIC, Australia
| | - Marc Somssich
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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Abobatta WF. Plant Responses and Tolerance to Extreme Salinity: Learning from Halophyte Tolerance to Extreme Salinity. SALT AND DROUGHT STRESS TOLERANCE IN PLANTS 2020. [DOI: 10.1007/978-3-030-40277-8_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Doucet J, Lee HK, Udugama N, Xu J, Qi B, Goring DR. Investigations into a putative role for the novel BRASSIKIN pseudokinases in compatible pollen-stigma interactions in Arabidopsis thaliana. BMC PLANT BIOLOGY 2019; 19:549. [PMID: 31829135 PMCID: PMC6907349 DOI: 10.1186/s12870-019-2160-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/25/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND In the Brassicaceae, the early stages of compatible pollen-stigma interactions are tightly controlled with early checkpoints regulating pollen adhesion, hydration and germination, and pollen tube entry into the stigmatic surface. However, the early signalling events in the stigma which trigger these compatible interactions remain unknown. RESULTS A set of stigma-expressed pseudokinase genes, termed BRASSIKINs (BKNs), were identified and found to be present in only core Brassicaceae genomes. In Arabidopsis thaliana Col-0, BKN1 displayed stigma-specific expression while the BKN2 gene was expressed in other tissues as well. CRISPR deletion mutations were generated for the two tandemly linked BKNs, and very mild hydration defects were observed for wild-type Col-0 pollen when placed on the bkn1/2 mutant stigmas. In further analyses, the predominant transcript for the stigma-specific BKN1 was found to have a premature stop codon in the Col-0 ecotype, but a survey of the 1001 Arabidopsis genomes uncovered three ecotypes that encoded a full-length BKN1 protein. Furthermore, phylogenetic analyses identified intact BKN1 orthologues in the closely related outcrossing Arabidopsis species, A. lyrata and A. halleri. Finally, the BKN pseudokinases were found to be plasma-membrane localized through the dual lipid modification of myristoylation and palmitoylation, and this localization would be consistent with a role in signaling complexes. CONCLUSION In this study, we have characterized the novel Brassicaceae-specific family of BKN pseudokinase genes, and examined the function of BKN1 and BKN2 in the context of pollen-stigma interactions in A. thaliana Col-0. Additionally, premature stop codons were identified in the predicted stigma specific BKN1 gene in a number of the 1001 A. thaliana ecotype genomes, and this was in contrast to the out-crossing Arabidopsis species which carried intact copies of BKN1. Thus, understanding the function of BKN1 in other Brassicaceae species will be a key direction for future studies.
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Affiliation(s)
- Jennifer Doucet
- Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3B2 Canada
| | - Hyun Kyung Lee
- Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3B2 Canada
| | - Nethangi Udugama
- Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3B2 Canada
| | - Jianfeng Xu
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF UK
- College of Horticulture, Agricultural University of Hebei, Baoding City, 071001 Hebei Province China
| | - Baoxiu Qi
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF UK
| | - Daphne R. Goring
- Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3B2 Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, M5S 3B2 Canada
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Qian W, Yang X, Li J, Luo R, Yan X, Pang Q. Genome-wide characterization and expression analysis of aquaporins in salt cress ( Eutrema salsugineum). PeerJ 2019; 7:e7664. [PMID: 31565576 PMCID: PMC6745184 DOI: 10.7717/peerj.7664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 08/13/2019] [Indexed: 01/24/2023] Open
Abstract
Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237-323 amino acids, with a theoretical molecular weight (MW) of 24.31-31.80 kDa and an isoelectric point (pI) value of 4.73-10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger's position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.
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Affiliation(s)
- Weiguo Qian
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, China
| | - Xiaomin Yang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, China
| | - Jiawen Li
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, China
| | - Rui Luo
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, China
| | - Xiufeng Yan
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, China
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, China
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12
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Šinzar-Sekulić J, Stamenković UM, Tomović G, Tumi AF, Andrejić G, Mihailović N, Lazarević MR. Assessment of trace element accumulation potential of Noccaea kovatsii from ultramafics of Bosnia and Herzegovina and Serbia. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:540. [PMID: 31378832 DOI: 10.1007/s10661-019-7711-x] [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: 12/31/2018] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
In this work, we present the results of the investigation of trace elements (Fe, Mg, Ni, Zn, Cu, Cr, Co, Cd, Pb) accumulation potential of Noccaea kovatsii (Heuff.) F. K. Mey., from the Balkan Peninsula. The study included eight populations from ultramafic soils, six from Bosnia and Herzegovina, and two from Serbia. Principal component analysis (PCA) was used to reveal relationships of elements in soil, and Pearson's correlation coefficients for analysing associations of available quantities of elements in soil and those in roots and shoots of N. kovatsii. Uptake and translocation efficiency was assessed by using bioconcentration (BCF) and translocation factors (TF). All the analysed populations of N. kovatsii emerged as strong Ni accumulators, with the highest shoot concentrations of 12,505 mg kg-1. Even thought contents of Zn in plant tissues of N. kovatsii were under the hyperaccumulation level (602 mg kg-1 and 1120 mg kg-1 respectively), BCF was up to 667, indicating that certain surveyed populations have strong accumulative potential for this element.
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Affiliation(s)
- Jasmina Šinzar-Sekulić
- Department of Plant Ecology and Phytogeography, Institute of Botany and Botanical Garden "Jevremovac," Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia.
| | - Una Matko Stamenković
- Department of Plant Ecology and Phytogeography, Institute of Botany and Botanical Garden "Jevremovac," Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Gordana Tomović
- Department of Plant Ecology and Phytogeography, Institute of Botany and Botanical Garden "Jevremovac," Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Ahmed F Tumi
- Department of Plant Ecology and Phytogeography, Institute of Botany and Botanical Garden "Jevremovac," Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Gordana Andrejić
- Institute for Application of Nuclear Energy, University of Belgrade, Banatska 31b, Zemun, 11080, Serbia
| | - Nevena Mihailović
- Institute for Application of Nuclear Energy, University of Belgrade, Banatska 31b, Zemun, 11080, Serbia
| | - Maja R Lazarević
- Department of Plant Ecology and Phytogeography, Institute of Botany and Botanical Garden "Jevremovac," Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
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Sterckeman T, Cazes Y, Sirguey C. Breeding the hyperaccumulator Noccaea caerulescens for trace metal phytoextraction: first results of a pure-line selection. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 21:448-455. [PMID: 30698040 DOI: 10.1080/15226514.2018.1537250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To initiate the creation of phytoextraction cultivars, plants were selected from 60 populations of N. caerulescens for their high shoot biomass or Cd, Ni, and Zn concentrations. They were self-pollinated, and the selection and fixation were continued for three generations in greenhouse conditions. Selected plants showed a potential to produce 5-10 t dry matter ha-1, which is required to decontaminate soils which have been moderately contaminated with Cd. However, the high biomass genotypes could not be fixed, probably both because of their complexity and to the sensitivity of this trait to environmental conditions, and plant density in particular. The selection led to an improvement to the Cd and Zn accumulation capacities of the plants, yet caused a decrease in their Ni accumulation. This is most likely due to a decline in Ni availability in soil, rather than to a deleterious effect of inbreeding. Metal accumulation appeared to be more heritable than biomass production and fixation for the former trait should be quicker than for the latter. The accumulation capacities of the selected plants permitted offtakes representing around 25% of the soil Cd in a single cropping. This potential has to be confirmed in field conditions.
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Affiliation(s)
- Thibault Sterckeman
- a Laboratoire Sols et Environnement , Université de Lorraine, INRA , Nancy , France
| | - Yannick Cazes
- a Laboratoire Sols et Environnement , Université de Lorraine, INRA , Nancy , France
| | - Catherine Sirguey
- a Laboratoire Sols et Environnement , Université de Lorraine, INRA , Nancy , France
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14
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Yuan F, Xu Y, Leng B, Wang B. Beneficial Effects of Salt on Halophyte Growth: Morphology, Cells, and Genes. Open Life Sci 2019; 14:191-200. [PMID: 33817151 PMCID: PMC7874760 DOI: 10.1515/biol-2019-0021] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/26/2018] [Indexed: 11/17/2022] Open
Abstract
Halophytes can survive and complete their life cycle in the presence of ≥200 mM NaCl. These remarkable plants have developed various strategies to tolerate salinity and thrive in high-salt environments. At the appropriate levels, salt has a beneficial effect on the vegetative growth of halophytes but inhibits the growth of non-halophytes. In recent years, many studies have focused on elucidating the salt-tolerance mechanisms of halophytes at the molecular, physiological, and individual level. In this review, we focus on the mechanisms, from the macroscopic to the molecular, underlying the successful growth of halophytes in saline environments to explain why salt has beneficial effects on halophytes but harmful effects on non-halophytes. These mechanisms include the specialized organs of halophytes (for example, ion compartmentalization in succulent leaves), their unique structures (salt glands and hydrophobic barriers in roots), and their salt-tolerance genes. We hope to shed light on the use of halophytes for engineering salt-tolerant crops, soil conservation, and the protection of freshwater resources in the near future.
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Affiliation(s)
- Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
| | - Yanyu Xu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
| | - Bingying Leng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
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15
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Kazachkova Y, Eshel G, Pantha P, Cheeseman JM, Dassanayake M, Barak S. Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems? PLANT PHYSIOLOGY 2018; 178:972-988. [PMID: 30237204 PMCID: PMC6236594 DOI: 10.1104/pp.18.00863] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/31/2018] [Indexed: 05/06/2023]
Abstract
Halophytes are able to thrive in salt concentrations that would kill 99% of other plant species, and identifying their salt-adaptive mechanisms has great potential for improving the tolerance of crop plants to salinized soils. Much research has focused on the physiological basis of halophyte salt tolerance, whereas the elucidation of molecular mechanisms has traditionally lagged behind due to the absence of a model halophyte system. However, over the last decade and a half, two Arabidopsis (Arabidopsis thaliana) relatives, Eutrema salsugineum and Schrenkiella parvula, have been established as transformation-competent models with various genetic resources including high-quality genome assemblies. These models have facilitated powerful comparative analyses with salt-sensitive Arabidopsis to unravel the genetic adaptations that enable a halophytic lifestyle. The aim of this review is to explore what has been learned about halophytism using E. salsugineum and S. parvula We consider evidence from physiological and molecular studies suggesting that differences in salt tolerance between related halophytes and salt-sensitive plants are associated with alterations in the regulation of basic physiological, biochemical, and molecular processes. Furthermore, we discuss how salt tolerance mechanisms of the halophytic models are reflected at the level of their genomes, where evolutionary processes such as subfunctionalization and/or neofunctionalization have altered the expression and/or functions of genes to facilitate adaptation to saline conditions. Lastly, we summarize the many areas of research still to be addressed with E. salsugineum and S. parvula as well as obstacles hindering further progress in understanding halophytism.
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Affiliation(s)
- Yana Kazachkova
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Gil Eshel
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Pramod Pantha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - John M Cheeseman
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Simon Barak
- French Associates' Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
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16
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Sankoff D, Zheng C, Zhang Y, Meidanis J, Lyons E, Tang H. Models for Similarity Distributions of Syntenic Homologs and Applications to Phylogenomics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:727-737. [PMID: 30072336 DOI: 10.1109/tcbb.2018.2849377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We outline an integrated approach to speciation and whole genome duplication (WGD) to resolve the occurrence of these events in phylogenetic analysis. We propose a more principled way of estimating the parameters of gene divergence and fractionation than the standard mixture of normals analysis. We formulate an algorithm for resolving data on local peaks in the distributions of duplicate gene similarities for a number of related genomes. We illustrate with a comprehensive analysis of WGD-origin duplicate gene data from the family Brassicaceae.
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17
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Wang XJ, Hu QJ, Guo XY, Wang K, Ru DF, German DA, Weretilnyk EA, Abbott RJ, Lascoux M, Liu JQ. Demographic expansion and genetic load of the halophyte model plantEutrema salsugineum. Mol Ecol 2018; 27:2943-2955. [DOI: 10.1111/mec.14738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/16/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Xiao-Juan Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Quan-Jun Hu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Xin-Yi Guo
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Kun Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Da-Fu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Dmitry A. German
- Department of Biodiversity and Plant Systematics; Centre for Organismal Studies (COS Heidelberg); Heidelberg University; Heidelberg Germany
- South-Siberian Botanical Garden; Altai State University; Barnaul Russia
| | | | | | - Martin Lascoux
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; Uppsala Sweden
| | - Jian-quan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
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18
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Bechtold U. Plant Life in Extreme Environments: How Do You Improve Drought Tolerance? FRONTIERS IN PLANT SCIENCE 2018; 9:543. [PMID: 29868044 PMCID: PMC5962824 DOI: 10.3389/fpls.2018.00543] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/09/2018] [Indexed: 05/11/2023]
Abstract
Systems studies of drought stress in resurrection plants and other xerophytes are rapidly identifying a large number of genes, proteins and metabolites that respond to severe drought stress or desiccation. This has provided insight into drought resistance mechanisms, which allow xerophytes to persist under such extreme environmental conditions. Some of the mechanisms that ensure cellular protection during severe dehydration appear to be unique to desert species, while many other stress signaling pathways are in common with well-studied model and crop species. However, despite the identification of many desiccation inducible genes, there are few "gene-to-field" examples that have led to improved drought tolerance and yield stability derived from resurrection plants, and only few examples have emerged from model species. This has led to many critical reviews on the merit of the experimental approaches and the type of plants used to study drought resistance mechanisms. This article discusses the long-standing arguments between the ecophysiology and molecular biology communities, on how to "drought-proof" future crop varieties. It concludes that a more positive and inclusive dialogue between the different disciplines is needed, to allow us to move forward in a much more constructive way.
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Affiliation(s)
- Ulrike Bechtold
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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19
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Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, Schmutz J, Lyons E, Pires JC, Edger PP, Conant GC. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PLoS Genet 2018; 14:e1007267. [PMID: 29590103 PMCID: PMC5891031 DOI: 10.1371/journal.pgen.1007267] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 04/09/2018] [Accepted: 02/21/2018] [Indexed: 11/18/2022] Open
Abstract
Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms' successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers' yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages' history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.
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Affiliation(s)
- Marianne Emery
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - M. Madeline S. Willis
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Khouanchy Oakgrove
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Yi Peng
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - J. Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
- Informatics Institute, University of Missouri-Columbia, Columbia, Missouri, United States of America
- Bond Life Sciences Center, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Patrick P. Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - Gavin C. Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America
- Program in Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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20
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Neugebauer K, Broadley MR, El-Serehy HA, George TS, McNicol JW, Moraes MF, White PJ. Variation in the angiosperm ionome. PHYSIOLOGIA PLANTARUM 2018; 163:306-322. [PMID: 29412469 DOI: 10.1111/ppl.12700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/15/2018] [Accepted: 01/31/2018] [Indexed: 05/06/2023]
Abstract
The ionome is defined as the elemental composition of a subcellular structure, cell, tissue, organ or organism. The subset of the ionome comprising mineral nutrients is termed the functional ionome. A 'standard functional ionome' of leaves of an 'average' angiosperm, defined as the nutrient composition of leaves when growth is not limited by mineral nutrients, is presented and can be used to compare the effects of environment and genetics on plant nutrition. The leaf ionome of a plant is influenced by interactions between its environment and genetics. Examples of the effects of the environment on the leaf ionome are presented and the consequences of nutrient deficiencies on the leaf ionome are described. The physiological reasons for (1) allometric relationships between leaf nitrogen and phosphorus concentrations and (2) linear relationships between leaf calcium and magnesium concentrations are explained. It is noted that strong phylogenetic effects on the mineral composition of leaves of angiosperm species are observed even when sampled from diverse environments. The evolutionary origins of traits including (1) the small calcium concentrations of Poales leaves, (2) the large magnesium concentrations of Caryophyllales leaves and (3) the large sulphur concentrations of Brassicales leaves are traced using phylogenetic relationships among angiosperm orders, families and genera. The rare evolution of hyperaccumulation of toxic elements in leaves of angiosperms is also described. Consequences of variation in the leaf ionome for ecology, mineral cycling in the environment, strategies for phytoremediation of contaminated land, sustainable agriculture and the nutrition of livestock and humans are discussed.
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Affiliation(s)
- Konrad Neugebauer
- Ecological Science Group, The James Hutton Institute, Dundee, DD2 5DA, UK
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Martin R Broadley
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Timothy S George
- Ecological Science Group, The James Hutton Institute, Dundee, DD2 5DA, UK
| | | | - Milton F Moraes
- Graduate Program of Tropical Agriculture, Federal University of Mato Grosso, Barra do Garças, Mato Grosso, Brazil
| | - Philip J White
- Ecological Science Group, The James Hutton Institute, Dundee, DD2 5DA, UK
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, 11451, Saudi Arabia
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21
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Koch MA, German DA, Kiefer M, Franzke A. Database Taxonomics as Key to Modern Plant Biology. TRENDS IN PLANT SCIENCE 2018; 23:4-6. [PMID: 29146431 DOI: 10.1016/j.tplants.2017.10.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/25/2017] [Indexed: 05/06/2023]
Abstract
The advent of omic technologies opened new and multiple avenues to access higher levels of complexity. Taxonomy - discovering and naming biodiversity - has also entered a taxonomics epoch and serves as a tool not only to name biological diversity, but also to fully explore biological knowledge and to build bridges between disciplines.
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Affiliation(s)
- Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics/Botanical Garden and Herbarium (HEID), Heidelberg University, Heidelberg, Germany.
| | - Dmitry A German
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics/Botanical Garden and Herbarium (HEID), Heidelberg University, Heidelberg, Germany
| | - Markus Kiefer
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics/Botanical Garden and Herbarium (HEID), Heidelberg University, Heidelberg, Germany
| | - Andreas Franzke
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics/Botanical Garden and Herbarium (HEID), Heidelberg University, Heidelberg, Germany
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22
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Bothe H, Słomka A. Divergent biology of facultative heavy metal plants. JOURNAL OF PLANT PHYSIOLOGY 2017; 219:45-61. [PMID: 29028613 DOI: 10.1016/j.jplph.2017.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 05/04/2023]
Abstract
Among heavy metal plants (the metallophytes), facultative species can live both in soils contaminated by an excess of heavy metals and in non-affected sites. In contrast, obligate metallophytes are restricted to polluted areas. Metallophytes offer a fascinating biology, due to the fact that species have developed different strategies to cope with the adverse conditions of heavy metal soils. The literature distinguishes between hyperaccumulating, accumulating, tolerant and excluding metallophytes, but the borderline between these categories is blurred. Due to the fact that heavy metal soils are dry, nutrient limited and are not uniform but have a patchy distribution in many instances, drought-tolerant or low nutrient demanding species are often regarded as metallophytes in the literature. In only a few cases, the concentrations of heavy metals in soils are so toxic that only a few specifically adapted plants, the genuine metallophytes, can cope with these adverse soil conditions. Current molecular biological studies focus on the genetically amenable and hyperaccumulating Arabidopsis halleri and Noccaea (Thlaspi) caerulescens of the Brassicaceae. Armeria maritima ssp. halleri utilizes glands for the excretion of heavy metals and is, therefore, a heavy metal excluder. The two endemic zinc violets of Western Europe, Viola lutea ssp. calaminaria of the Aachen-Liège area and Viola lutea ssp. westfalica of the Pb-Cu-ditch of Blankenrode, Eastern Westphalia, as well as Viola tricolor ecotypes of Eastern Europe, keep their cells free of excess heavy metals by arbuscular mycorrhizal fungi which bind heavy metals. The Caryophyllaceae, Silene vulgaris f. humilis and Minuartia verna, apparently discard leaves when overloaded with heavy metals. All Central European metallophytes have close relatives that grow in areas outside of heavy metal soils, mainly in the Alps, and have, therefore, been considered as relicts of the glacial epoch in the past. However, the current literature favours the idea that hyperaccumulation of heavy metals serves plants as deterrent against attack by feeding animals (termed elemental defense hypothesis). The capability to hyperaccumulate heavy metals in A. halleri and N. caerulescens is achieved by duplications and alterations of the cis-regulatory properties of genes coding for heavy metal transporting/excreting proteins. Several metallophytes have developed ecotypes with a varying content of such heavy metal transporters as an adaption to the specific toxicity of a heavy metal site.
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Affiliation(s)
- Hermann Bothe
- Botanical Institute, The University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany.
| | - Aneta Słomka
- Department of Plant Cytology and Embryology, Jagiellonian University, Gronostajowa 9 Str., 30-387 Cracow, Poland.
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Barrero-Sicilia C, Silvestre S, Haslam RP, Michaelson LV. Lipid remodelling: Unravelling the response to cold stress in Arabidopsis and its extremophile relative Eutrema salsugineum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:194-200. [PMID: 28818375 PMCID: PMC5567406 DOI: 10.1016/j.plantsci.2017.07.017] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/20/2017] [Accepted: 07/12/2017] [Indexed: 05/19/2023]
Abstract
Environmental constraints limit the geographic distribution of many economically important crops. Cold stress is an important abiotic stress that affects plant growth and development, resulting in loss of vigour and surface lesions. These symptoms are caused by, among other metabolic processes, the altered physical and chemical composition of cell membranes. As a major component of cell membranes lipids have been recognized as having a significant role in cold stress, both as a mechanical defence through leaf surface protection and plasma membrane remodelling, and as signal transduction molecules. We present an overview integrating gene expression and lipidomic data published so far in Arabidopsis and its relative the extremophile Eutrema salsugineum. This data enables a better understanding of the contribution of the lipidome in determining the ability to tolerate suboptimal temperature conditions. Collectively this information will allow us to identify the key lipids and pathways responsible for resilience, enabling the development of new approaches for crop tolerance to stress.
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Affiliation(s)
| | - Susana Silvestre
- Plant Sciences, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Richard P Haslam
- Plant Sciences, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK.
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24
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Khanal N, Bray GE, Grisnich A, Moffatt BA, Gray GR. Differential Mechanisms of Photosynthetic Acclimation to Light and Low Temperature in Arabidopsis and the Extremophile Eutrema salsugineum. PLANTS (BASEL, SWITZERLAND) 2017; 6:E32. [PMID: 28792470 PMCID: PMC5620588 DOI: 10.3390/plants6030032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/19/2017] [Accepted: 08/01/2017] [Indexed: 12/21/2022]
Abstract
Photosynthetic organisms are able to sense energy imbalances brought about by the overexcitation of photosystem II (PSII) through the redox state of the photosynthetic electron transport chain, estimated as the chlorophyll fluorescence parameter 1-qL, also known as PSII excitation pressure. Plants employ a wide array of photoprotective processes that modulate photosynthesis to correct these energy imbalances. Low temperature and light are well established in their ability to modulate PSII excitation pressure. The acquisition of freezing tolerance requires growth and development a low temperature (cold acclimation) which predisposes the plant to photoinhibition. Thus, photosynthetic acclimation is essential for proper energy balancing during the cold acclimation process. Eutrema salsugineum (Thellungiella salsuginea) is an extremophile, a close relative of Arabidopsis thaliana, but possessing much higher constitutive levels of tolerance to abiotic stress. This comparative study aimed to characterize the photosynthetic properties of Arabidopsis (Columbia accession) and two accessions of Eutrema (Yukon and Shandong) isolated from contrasting geographical locations at cold acclimating and non-acclimating conditions. In addition, three different growth regimes were utilized that varied in temperature, photoperiod and irradiance which resulted in different levels of PSII excitation pressure. This study has shown that these accessions interact differentially to instantaneous (measuring) and long-term (acclimation) changes in PSII excitation pressure with regard to their photosynthetic behaviour. Eutrema accessions contained a higher amount of photosynthetic pigments, showed higher oxidation of P700 and possessed more resilient photoprotective mechanisms than that of Arabidopsis, perhaps through the prevention of PSI acceptor-limitation. Upon comparison of the two Eutrema accessions, Shandong demonstrated the greatest PSII operating efficiency (ΦPSII) and P700 oxidizing capacity, while Yukon showed greater growth plasticity to irradiance. Both of these Eutrema accessions are able to photosynthetically acclimate but do so by different mechanisms. The Shandong accessions demonstrate a stable response, favouring energy partitioning to photochemistry while the Yukon accession shows a more rapid response with partitioning to other (non-photochemical) strategies.
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Affiliation(s)
- Nityananda Khanal
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Geoffrey E Bray
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Anna Grisnich
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Barbara A Moffatt
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | - Gordon R Gray
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
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25
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Han T, Dong H, Cui J, Li M, Lin S, Cao J, Huang L. Genomic, Molecular Evolution, and Expression Analysis of Genes Encoding Putative Classical AGPs, Lysine-Rich AGPs, and AG Peptides in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2017; 8:397. [PMID: 28424711 PMCID: PMC5372829 DOI: 10.3389/fpls.2017.00397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/08/2017] [Indexed: 05/27/2023]
Abstract
Arabinogalactan proteins (AGPs) belong to a class of Pro/Hyp-rich glycoproteins and are some of the most complex types of macromolecules found in plants. In the economically important plant species, Brassica rapa, only chimeric AGPs have been identified to date. This has significantly limited our understanding of the functional roles of AGPs in this plant. In this study, 64 AGPs were identified in the genome of B. rapa, including 33 classical AGPs, 28 AG peptides and three lys-rich AGPs. Syntenic gene analysis between B. rapa and A. thaliana suggested that the whole genome triplication event dominated the expansion of the AGP gene family in B. rapa. This resulted in a high retained proportion of the AGP family in the B. rapa genome, especially in the least fractionated subgenome. Phylogenetic and motif analysis classified the classical AGPs into six clades and three orphan genes, and the AG peptides into three clades and five orphan genes. Classical AGPs has a faster rate of molecular evolution than AG peptides revealed by estimation of molecular evolution rates. However, no significant differences were observed between classical AGPs and lys-rich AGPs. Under control conditions and in response to phytohormones treatment, a complete expression profiling experiment has identified five anther-specific AGPs and quite a number of AGPs responding to abscisic acid, methyl jasmonate and/or gibberellin. In this study, we presented a bioinformatics approach to identify important types of AGPs. Moreover, the association between their function and their protein structure, as well as the evolution and the expression of AGP genes were investigated, which might provide fundamental information for revealing the roles of AGPs in B. rapa.
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Affiliation(s)
- Tianyu Han
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang UniversityHangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of AgricultureHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Heng Dong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang UniversityHangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of AgricultureHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Jie Cui
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang UniversityHangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of AgricultureHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Ming Li
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang UniversityHangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of AgricultureHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Sue Lin
- Institute of Vegetable Science, Wenzhou Vocational College of Science and TechnologyWenzhou, China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang UniversityHangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of AgricultureHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
| | - Li Huang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang UniversityHangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of AgricultureHangzhou, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyHangzhou, China
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26
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Blande D, Halimaa P, Tervahauta AI, Aarts MG, Kärenlampi SO. De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. Sci Data 2017; 4:160131. [PMID: 28140388 PMCID: PMC5283065 DOI: 10.1038/sdata.2016.131] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/24/2016] [Indexed: 11/09/2022] Open
Abstract
Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition. Transcriptomes from root and shoot tissues of four N. caerulescens accessions with contrasting Zn, Cd and Ni hyperaccumulation and tolerance traits were sequenced with Illumina Hiseq2000. Transcriptomes were assembled using the Trinity de novo assembler and were annotated and the protein sequences predicted. The comparison against the BUSCO plant early release dataset indicated high-quality assemblies. The predicted protein sequences have been clustered into ortholog groups with closely related species. The data serve as important reference sequences in whole transcriptome studies, in analyses of genetic differences between the accessions and other species, and for primer design.
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Affiliation(s)
- Daniel Blande
- University of Eastern Finland, Department of Environmental and Biological Sciences, Kuopio 70210, Finland
| | - Pauliina Halimaa
- University of Eastern Finland, Department of Environmental and Biological Sciences, Kuopio 70210, Finland
| | - Arja I Tervahauta
- University of Eastern Finland, Department of Environmental and Biological Sciences, Kuopio 70210, Finland
| | - Mark G.M. Aarts
- Wageningen University, Laboratory of Genetics, Wageningen 6708 PB, The Netherlands
| | - Sirpa O Kärenlampi
- University of Eastern Finland, Department of Environmental and Biological Sciences, Kuopio 70210, Finland
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27
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Eshel G, Shaked R, Kazachkova Y, Khan A, Eppel A, Cisneros A, Acuna T, Gutterman Y, Tel-Zur N, Rachmilevitch S, Fait A, Barak S. Anastatica hierochuntica, an Arabidopsis Desert Relative, Is Tolerant to Multiple Abiotic Stresses and Exhibits Species-Specific and Common Stress Tolerance Strategies with Its Halophytic Relative, Eutrema ( Thellungiella) salsugineum. FRONTIERS IN PLANT SCIENCE 2017; 7:1992. [PMID: 28144244 PMCID: PMC5239783 DOI: 10.3389/fpls.2016.01992] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/15/2016] [Indexed: 05/08/2023]
Abstract
The search for novel stress tolerance determinants has led to increasing interest in plants native to extreme environments - so called "extremophytes." One successful strategy has been comparative studies between Arabidopsis thaliana and extremophyte Brassicaceae relatives such as the halophyte Eutrema salsugineum located in areas including cold, salty coastal regions of China. Here, we investigate stress tolerance in the desert species, Anastatica hierochuntica (True Rose of Jericho), a member of the poorly investigated lineage III Brassicaceae. We show that A. hierochuntica has a genome approximately 4.5-fold larger than Arabidopsis, divided into 22 diploid chromosomes, and demonstrate that A. hierochuntica exhibits tolerance to heat, low N and salt stresses that are characteristic of its habitat. Taking salt tolerance as a case study, we show that A. hierochuntica shares common salt tolerance mechanisms with E. salsugineum such as tight control of shoot Na+ accumulation and resilient photochemistry features. Furthermore, metabolic profiling of E. salsugineum and A. hierochuntica shoots demonstrates that the extremophytes exhibit both species-specific and common metabolic strategies to cope with salt stress including constitutive up-regulation (under control and salt stress conditions) of ascorbate and dehydroascorbate, two metabolites involved in ROS scavenging. Accordingly, A. hierochuntica displays tolerance to methyl viologen-induced oxidative stress suggesting that a highly active antioxidant system is essential to cope with multiple abiotic stresses. We suggest that A. hierochuntica presents an excellent extremophyte Arabidopsis relative model system for understanding plant survival in harsh desert conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Simon Barak
- French Associates Institute for Biotechnology and Agriculture of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSde Boker, Israel
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28
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German DA, Koch MA. Eutrema salsugineum (Cruciferae) new to Mexico: a surprising generic record for the flora of Middle America. PHYTOKEYS 2017:13-21. [PMID: 28228683 PMCID: PMC5301981 DOI: 10.3897/phytokeys.76.9731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/12/2016] [Indexed: 05/14/2023]
Abstract
The paper reports Eutrema salsugineum as a novelty to the flora of Mexico and Middle America in general. The finding stands ca. 1600 km apart from the closest known locality in the Rocky Mountains of Colorado, USA. The species is considered native to NW Mexico and its late discovery in the region is presumably explained by its tiny habit, early flowering time, and subephemeral life cycle. The phylogenetic position of this Mexican population in a haplotype network based on the chloroplast DNA fragment psbA-trnH confirms this hypothesis and also suggests, in contrast to the previously held viewpoint, multiple colonizations of North American continent from Asia.
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Affiliation(s)
- Dmitry A. German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
- South-Siberian Botanical Garden, Altai State University, Lenin Str. 61, 656049 Barnaul, Russia
| | - Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
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29
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Gonneau C, Noret N, Godé C, Frérot H, Sirguey C, Sterckeman T, Pauwels M. Demographic history of the trace metal hyperaccumulator Noccaea caerulescens (J. Presl and C. Presl) F. K. Mey. in Western Europe. Mol Ecol 2016; 26:904-922. [PMID: 27914207 DOI: 10.1111/mec.13942] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/27/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
Abstract
Noccaea caerulescens (Brassicaceae) is a major pseudometallophyte model for the investigation of the genetics and evolution of metal hyperaccumulation in plants. We studied the population genetics and demographic history of this species to advance the understanding of among-population differences in metal hyperaccumulation and tolerance abilities. Sampling of seven to 30 plants was carried out in 62 sites in Western Europe. Genotyping was carried out using a combination of new chloroplast and nuclear neutral markers. A strong genetic structure was detected, allowing the definition of three genetic subunits. Subunits showed a good geographic coherence. Accordingly, distant metallicolous populations generally belonged to distinct subunits. Approximate Bayesian computation analysis of demographic scenarios among subunits further supported a primary isolation of populations from the southern Massif Central prior to last glacial maximum, whereas northern populations may have derived during postglacial recolonization events. Estimated divergence times among subunits were rather recent in comparison with the species history, but certainly before the establishment of anthropogenic metalliferous sites. Our results suggest that the large-scale genetic structure of N. caerulescens populations pre-existed to the local adaptation to metalliferous sites. The population structure of quantitative variation for metal-related adaptive traits must have established independently in isolated gene pools. However, features of the most divergent genetic unit (e.g. extreme levels of Cd accumulation observed in previous studies) question the putative relationships between adaptive evolution of metal-related traits and subunits isolation. Finally, admixture signals among distant metallicolous populations suggest a putative role of human activities in facilitating long-distance genetic exchanges.
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Affiliation(s)
- Cédric Gonneau
- Laboratoire Sols et Environnement UMR1120, Université de Lorraine, TSA 40602, Vandœuvre-lès-Nancy Cedex, F-54518, France.,Laboratoire Sols et Environnement UMR1120, INRA, Vandœuvre-lès-Nancy Cedex, F-54518, France
| | - Nausicaa Noret
- Laboratoire d'Écologie Végétale et Biogéochimie, Université libre de Bruxelles, Campus de la Plaine - CP244, Boulevard du Triomphe, B-1050, Ixelles, Belgium
| | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Hélène Frérot
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Catherine Sirguey
- Laboratoire Sols et Environnement UMR1120, Université de Lorraine, TSA 40602, Vandœuvre-lès-Nancy Cedex, F-54518, France.,Laboratoire Sols et Environnement UMR1120, INRA, Vandœuvre-lès-Nancy Cedex, F-54518, France
| | - Thibault Sterckeman
- Laboratoire Sols et Environnement UMR1120, Université de Lorraine, TSA 40602, Vandœuvre-lès-Nancy Cedex, F-54518, France.,Laboratoire Sols et Environnement UMR1120, INRA, Vandœuvre-lès-Nancy Cedex, F-54518, France
| | - Maxime Pauwels
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
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30
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Lee YP, Funk C, Erban A, Kopka J, Köhl KI, Zuther E, Hincha DK. Salt stress responses in a geographically diverse collection of Eutrema/Thellungiella spp. accessions. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:590-606. [PMID: 32480489 DOI: 10.1071/fp15285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/10/2015] [Indexed: 05/13/2023]
Abstract
Salinity strongly impairs plant growth and development. Natural genetic variation can be used to dissect complex traits such as plant salt tolerance. We used 16 accessions of the halophytic species Eutrema salsugineum (previously called Thellungiella salsuginea (Pallas) O.E.Schulz, Thellungiella halophila (C.A.Meyer) O.E. Schulz and Thellungiella botschantzevii D.A.German to investigate their natural variation in salinity tolerance. Although all accessions showed survival and growth up to 700mM NaCl in hydroponic culture, their relative salt tolerance varied considerably. All accessions accumulated the compatible solutes proline, sucrose, glucose and fructose and the polyamines putrescine and spermine. Relative salt tolerance was not correlated with the content of any of the investigated solutes. We compared the metabolomes and transcriptomes of Arabidopsis thaliana (L. Heynh.) Col-0 and E. salsugineum Yukon under control and salt stress conditions. Higher content of several metabolites in Yukon compared with Col-0 under control conditions indicated metabolic pre-adaptation to salinity in the halophyte. Most metabolic salt responses in Yukon took place at 200mM NaCl, whereas few additional changes were observed between 200 and 500mM. The opposite trend was observed for the transcriptome, with only little overlap between salt-regulated genes in the two species. In addition, only about half of the salt-regulated Yukon unigenes had orthologues in Col-0.
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Affiliation(s)
- Yang Ping Lee
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Christian Funk
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Karin I Köhl
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
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31
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Horn PJ, Liu J, Cocuron JC, McGlew K, Thrower NA, Larson M, Lu C, Alonso AP, Ohlrogge J. Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:322-348. [PMID: 26991237 DOI: 10.1111/tpj.13163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 03/02/2016] [Accepted: 03/07/2016] [Indexed: 06/05/2023]
Abstract
Two Brassicaceae species, Physaria fendleri and Camelina sativa, are genetically very closely related to each other and to Arabidopsis thaliana. Physaria fendleri seeds contain over 50% hydroxy fatty acids (HFAs), while Camelina sativa and Arabidopsis do not accumulate HFAs. To better understand how plants evolved new biochemical pathways with the capacity to accumulate high levels of unusual fatty acids, transcript expression and protein sequences of developing seeds of Physaria fendleri, wild-type Camelina sativa, and Camelina sativa expressing a castor bean (Ricinus communis) hydroxylase were analyzed. A number of potential evolutionary adaptations within lipid metabolism that probably enhance HFA production and accumulation in Physaria fendleri, and, in their absence, limit accumulation in transgenic tissues were revealed. These adaptations occurred in at least 20 genes within several lipid pathways from the onset of fatty acid synthesis and its regulation to the assembly of triacylglycerols. Lipid genes of Physaria fendleri appear to have co-evolved through modulation of transcriptional abundances and alterations within protein sequences. Only a handful of genes showed evidence for sequence adaptation through gene duplication. Collectively, these evolutionary changes probably occurred to minimize deleterious effects of high HFA amounts and/or to enhance accumulation for physiological advantage. These results shed light on the evolution of pathways for novel fatty acid production in seeds, help explain some of the current limitations to accumulation of HFAs in transgenic plants, and may provide improved strategies for future engineering of their production.
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Affiliation(s)
- Patrick J Horn
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Jinjie Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
| | | | - Kathleen McGlew
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Nicholas A Thrower
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
| | - Matt Larson
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA
| | - Ana P Alonso
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, USA
| | - John Ohlrogge
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
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32
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Martos S, Gallego B, Sáez L, López-Alvarado J, Cabot C, Poschenrieder C. Characterization of Zinc and Cadmium Hyperaccumulation in Three Noccaea (Brassicaceae) Populations from Non-metalliferous Sites in the Eastern Pyrenees. FRONTIERS IN PLANT SCIENCE 2016; 7:128. [PMID: 26904085 PMCID: PMC4746256 DOI: 10.3389/fpls.2016.00128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/23/2016] [Indexed: 05/08/2023]
Abstract
The Southern slope of the Pyrenees is the meridional limit for the distribution of several Noccaea populations. However, the systematic description of these populations and their hyperaccumulation mechanisms are not well established. Morphological and genetic analysis (ITS and 3 chloroplast regions) were used to identify Noccaea populations localized on non-metallicolous soils during a survey in the Catalonian Pyrenees. Cd and Zn concentrations were analyzed in soils and plants both sampled in the field and grown hydroponically. The expression of selected metal transporter genes was assessed by quantitative PCR. The populations were identified as Noccaea brachypetala (Jord.) F.K. Mey by conspicuous morphological traits. Principal component analysis provided a clear separation among N. brachypetala, Noccaea caerulescens J. Presl & C. Presl and Noccaea occitanica (Jord.) F.K. Mey., three Noccaea species reported in the Pyrenees. Contrastingly, ITS and cpDNA analyses were unable to clearly differentiate these taxa. Differences in the expression of the metal transporter genes HMA3, HMA4, and MTP1 between N. caerulescens and N. brachypetala, and those amongst the N. brachypetala populations suggest differences in the strategies for handling enhanced Cd and Zn availability. This is the first report demonstrating Cd and Zn hyperaccumulation by N. brachypetala both in the field and in hydroponics. This comprehensive study based on taxonomic, molecular, and physiological data allows both the correct identification of this species and the characterization of population differences in hyperaccumulation and tolerance of Zn and Cd.
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Affiliation(s)
- Soledad Martos
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Berta Gallego
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Llorenç Sáez
- Botany Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Javier López-Alvarado
- Botany Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Catalina Cabot
- Biology Department, Universitat de les Illes BalearsPalma de Mallorca, Spain
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
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33
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Kazachkova Y, Khan A, Acuña T, López-Díaz I, Carrera E, Khozin-Goldberg I, Fait A, Barak S. Salt Induces Features of a Dormancy-Like State in Seeds of Eutrema (Thellungiella) salsugineum, a Halophytic Relative of Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:1071. [PMID: 27536302 PMCID: PMC4971027 DOI: 10.3389/fpls.2016.01071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/07/2016] [Indexed: 05/08/2023]
Abstract
The salinization of land is a major factor limiting crop production worldwide. Halophytes adapted to high levels of salinity are likely to possess useful genes for improving crop tolerance to salt stress. In addition, halophytes could provide a food source on marginal lands. However, despite halophytes being salt-tolerant plants, the seeds of several halophytic species will not germinate on saline soils. Yet, little is understood regarding biochemical and gene expression changes underlying salt-mediated inhibition of halophyte seed germination. We have used the halophytic Arabidopsis relative model system, Eutrema (Thellungiella) salsugineum to explore salt-mediated inhibition of germination. We show that E. salsugineum seed germination is inhibited by salt to a far greater extent than in Arabidopsis, and that this inhibition is in response to the osmotic component of salt exposure. E. salsugineum seeds remain viable even when germination is completely inhibited, and germination resumes once seeds are transferred to non-saline conditions. Moreover, removal of the seed coat from salt-treated seeds allows embryos to germinate on salt-containing medium. Mobilization of seed storage reserves is restricted in salt-treated seeds, while many germination-associated metabolic changes are arrested or progress to a lower extent. Salt-exposed seeds are further characterized by a reduced GA/ABA ratio and increased expression of the germination repressor genes, RGL2, ABI5, and DOG1. Furthermore, a salt-mediated increase in expression of a LATE EMBRYOGENESIS ABUNDANT gene and accretion of metabolites involved in osmoprotection indicates induction of processes associated with stress tolerance, and accumulation of easily mobilized carbon reserves. Overall, our results suggest that salt inhibits E. salsugineum seed germination by inducing a seed state with molecular features of dormancy while a physical constraint to radicle emergence is provided by the seed coat layers. This seed state could facilitate survival on saline soils until a rain event(s) increases soil water potential indicating favorable conditions for seed germination and establishment of salt-tolerant E. salsugineum seedlings.
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Affiliation(s)
- Yana Kazachkova
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Sde BokerIsrael
| | - Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Sde BokerIsrael
| | - Tania Acuña
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Sde BokerIsrael
| | - Isabel López-Díaz
- Instituto de Biología Molecular y Celular de Plantas, CSIC–UPV, ValenciaSpain
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas, CSIC–UPV, ValenciaSpain
| | - Inna Khozin-Goldberg
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Sde BokerIsrael
| | - Aaron Fait
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Sde BokerIsrael
- *Correspondence: Simon Barak, Aaron Fait,
| | - Simon Barak
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Sde BokerIsrael
- *Correspondence: Simon Barak, Aaron Fait,
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Mousset M, Flaven E, Justy F, Pouzadoux J, Gode C, Pauwels M, Gonneau C. Characterization and multiplexing of 21 microsatellite markers for the herb Noccaea caerulescens (Brassicaceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps.1500052. [PMID: 26697274 PMCID: PMC4683039 DOI: 10.3732/apps.1500052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/04/2015] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY Multiplexed microsatellite markers were developed for population genetic studies in the pseudometallophyte Noccaea caerulescens (Brassicaceae), a model species to investigate metal tolerance and hyperaccumulation in higher plants. METHODS AND RESULTS Microsatellite loci were isolated through pyrosequencing of an enriched DNA library. Three multiplexes combining four previously published and 17 newly designed markers were developed. The new markers were screened in metallicolous and nonmetallicolous populations from southern France. The total number of alleles per locus ranged from five to 18. The observed heterozygosity per locus and per population ranged from 0 to 0.83, and expected heterozygosity ranged from 0 to 0.89. CONCLUSIONS The investigated loci showed reasonable to high levels of polymorphism at the regional scale. The multiplex set should be helpful in investigating genetic diversity, population structure, and demographic history in N. caerulescens at various spatial scales.
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Affiliation(s)
- Mathilde Mousset
- Institut des Sciences de l’Évolution, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon 34095, Montpellier CEDEX 05, France
| | - Elodie Flaven
- Institut des Sciences de l’Évolution, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon 34095, Montpellier CEDEX 05, France
| | - Fabienne Justy
- Institut des Sciences de l’Évolution, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon 34095, Montpellier CEDEX 05, France
| | - Juliette Pouzadoux
- Institut des Sciences de l’Évolution, Université de Montpellier, CNRS, IRD, EPHE, CC 065, Place Eugène Bataillon 34095, Montpellier CEDEX 05, France
| | - Cécile Gode
- Université Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Maxime Pauwels
- Université Lille, CNRS, UMR 8198, Evo-Eco-Paleo, F-59000 Lille, France
| | - Cédric Gonneau
- Université de Lorraine, Laboratoire Sols et Environnement (UMR 1120), F-54518 Vandœuvre-lès-Nancy CEDEX, France
- INRA, Laboratoire Sols et Environnement (UMR 1120), F-54518 Vandœuvre-lès-Nancy CEDEX, France
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Hohmann N, Wolf EM, Lysak MA, Koch MA. A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History. THE PLANT CELL 2015; 27:2770-84. [PMID: 26410304 PMCID: PMC4682323 DOI: 10.1105/tpc.15.00482] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/13/2015] [Accepted: 09/05/2015] [Indexed: 05/18/2023]
Abstract
The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.
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Affiliation(s)
- Nora Hohmann
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Eva M Wolf
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
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Hao G, Bi H, Li Y, He Q, Ma Y, Guo X, Ma T. The whole chloroplast genomes of two Eutrema species (Brassicaceae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3727-8. [PMID: 26329763 DOI: 10.3109/19401736.2015.1079877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we determined the complete chloroplast genomes from two crucifer species of the Eutrema genus. The sizes of the two cp genomes were 153 948 bp (E. yunnanense) and 153 876 bp (E. heterophyllum). Both genomes have the typical quadripartite structure consisting of a large single copy region, a small single copy region and two inverted repeats. Gene contents and their relative positions of the 132 individual genes (87 protein-coding genes, eight rRNA, and 37 tRNA genes) of either genome were identical to each other. Phylogenetic analysis supports the idea that the currently recognized Eutrema genus is monophyletic and that E. salsugineum and Schrenkiella parvula evolved salt tolerance independently.
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Affiliation(s)
- Guoqian Hao
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Hao Bi
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Yuanshuo Li
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Qi He
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Yazhen Ma
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Xinyi Guo
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
| | - Tao Ma
- a MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University , Chengdu , China
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Mandáková T, Singh V, Krämer U, Lysak MA. Genome Structure of the Heavy Metal Hyperaccumulator Noccaea caerulescens and Its Stability on Metalliferous and Nonmetalliferous Soils. PLANT PHYSIOLOGY 2015; 169:674-89. [PMID: 26195571 PMCID: PMC4577401 DOI: 10.1104/pp.15.00619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/16/2015] [Indexed: 05/05/2023]
Abstract
Noccaea caerulescens (formerly known as Thlaspi caerulescens), an extremophile heavy metal hyperaccumulator model plant in the Brassicaceae family, is a morphologically and phenotypically diverse species exhibiting metal tolerance and leaf accumulation of zinc, cadmium, and nickel. Here, we provide a detailed genome structure of the approximately 267-Mb N. caerulescens genome, which has descended from seven chromosomes of the ancestral proto-Calepineae Karyotype (n = 7) through an unusually high number of pericentric inversions. Genome analysis in two other related species, Noccaea jankae and Raparia bulbosa, showed that all three species, and thus probably the entire Coluteocarpeae tribe, have descended from the proto-Calepineae Karyotype. All three analyzed species share the chromosome structure of six out of seven chromosomes and an unusually high metal accumulation in leaves, which remains moderate in N. jankae and R. bulbosa and is extreme in N. caerulescens. Among these species, N. caerulescens has the most derived karyotype, with species-specific inversions on chromosome NC6, which grouped onto its bottom arm functionally related genes of zinc and iron metal homeostasis comprising the major candidate genes NICOTIANAMINE SYNTHASE2 and ZINC-INDUCED FACILITATOR-LIKE1. Concurrently, copper and organellar metal homeostasis genes, which are functionally unrelated to the extreme traits characteristic of N. caerulescens, were grouped onto the top arm of NC6. Compared with Arabidopsis thaliana, more distal chromosomal positions in N. caerulescens were enriched among more highly expressed metal homeostasis genes but not among other groups of genes. Thus, chromosome rearrangements could have facilitated the evolution of enhanced metal homeostasis gene expression, a known hallmark of metal hyperaccumulation.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic (T.M., M.A.L.); andRuhr-Universität Bochum, 44780 Bochum, Germany (V.S., U.K.)
| | - Vasantika Singh
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic (T.M., M.A.L.); andRuhr-Universität Bochum, 44780 Bochum, Germany (V.S., U.K.)
| | - Ute Krämer
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic (T.M., M.A.L.); andRuhr-Universität Bochum, 44780 Bochum, Germany (V.S., U.K.)
| | - Martin A Lysak
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic (T.M., M.A.L.); andRuhr-Universität Bochum, 44780 Bochum, Germany (V.S., U.K.)
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38
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Mucha S, Walther D, Müller TM, Hincha DK, Glawischnig E. Substantial reprogramming of the Eutrema salsugineum (Thellungiella salsuginea) transcriptome in response to UV and silver nitrate challenge. BMC PLANT BIOLOGY 2015; 15:137. [PMID: 26063239 PMCID: PMC4464140 DOI: 10.1186/s12870-015-0506-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/24/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cruciferous plants synthesize a large variety of tryptophan-derived phytoalexins in response to pathogen infection, UV irradiation, or high dosages of heavy metals. The major phytoalexins of Eutrema salsugineum (Thellungiella salsuginea), which has recently been established as an extremophile model plant, are probably derivatives of indole glucosinolates, in contrast to Arabidopsis, which synthesizes characteristic camalexin from the glucosinolate precursor indole-3-acetaldoxime. RESULTS The transcriptional response of E. salsugineum to UV irradiation and AgNO3 was monitored by RNAseq and microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated. The putative Eutrema WRKY33 ortholog was functionally tested and shown to complement camalexin deficiency in Atwrky33 mutant. CONCLUSIONS In E. salsugineum, UV irradiation or heavy metal application resulted in substantial transcriptional reprogramming. Consistently induced genes of indole glucosinolate biosynthesis and modification will serve as candidate genes for the biosynthesis of Eutrema-specific phytoalexins.
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MESH Headings
- Biosynthetic Pathways/genetics
- Brassicaceae/drug effects
- Brassicaceae/genetics
- Brassicaceae/radiation effects
- Cellular Reprogramming/drug effects
- Cellular Reprogramming/radiation effects
- Gene Expression Regulation, Plant/drug effects
- Gene Expression Regulation, Plant/radiation effects
- Gene Knockout Techniques
- Glucosinolates/biosynthesis
- Indoles/metabolism
- Metals, Heavy/toxicity
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Sesquiterpenes/metabolism
- Silver Nitrate/pharmacology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Stress, Physiological/radiation effects
- Thiazoles/metabolism
- Transcription Factors/metabolism
- Transcription, Genetic/drug effects
- Transcription, Genetic/radiation effects
- Transcriptome/drug effects
- Transcriptome/genetics
- Transcriptome/radiation effects
- Tryptophan/biosynthesis
- Ultraviolet Rays
- Phytoalexins
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Affiliation(s)
- Stefanie Mucha
- Lehrstuhl für Genetik, Technische Universität München, D-85354, Freising, Germany.
| | - Dirk Walther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Germany.
| | - Teresa M Müller
- Lehrstuhl für Genetik, Technische Universität München, D-85354, Freising, Germany.
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Germany.
| | - Erich Glawischnig
- Lehrstuhl für Genetik, Technische Universität München, D-85354, Freising, Germany.
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Milia G, Camiolo S, Avesani L, Porceddu A. The dynamic loss and gain of introns during the evolution of the Brassicaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:915-924. [PMID: 25899207 DOI: 10.1111/tpj.12860] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/02/2015] [Accepted: 04/09/2015] [Indexed: 06/04/2023]
Abstract
Sequence comparison allows the detailed analysis of evolution at the nucleotide and amino acid levels, but much less information is known about the structural evolution of genes, i.e. how the number, length and distribution of introns change over time. We constructed a parsimonious model for the evolutionary rate of intron loss (IL) and intron gain (IG) within the Brassicaceae and found that IL/IG has been highly dynamic, with substantial differences between and even within lineages. The divergence of the Brassicaceae lineages I and II marked a dramatic change in the IL rate, with the common ancestor of lineage I losing introns three times more rapidly than the common ancestor of lineage II. Our data also indicate a subsequent declining trend in the rate of IL, although in Arabidopsis thaliana introns continue to be lost at approximately the ancestral rate. Variations in the rate of IL/IG within lineage II have been even more remarkable. Brassica rapa appears to have lost introns approximately 15 times more rapidly than the common ancestor of B. rapa and Schenkiella parvula, and approximately 25 times more rapidly than its sister species Eutrema salsugineum. Microhomology was detected at the splice sites of several dynamic introns suggesting that the non-homologous end-joining and double-strand break repair is a common pathway underlying IL/IG in these species. We also detected molecular signatures typical of mRNA-mediated IL, but only in B. rapa.
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Affiliation(s)
- Giampiera Milia
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
| | - Salvatore Camiolo
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
| | - Linda Avesani
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Andrea Porceddu
- Department of Agricultural Sciences, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
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40
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Khanal N, Moffatt BA, Gray GR. Acquisition of freezing tolerance in Arabidopsis and two contrasting ecotypes of the extremophile Eutrema salsugineum (Thellungiella salsuginea). JOURNAL OF PLANT PHYSIOLOGY 2015; 180:35-44. [PMID: 25889872 DOI: 10.1016/j.jplph.2015.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 05/28/2023]
Abstract
Eutrema salsugineum (Thellungiella salsuginea) is an extremophile, a close relative of Arabidopsis, but possessing much higher constitutive levels of tolerance to abiotic stress. This study aimed to characterize the freezing tolerance of Arabidopsis (Columbia ecotype) and two ecotypes of Eutrema (Yukon and Shandong) isolated from contrasting geographical locations. Under our growth conditions, maximal freezing tolerance was observed after two- and three-weeks of cold acclimation for Arabidopsis and Eutrema, respectively. The ecotypes of Eutrema and Arabidopsis do not differ in their constitutive level of freezing tolerance or short-term cold acclimation capacity. However Eutrema remarkably outperforms Arabidopsis in long-term acclimation capacity suggesting a wider phenotypic plasticity for the trait of freezing tolerance. The combination of drought treatment and one-week of cold acclimation was more effective than long-term cold acclimation in achieving maximum levels of freezing tolerance in Eutrema, but not Arabidopsis. Furthermore, it was demonstrated growth conditions, particularly irradiance, are determinates of the level of freezing tolerance attained during cold acclimation suggesting a role for photosynthetic processes in adaptive stress responses.
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Affiliation(s)
- Nityananda Khanal
- Department of Plant Sciences, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
| | - Barbara A Moffatt
- Department of Biology, University of Waterloo, Waterloo ON N2L 3G1, Canada
| | - Gordon R Gray
- Department of Plant Sciences, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada.
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Wang XJ, Shi DC, Wang XY, Wang J, Sun YS, Liu JQ. Evolutionary Migration of the Disjunct Salt Cress Eutrema salsugineum (= Thellungiella salsuginea, Brassicaceae) between Asia and North America. PLoS One 2015; 10:e0124010. [PMID: 25970468 PMCID: PMC4430283 DOI: 10.1371/journal.pone.0124010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/09/2015] [Indexed: 12/14/2022] Open
Abstract
Eutrema salsugineum (= Thellungiella salsuginea Brassicaceae), a species growing in highly saline habitats, is a good model for use in salt-stress research. However, its evolutionary migrations and genetic variations within and between disjunct regions from central Asia to northern China and North America remain largely unknown. We examined genetic variations and phylogeographic patterns of this species by sequencing ITS, 9 chloroplast (cp) DNA fragments (4379 bp) and 10 unlinked nuclear loci (6510 bp) of 24 populations across its distributional range. All markers suggested the high genetic poverty of this species and the limited number of genetic variations recovered was congruently partitioned between central Asia, northern China and North America. Further modelling of nuclear population-genetic data based on approximate bayesian computation (ABC) analyses indicated that the long-distance dispersals after the recent origin of E. salsugineum may have occurred from central Asia to the other two regions respectively within 20000 years. The fast demographic expansions should have occurred in northern China in a more recent past. Our study highlights the importance of using ABC analyses and nuclear population genetic data to trace evolutionary migrations of the disjunct distributions of the plants in the recent past.
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Affiliation(s)
- Xiao-Juan Wang
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
| | - Da-Chuan Shi
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou, China
| | - Xin-Yu Wang
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
| | - Juan Wang
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yong-Shuai Sun
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
| | - Jian-Quan Liu
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, School of Life Science, Lanzhou University, Lanzhou, China
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Slama I, Abdelly C, Bouchereau A, Flowers T, Savouré A. Diversity, distribution and roles of osmoprotective compounds accumulated in halophytes under abiotic stress. ANNALS OF BOTANY 2015; 115:433-47. [PMID: 25564467 PMCID: PMC4332610 DOI: 10.1093/aob/mcu239] [Citation(s) in RCA: 339] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/19/2014] [Accepted: 10/21/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Osmolytes are low-molecular-weight organic solutes, a broad group that encompasses a variety of compounds such as amino acids, tertiary sulphonium and quaternary ammonium compounds, sugars and polyhydric alcohols. Osmolytes are accumulated in the cytoplasm of halophytic species in order to balance the osmotic potential of the Na(+) and Cl(-) accumulated in the vacuole. The advantages of the accumulation of osmolytes are that they keep the main physiological functions of the cell active, the induction of their biosynthesis is controlled by environmental cues, and they can be synthesized at all developmental stages. In addition to their role in osmoregulation, osmolytes have crucial functions in protecting subcellular structures and in scavenging reactive oxygen species. SCOPE This review discusses the diversity of osmolytes among halophytes and their distribution within taxonomic groups, the intrinsic and extrinsic factors that influence their accumulation, and their role in osmoregulation and osmoprotection. Increasing the osmolyte content in plants is an interesting strategy to improve the growth and yield of crops upon exposure to salinity. Examples of transgenic plants as well as exogenous applications of some osmolytes are also discussed. Finally, the potential use of osmolytes in protein stabilization and solvation in biotechnology, including the pharmaceutical industry and medicine, are considered.
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Affiliation(s)
- Inès Slama
- Laboratoire des Plantes Extremophiles, Centre de Biotechnologie de Borj-Cedria (CBBC), BP 901, Hammam-Lif 2050, Tunisia, UMR 1349 IGEPP, INRA/Agrocampus Ouest/Université de Rennes 1, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK and Sorbonne Universités, UPMC Université Paris 06, Adaptation de Plantes aux Contraintes Environnementales, URF5, Case 156, 4 place Jussieu, F-75252 Paris cedex 05, France
| | - Chedly Abdelly
- Laboratoire des Plantes Extremophiles, Centre de Biotechnologie de Borj-Cedria (CBBC), BP 901, Hammam-Lif 2050, Tunisia, UMR 1349 IGEPP, INRA/Agrocampus Ouest/Université de Rennes 1, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK and Sorbonne Universités, UPMC Université Paris 06, Adaptation de Plantes aux Contraintes Environnementales, URF5, Case 156, 4 place Jussieu, F-75252 Paris cedex 05, France
| | - Alain Bouchereau
- Laboratoire des Plantes Extremophiles, Centre de Biotechnologie de Borj-Cedria (CBBC), BP 901, Hammam-Lif 2050, Tunisia, UMR 1349 IGEPP, INRA/Agrocampus Ouest/Université de Rennes 1, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK and Sorbonne Universités, UPMC Université Paris 06, Adaptation de Plantes aux Contraintes Environnementales, URF5, Case 156, 4 place Jussieu, F-75252 Paris cedex 05, France
| | - Tim Flowers
- Laboratoire des Plantes Extremophiles, Centre de Biotechnologie de Borj-Cedria (CBBC), BP 901, Hammam-Lif 2050, Tunisia, UMR 1349 IGEPP, INRA/Agrocampus Ouest/Université de Rennes 1, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK and Sorbonne Universités, UPMC Université Paris 06, Adaptation de Plantes aux Contraintes Environnementales, URF5, Case 156, 4 place Jussieu, F-75252 Paris cedex 05, France
| | - Arnould Savouré
- Laboratoire des Plantes Extremophiles, Centre de Biotechnologie de Borj-Cedria (CBBC), BP 901, Hammam-Lif 2050, Tunisia, UMR 1349 IGEPP, INRA/Agrocampus Ouest/Université de Rennes 1, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK and Sorbonne Universités, UPMC Université Paris 06, Adaptation de Plantes aux Contraintes Environnementales, URF5, Case 156, 4 place Jussieu, F-75252 Paris cedex 05, France
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Dorn KM, Fankhauser JD, Wyse DL, Marks MD. A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop. DNA Res 2015; 22:121-31. [PMID: 25632110 PMCID: PMC4401323 DOI: 10.1093/dnares/dsu045] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/21/2014] [Indexed: 12/30/2022] Open
Abstract
Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress.
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Affiliation(s)
- Kevin M Dorn
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | | | - Donald L Wyse
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - M David Marks
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
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Cappa JJ, Yetter C, Fakra S, Cappa PJ, DeTar R, Landes C, Pilon-Smits EAH, Simmons MP. Evolution of selenium hyperaccumulation in Stanleya (Brassicaceae) as inferred from phylogeny, physiology and X-ray microprobe analysis. THE NEW PHYTOLOGIST 2015; 205:583-95. [PMID: 25262627 DOI: 10.1111/nph.13071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/07/2014] [Indexed: 05/20/2023]
Abstract
Past studies have identified herbivory as a likely selection pressure for the evolution of hyperaccumulation, but few have tested the origin(s) of hyperaccumulation in a phylogenetic context. We focused on the evolutionary history of selenium (Se) hyperaccumulation in Stanleya (Brassicaceae). Multiple accessions were collected for all Stanleya taxa and two outgroup species. We sequenced four nuclear gene regions and performed a phylogenetic analysis. Ancestral reconstruction was used to predict the states for Se-related traits in a parsimony framework. Furthermore, we tested the taxa for Se localization and speciation using X-ray microprobe analyses. True hyperaccumulation was found in three taxa within the S. pinnata/bipinnata clade. Tolerance to hyperaccumulator Se concentrations was found in several taxa across the phylogeny, including the hyperaccumulators. X-ray analysis revealed two distinct patterns of leaf Se localization across the genus: marginal and vascular. All taxa accumulated predominantly (65-96%) organic Se with the C-Se-C configuration. These results give insight into the evolution of Se hyperaccumulation in Stanleya and suggest that Se tolerance and the capacity to produce organic Se are likely prerequisites for Se hyperaccumulation in Stanleya.
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Affiliation(s)
- Jennifer J Cappa
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
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Hohmann N, Schmickl R, Chiang TY, Lučanová M, Kolář F, Marhold K, Koch MA. Taming the wild: resolving the gene pools of non-model Arabidopsis lineages. BMC Evol Biol 2014; 14:224. [PMID: 25344686 PMCID: PMC4216345 DOI: 10.1186/s12862-014-0224-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/15/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses. RESULTS Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins. CONCLUSIONS Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
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Affiliation(s)
- Nora Hohmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
| | - Roswitha Schmickl
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, Cheng-Kung University, Tainan, Taiwan.
| | - Magdalena Lučanová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic.
| | - Filip Kolář
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic.
| | - Karol Marhold
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-25243, Czech Republic.
- Institute of Botany Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, SK-845 23, Slovakia.
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, 69120, Germany.
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Sedbrook JC, Phippen WB, Marks MD. New approaches to facilitate rapid domestication of a wild plant to an oilseed crop: example pennycress (Thlaspi arvense L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 227:122-32. [PMID: 25219314 DOI: 10.1016/j.plantsci.2014.07.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 05/22/2023]
Abstract
Oilseed crops are sources of oils and seed meal having a multitude of uses. While the domestication of soybean and rapeseed took extended periods of time, new genome-based techniques have ushered in an era where crop domestication can occur rapidly. One attractive target for rapid domestication is the winter annual plant Field Pennycress (Thlaspi arvense L.; pennycress; Brassicaceae). Pennycress grows widespread throughout temperate regions of the world and could serve as a winter oilseed-producing cover crop. If grown throughout the USA Midwest Corn Belt, for example, pennycress could produce as much as 840L/ha oils and 1470kg/ha press-cake annually on 16 million hectares of farmland currently left fallow during the fall through spring months. However, wild pennycress strains have inconsistent germination and stand establishment, un-optimized maturity for a given growth zone, suboptimal oils and meal quality for biofuels and food production, and significant harvest loss due to pod shatter. In this review, we describe the virtues and current shortcomings of pennycress and discuss how knowledge from studying Arabidopsis thaliana and other Brassicas, in combination with the advent of affordable next generation sequencing, can bring about the rapid domestication and improvement of pennycress and other crops.
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Affiliation(s)
- John C Sedbrook
- School of Biological Sciences, Illinois State University, Campus Box 4120, Normal, IL 61790 USA.
| | - Winthrop B Phippen
- School of Agriculture, Western Illinois University, 1 University Circle, Macomb, IL 61455, USA
| | - M David Marks
- Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN 55108, USA
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Lin YF, Severing EI, te Lintel Hekkert B, Schijlen E, Aarts MGM. A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens. FRONTIERS IN PLANT SCIENCE 2014; 5:261. [PMID: 24999345 PMCID: PMC4064536 DOI: 10.3389/fpls.2014.00261] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 05/21/2014] [Indexed: 05/06/2023]
Abstract
Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession "Ganges" by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure.
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Affiliation(s)
- Ya-Fen Lin
- Laboratory of Genetics, Wageningen UniversityWageningen, Netherlands
| | - Edouard I. Severing
- Laboratory of Genetics, Wageningen UniversityWageningen, Netherlands
- Laboratory of Bioinformatics, Wageningen UniversityWageningen, Netherlands
| | - Bas te Lintel Hekkert
- Business Unit Bioscience, Plant Research International, Wageningen University and Research CentresWageningen, Netherlands
| | - Elio Schijlen
- Business Unit Bioscience, Plant Research International, Wageningen University and Research CentresWageningen, Netherlands
| | - Mark G. M. Aarts
- Laboratory of Genetics, Wageningen UniversityWageningen, Netherlands
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Halimaa P, Blande D, Aarts MGM, Tuomainen M, Tervahauta A, Kärenlampi S. Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens. FRONTIERS IN PLANT SCIENCE 2014; 5:213. [PMID: 24904610 PMCID: PMC4033236 DOI: 10.3389/fpls.2014.00213] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 04/30/2014] [Indexed: 05/20/2023]
Abstract
The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics.
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Affiliation(s)
- Pauliina Halimaa
- Department of Biology, University of Eastern FinlandKuopio, Finland
| | - Daniel Blande
- Department of Biology, University of Eastern FinlandKuopio, Finland
| | - Mark G. M. Aarts
- Laboratory of Genetics, Wageningen UniversityWageningen, Netherlands
| | - Marjo Tuomainen
- Department of Biology, University of Eastern FinlandKuopio, Finland
| | - Arja Tervahauta
- Department of Biology, University of Eastern FinlandKuopio, Finland
| | - Sirpa Kärenlampi
- Department of Biology, University of Eastern FinlandKuopio, Finland
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Jarvis DE, Ryu CH, Beilstein MA, Schumaker KS. Distinct Roles for SOS1 in the Convergent Evolution of Salt Tolerance in Eutrema salsugineum and Schrenkiella parvula. Mol Biol Evol 2014; 31:2094-107. [DOI: 10.1093/molbev/msu152] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Vekemans X, Poux C, Goubet PM, Castric V. The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S-locus? J Evol Biol 2014; 27:1372-85. [PMID: 24725152 DOI: 10.1111/jeb.12372] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
Abstract
Evolutionary transitions between mating systems have occurred repetitively and independently in flowering plants. One of the most spectacular advances of the recent empirical literature in the field was the discovery of the underlying genetic machinery, which provides the opportunity to retrospectively document the scenario of the outcrossing to selfing transitions in a phylogenetic perspective. In this review, we explore the literature describing patterns of polymorphism and molecular evolution of the locus controlling self-incompatibility (S-locus) in selfing species of the Brassicaceae family in order to document the transition from outcrossing to selfing, a retrospective approach that we describe as the 'mating system genes approach'. The data point to strikingly contrasted scenarios of transition from outcrossing to selfing. We also perform original analyses of the fully sequenced genomes of four species showing self-compatibility, to compare the orthologous S-locus region with that of functional S-locus haplotypes. Phylogenetic analyses suggest that all species we investigated evolved independently towards loss of self-incompatibility, and in most cases almost intact sequences of either of the two S-locus genes suggest that these transitions occurred relatively recently. The S-locus region in Aethionema arabicum, representing the most basal lineage of Brassicaceae, showed unusual patterns so that our analysis could not determine whether self-incompatibility was lost secondarily, or evolved in the core Brassicaceae after the split with this basal lineage. Although the approach we detail can only be used when mating system genes have been identified in a clade, we suggest that its integration with phylogenetic and population genetic approaches should help determine the main routes of this predominant mating system shift in plants.
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Affiliation(s)
- X Vekemans
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université Lille 1, Villeneuve d'Ascq Cedex, France
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