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Shen L, Feng J. NIN-at the heart of NItrogen-fixing Nodule symbiosis. FRONTIERS IN PLANT SCIENCE 2024; 14:1284720. [PMID: 38283980 PMCID: PMC10810997 DOI: 10.3389/fpls.2023.1284720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
Legumes and actinorhizal plants establish symbiotic relationships with nitrogen-fixing bacteria, resulting in the formation of nodules. Nodules create an ideal environment for nitrogenase to convert atmospheric nitrogen into biological available ammonia. NODULE INCEPTION (NIN) is an indispensable transcription factor for all aspects of nodule symbiosis. Moreover, NIN is consistently lost in non-nodulating species over evolutions. Here we focus on recent advances in the signaling mechanisms of NIN during nodulation and discuss the role of NIN in the evolution of nitrogen-fixing nodule symbiosis.
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Affiliation(s)
- Lisha Shen
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jian Feng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- CAS−JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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2
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García-Soto I, Andersen SU, Monroy-Morales E, Robledo-Gamboa M, Guadarrama J, Aviles-Baltazar NY, Serrano M, Stougaard J, Montiel J. A collection of novel Lotus japonicus LORE1 mutants perturbed in the nodulation program induced by the Agrobacterium pusense strain IRBG74. FRONTIERS IN PLANT SCIENCE 2024; 14:1326766. [PMID: 38250449 PMCID: PMC10796720 DOI: 10.3389/fpls.2023.1326766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
The Lotus japonicus population carrying new Lotus retrotransposon 1 (LORE1) insertions represents a valuable biological resource for genetic research. New insertions were generated by activation of the endogenous retroelement LORE1a in the germline of the G329-3 plant line and arranged in a 2-D system for reverse genetics. LORE1 mutants identified in this collection contributes substantially to characterize candidate genes involved in symbiotic association of L. japonicus with its cognate symbiont, the nitrogen-fixing bacteria Mesorhizobium loti that infects root nodules intracellularly. In this study we aimed to identify novel players in the poorly explored intercellular infection induced by Agrobacterium pusense IRBG74 sp. For this purpose, a forward screen of > 200,000 LORE1 seedlings, obtained from bulk propagation of G329-3 plants, inoculated with IRBG74 was performed. Plants with perturbed nodulation were scored and the offspring were further tested on plates to confirm the symbiotic phenotype. A total of 110 Lotus mutants with impaired nodulation after inoculation with IRBG74 were obtained. A comparative analysis of nodulation kinetics in a subset of 20 mutants showed that most of the lines were predominantly affected in nodulation by IRBG74. Interestingly, additional defects in the main root growth were observed in some mutant lines. Sequencing of LORE1 flanking regions in 47 mutants revealed that 92 Lotus genes were disrupted by novel LORE1 insertions in these lines. In the IM-S34 mutant, one of the insertions was located in the 5´UTR of the LotjaGi5g1v0179800 gene, which encodes the AUTOPHAGY9 protein. Additional mutant alleles, named atg9-2 and atg9-3, were obtained in the reverse genetic collection. Nodule formation was significantly reduced in these mutant alleles after M. loti and IRBG74 inoculation, confirming the effectiveness of the mutant screening. This study describes an effective forward genetic approach to obtain novel mutants in Lotus with a phenotype of interest and to identify the causative gene(s).
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Affiliation(s)
- Ivette García-Soto
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Elizabeth Monroy-Morales
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Mariana Robledo-Gamboa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Jesús Guadarrama
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | | | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jesús Montiel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
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3
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Hassan AH, Mokhtar MM, El Allali A. Transposable elements: multifunctional players in the plant genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1330127. [PMID: 38239225 PMCID: PMC10794571 DOI: 10.3389/fpls.2023.1330127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.
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Affiliation(s)
- Asmaa H. Hassan
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Morad M. Mokhtar
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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4
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Ramakrishnan M, Papolu PK, Mullasseri S, Zhou M, Sharma A, Ahmad Z, Satheesh V, Kalendar R, Wei Q. The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome. PLANT CELL REPORTS 2023; 42:3-15. [PMID: 36401648 DOI: 10.1007/s00299-022-02945-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement. Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert's College (Autonomous), Kochi, 682018, Kerala, India
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, University of Helsinki, Biocenter 3, Viikinkaari 1, F1-00014, Helsinki, Finland.
- Institute of Plant Biology and Biotechnology (IPBB), Timiryazev Street 45, 050040, Almaty, Kazakhstan.
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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5
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Fukai E, Yoshikawa M, Shah N, Sandal N, Miyao A, Ono S, Hirakawa H, Akyol TY, Umehara Y, Nonomura KI, Stougaard J, Hirochika H, Hayashi M, Sato S, Andersen SU, Okazaki K. Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1397-1410. [PMID: 35792830 DOI: 10.1111/tpj.15896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.
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Affiliation(s)
- Eigo Fukai
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Manabu Yoshikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Niraj Shah
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Akio Miyao
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Seijiro Ono
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hideki Hirakawa
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Yosuke Umehara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Ken-Ichi Nonomura
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Hirohiko Hirochika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Makoto Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Shusei Sato
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | | | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
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6
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Villar I, Rubio MC, Calvo-Begueria L, Pérez-Rontomé C, Larrainzar E, Wilson MT, Sandal N, Mur LA, Wang L, Reeder B, Duanmu D, Uchiumi T, Stougaard J, Becana M. Three classes of hemoglobins are required for optimal vegetative and reproductive growth of Lotus japonicus: genetic and biochemical characterization of LjGlb2-1. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7778-7791. [PMID: 34387337 PMCID: PMC8664582 DOI: 10.1093/jxb/erab376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Legumes express two major types of hemoglobins, namely symbiotic (leghemoglobins) and non-symbiotic (phytoglobins), with the latter being categorized into three classes according to phylogeny and biochemistry. Using knockout mutants, we show that all three phytoglobin classes are required for optimal vegetative and reproductive development of Lotus japonicus. The mutants of two class 1 phytoglobins showed different phenotypes: Ljglb1-1 plants were smaller and had relatively more pods, whereas Ljglb1-2 plants had no distinctive vegetative phenotype and produced relatively fewer pods. Non-nodulated plants lacking LjGlb2-1 showed delayed growth and alterations in the leaf metabolome linked to amino acid processing, fermentative and respiratory pathways, and hormonal balance. The leaves of mutant plants accumulated salicylic acid and contained relatively less methyl jasmonic acid, suggesting crosstalk between LjGlb2-1 and the signaling pathways of both hormones. Based on the expression of LjGlb2-1 in leaves, the alterations of flowering and fruiting of nodulated Ljglb2-1 plants, the developmental and biochemical phenotypes of the mutant fed on ammonium nitrate, and the heme coordination and reactivity of the protein toward nitric oxide, we conclude that LjGlb2-1 is not a leghemoglobin but an unusual class 2 phytoglobin. For comparison, we have also characterized a close relative of LjGlb2-1 in Medicago truncatula, MtLb3, and conclude that this is an atypical leghemoglobin.
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Affiliation(s)
- Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Maria C Rubio
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Laura Calvo-Begueria
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Carmen Pérez-Rontomé
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Estibaliz Larrainzar
- Department of Sciences, Institute for Multidisciplinary Research in Applied Biology, Campus Arrosadía, Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - Michael T Wilson
- School of Life Sciences, Essex University, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Luis A Mur
- Aberystwyth University, Institute of Biological, Environmental and Rural Sciences, Aberystwyth, SY23 3DA, Wales, UK
| | - Longlong Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Brandon Reeder
- School of Life Sciences, Essex University, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
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Orłowska R, Pachota KA, Dynkowska WM, Niedziela A, Bednarek PT. Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley. Int J Mol Sci 2021; 22:ijms22136783. [PMID: 34202586 PMCID: PMC8268840 DOI: 10.3390/ijms22136783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.
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Orozco-Arias S, Isaza G, Guyot R. Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. Int J Mol Sci 2019; 20:E3837. [PMID: 31390781 PMCID: PMC6696364 DOI: 10.3390/ijms20153837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170001, Colombia
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170001, Colombia.
- Institut de Recherche pour le Développement, CIRAD, University Montpellier, 34000 Montpellier, France.
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9
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Wong JEMM, Nadzieja M, Madsen LH, Bücherl CA, Dam S, Sandal NN, Couto D, Derbyshire P, Uldum-Berentsen M, Schroeder S, Schwämmle V, Nogueira FCS, Asmussen MH, Thirup S, Radutoiu S, Blaise M, Andersen KR, Menke FLH, Zipfel C, Stougaard J. A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation. Proc Natl Acad Sci U S A 2019; 116:14339-14348. [PMID: 31239345 PMCID: PMC6628658 DOI: 10.1073/pnas.1815425116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The establishment of nitrogen-fixing root nodules in legume-rhizobia symbiosis requires an intricate communication between the host plant and its symbiont. We are, however, limited in our understanding of the symbiosis signaling process. In particular, how membrane-localized receptors of legumes activate signal transduction following perception of rhizobial signaling molecules has mostly remained elusive. To address this, we performed a coimmunoprecipitation-based proteomics screen to identify proteins associated with Nod factor receptor 5 (NFR5) in Lotus japonicus. Out of 51 NFR5-associated proteins, we focused on a receptor-like cytoplasmic kinase (RLCK), which we named NFR5-interacting cytoplasmic kinase 4 (NiCK4). NiCK4 associates with heterologously expressed NFR5 in Nicotiana benthamiana, and directly binds and phosphorylates the cytoplasmic domains of NFR5 and NFR1 in vitro. At the cellular level, Nick4 is coexpressed with Nfr5 in root hairs and nodule cells, and the NiCK4 protein relocates to the nucleus in an NFR5/NFR1-dependent manner upon Nod factor treatment. Phenotyping of retrotransposon insertion mutants revealed that NiCK4 promotes nodule organogenesis. Together, these results suggest that the identified RLCK, NiCK4, acts as a component of the Nod factor signaling pathway downstream of NFR5.
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Affiliation(s)
- Jaslyn E M M Wong
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Lene H Madsen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Christoph A Bücherl
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Svend Dam
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Niels N Sandal
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Daniel Couto
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Mette Uldum-Berentsen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Sina Schroeder
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Fábio C S Nogueira
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Mette H Asmussen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Søren Thirup
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Mickaël Blaise
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark;
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10
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Hashiguchi M, Tanaka H, Muguerza M, Akashi R, Sandal NN, Andersen SU, Sato S. Lotus japonicus Genetic, Mutant, and Germplasm Resources. ACTA ACUST UNITED AC 2018; 3:e20070. [PMID: 29927119 DOI: 10.1002/cppb.20070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A quarter of a century has passed since Lotus japonicus was proposed as a model legume because of its suitability for molecular genetic studies. Since then, a comprehensive set of genetic resources and tools has been developed, including recombinant inbred lines, a collection of wild accessions, published mutant lines, a large collection of mutant lines tagged with LORE1 insertions, cDNA clones with expressed sequence tag (EST) information, genomic clones with end-sequence information, and a reference genome sequence. Resource centers in Japan and Denmark ensure easy access to data and materials, and the resources have greatly facilitated L. japonicus research, thereby contributing to the molecular understanding of characteristic legume features such as endosymbiosis. Here, we provide detailed instructions for L. japonicus cultivation and describe how to order materials and access data using the resource center websites. The comprehensive overview presented here will make L. japonicus more easily accessible as a model system, especially for research groups new to L. japonicus research. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Hidenori Tanaka
- University of Miyazaki, Faculty of Agriculture, Miyazaki, Japan
| | - Melody Muguerza
- University of Miyazaki, Faculty of Agriculture, Miyazaki, Japan
| | - Ryo Akashi
- University of Miyazaki, Faculty of Agriculture, Miyazaki, Japan
| | | | | | - Shusei Sato
- Tohoku University, Graduate School of Life Sciences, Sendai, Japan
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11
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Masuta Y, Kawabe A, Nozawa K, Naito K, Kato A, Ito H. Characterization of a heat-activated retrotransposon in Vigna angularis. BREEDING SCIENCE 2018; 68:168-176. [PMID: 29875600 PMCID: PMC5982181 DOI: 10.1270/jsbbs.17085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 05/14/2023]
Abstract
In plants, several transposable elements are conserved across species. We found a homolog of ONSEN, which is a heat-activated retrotransposon originally isolated from Arabidopsis thaliana, in Vigna. The ONSEN-like elements (VaONS) were detected in all the analyzed Japanese accessions of Vigna angularis (adzuki bean) by Southern blot analysis. However, VaONS sequences were observed to be polymorphic in the different accessions. Interestingly, extrachromosomal DNA (ecDNA) was detected in some accessions of adzuki bean, indicating the conserved heat-activation of VaONS. Furthermore, we successfully induced retrotransposition of VaONS in adzuki plant regenerated through callus. Findings of our study should provide a new tool for molecular breeding of adzuki bean.
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Affiliation(s)
- Yukari Masuta
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo Motoyama, Kita-ku, Kyoto 603-8555,
Japan
| | - Kosuke Nozawa
- Graduate School of Life Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Ken Naito
- Genetic Resource Center, National Agriculture and Food Research Organization,
2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Atsushi Kato
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
- Corresponding author (e-mail: )
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12
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Pedersen CT, Loke I, Lorentzen A, Wolf S, Kamble M, Kristensen SK, Munch D, Radutoiu S, Spillner E, Roepstorff P, Thaysen-Andersen M, Stougaard J, Dam S. N-glycan maturation mutants in Lotus japonicus for basic and applied glycoprotein research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:394-407. [PMID: 28407380 DOI: 10.1111/tpj.13570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/27/2017] [Accepted: 04/03/2017] [Indexed: 05/11/2023]
Abstract
Studies of protein N-glycosylation are important for answering fundamental questions on the diverse functions of glycoproteins in plant growth and development. Here we generated and characterised a comprehensive collection of Lotus japonicusLORE1 insertion mutants, each lacking the activity of one of the 12 enzymes required for normal N-glycan maturation in the glycosylation machinery. The inactivation of the individual genes resulted in altered N-glycan patterns as documented using mass spectrometry and glycan-recognising antibodies, indicating successful identification of null mutations in the target glyco-genes. For example, both mass spectrometry and immunoblotting experiments suggest that proteins derived from the α1,3-fucosyltransferase (Lj3fuct) mutant completely lacked α1,3-core fucosylation. Mass spectrometry also suggested that the Lotus japonicus convicilin 2 was one of the main glycoproteins undergoing differential expression/N-glycosylation in the mutants. Demonstrating the functional importance of glycosylation, reduced growth and seed production phenotypes were observed for the mutant plants lacking functional mannosidase I, N-acetylglucosaminyltransferase I, and α1,3-fucosyltransferase, even though the relative protein composition and abundance appeared unaffected. The strength of our N-glycosylation mutant platform is the broad spectrum of resulting glycoprotein profiles and altered physiological phenotypes that can be produced from single, double, triple and quadruple mutants. This platform will serve as a valuable tool for elucidating the functional role of protein N-glycosylation in plants. Furthermore, this technology can be used to generate stable plant mutant lines for biopharmaceutical production of glycoproteins displaying relative homogeneous and mammalian-like N-glycosylation features.
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Affiliation(s)
- Carina T Pedersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Ian Loke
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Andrea Lorentzen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Sara Wolf
- Department of Engineering, Aarhus University, DK-8000, Aarhus, Denmark
| | - Manoj Kamble
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Sebastian K Kristensen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - David Munch
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Simona Radutoiu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Edzard Spillner
- Department of Engineering, Aarhus University, DK-8000, Aarhus, Denmark
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Morten Thaysen-Andersen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Svend Dam
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
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Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species. Sci Rep 2017; 7:5966. [PMID: 28729554 PMCID: PMC5519738 DOI: 10.1038/s41598-017-06084-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023] Open
Abstract
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
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Kawaharada Y, James EK, Kelly S, Sandal N, Stougaard J. The Ethylene Responsive Factor Required for Nodulation 1 (ERN1) Transcription Factor Is Required for Infection-Thread Formation in Lotus japonicus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:194-204. [PMID: 28068194 DOI: 10.1094/mpmi-11-16-0237-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Several hundred genes are transcriptionally regulated during infection-thread formation and development of nitrogen-fixing root nodules. We have characterized a set of Lotus japonicus mutants impaired in root-nodule formation and found that the causative gene, Ern1, encodes a protein with a characteristic APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription-factor domain. Phenotypic characterization of four ern1 alleles shows that infection pockets are formed but root-hair infection threads are absent. Formation of root-nodule primordia is delayed and no normal transcellular infection threads are found in the infected nodules. Corroborating the role of ERN1 (ERF Required for Nodulation1) in nodule organogenesis, spontaneous nodulation induced by an autoactive CCaMK and cytokinin-induced nodule primordia were not observed in ern1 mutants. Expression of Ern1 is induced in the susceptible zone by Nod factor treatment or rhizobial inoculation. At the cellular level, the pErn1:GUS reporter is highly expressed in root epidermal cells of the susceptible zone and in the cortical cells that form nodule primordia. The genetic regulation of this cellular expression pattern was further investigated in symbiotic mutants. Nod factor induction of Ern1 in epidermal cells was found to depend on Nfr1, Cyclops, and Nsp2 but was independent of Nin and Nf-ya1. These results suggest that ERN1 functions as a transcriptional regulator involved in the formation of infection threads and development of nodule primordia and may coordinate these two processes.
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Affiliation(s)
- Yasuyuki Kawaharada
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Euan K James
- 2 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Simon Kelly
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Niels Sandal
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Jens Stougaard
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
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15
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Masuta Y, Nozawa K, Takagi H, Yaegashi H, Tanaka K, Ito T, Saito H, Kobayashi H, Matsunaga W, Masuda S, Kato A, Ito H. Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture. PLANT & CELL PHYSIOLOGY 2017; 58:375-384. [PMID: 28013279 DOI: 10.1093/pcp/pcw202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation. The heat activation of ONSEN transcripts was not significantly up-regulated in tissue culture compared with that in heat-stressed seedlings, indicating that the transposition of ONSEN was regulated independently of the transcript level. RdDM-related genes were up-regulated by heat stress in both tissue culture and seedlings. The level of DNA methylation of ONSEN did not show any change in tissue culture, and the amount of ONSEN-derived small RNAs was not affected by heat stress. The results indicated that the transposition of ONSEN was regulated by an alternative mechanism in addition to the RdDM-mediated epigenetic regulation in tissue culture. We applied the tissue culture-induced transposition of ONSEN to Japanese radish, an important breeding species of the family Brassicaceae. Several new insertions were detected in a regenerated plant derived from heat-stressed tissues and its self-fertilized progeny, revealing the possibility of molecular breeding without genetic modification.
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Affiliation(s)
- Yukari Masuta
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Kosuke Nozawa
- Faculty of Science, Hokkaido University, Sappor, Japan
| | | | | | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Tasuku Ito
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Hideyuki Saito
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Seiji Masuda
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Atsushi Kato
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University, Sappor, Japan
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16
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Mun T, Małolepszy A, Sandal N, Stougaard J, Andersen SU. User Guide for the LORE1 Insertion Mutant Resource. Methods Mol Biol 2017; 1610:13-23. [PMID: 28439854 DOI: 10.1007/978-1-4939-7003-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Lotus japonicus is a model legume used in the study of plant-microbe interactions, especially in the field of biological nitrogen fixation due to its ability to enter into a symbiotic relationship with a soil bacterium, Mesorhizobium loti. The LORE1 mutant population is a valuable resource for reverse genetics in L. japonicus due to its non-transgenic nature, high tagging efficiency, and low copy count. Here, we outline a workflow for identifying, ordering, and establishing homozygous LORE1 mutant lines for a gene of interest, LjFls2, including protocols for growth and genotyping of a segregating LORE1 population.
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Affiliation(s)
- Terry Mun
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Anna Małolepszy
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
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17
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Negi P, Rai AN, Suprasanna P. Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1448. [PMID: 27777577 PMCID: PMC5056178 DOI: 10.3389/fpls.2016.01448] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/12/2016] [Indexed: 05/02/2023]
Abstract
The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.
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Affiliation(s)
| | | | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreTrombay, India
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18
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Małolepszy A, Mun T, Sandal N, Gupta V, Dubin M, Urbański D, Shah N, Bachmann A, Fukai E, Hirakawa H, Tabata S, Nadzieja M, Markmann K, Su J, Umehara Y, Soyano T, Miyahara A, Sato S, Hayashi M, Stougaard J, Andersen SU. The LORE1 insertion mutant resource. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:306-317. [PMID: 27322352 DOI: 10.1111/tpj.13243] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 05/08/2023]
Abstract
Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.
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Affiliation(s)
- Anna Małolepszy
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Terry Mun
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niels Sandal
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Vikas Gupta
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Manu Dubin
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Dorian Urbański
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niraj Shah
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Asger Bachmann
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Eigo Fukai
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Marcin Nadzieja
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Katharina Markmann
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Junyi Su
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Yosuke Umehara
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Takashi Soyano
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Akira Miyahara
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Makoto Hayashi
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Stig U Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
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19
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Grandbastien MA. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:403-16. [DOI: 10.1016/j.bbagrm.2014.07.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
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20
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Alzohairy AM, Sabir JSM, Gyulai GB, Younis RAA, Jansen RK, Bahieldin A. Environmental stress activation of plant long-terminal repeat retrotransposons. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:557-567. [PMID: 32481013 DOI: 10.1071/fp13339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/23/2014] [Indexed: 06/11/2023]
Abstract
Genomic retrotransposons (RTs) are major components of most plant genomes. They spread throughout the genomes by a process termed retrotransposition, which consists of reverse transcription and reinsertion of the copied element into a new genomic location (a copy-and-paste system). Abiotic and biotic stresses activate long-terminal repeat (LTR) RTs in photosynthetic eukaryotes from algae to angiosperms. LTR RTs could represent a threat to the integrity of host genomes because of their activity and mutagenic potential by epigenetic regulation. Host genomes have developed mechanisms to control the activity of the retroelements and their mutagenic potential. Some LTR RTs escape these defense mechanisms, and maintain their ability to be activated and transpose as a result of biotic or abiotic stress stimuli. These stimuli include pathogen infection, mechanical damage, in vitro tissue culturing, heat, drought and salt stress, generation of doubled haploids, X-ray irradiation and many others. Reactivation of LTR RTs differs between different plant genomes. The expression levels of reactivated RTs are influenced by the transcriptional and post-transcriptional gene silencing mechanisms (e.g. DNA methylation, heterochromatin formation and RNA interference). Moreover, the insertion of RTs (e.g. Triticum aestivum L. Wis2-1A) into or next to coding regions of the host genome can generate changes in the expression of adjacent host genes of the host. In this paper, we review the ways that plant genomic LTR RTs are activated by environmental stimuli to affect restructuring and diversification of the host genome.
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Affiliation(s)
- Ahmed M Alzohairy
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Jamal S M Sabir
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - G Bor Gyulai
- Institute of Genetics and Biotechnology, St. Stephanus University, Gödöll? H-2103, Hungary
| | - Rania A A Younis
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Robert K Jansen
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
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Urbański DF, Małolepszy A, Stougaard J, Andersen SU. High-throughput and targeted genotyping of Lotus japonicus LORE1 insertion mutants. Methods Mol Biol 2013; 1069:119-46. [PMID: 23996313 DOI: 10.1007/978-1-62703-613-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The Lotus Retrotransposon 1 (LORE1) is used for genome-wide mutagenesis of the model legume Lotus japonicus. Characterization of the LORE1 insertion sites in individual mutant lines is critical for development and use of the resource. Here we present guidelines for use of the LORE1 reverse genetics resource and provide detailed protocols for insertion site identification and validation. For high-throughput identification of insertions in up to 9,216 pooled lines, the FSTpoolit protocol takes advantage of Splinkerette adapters, molecular barcoding, 2D pooling, Illumina sequencing, and automated data analysis using the freely available FSTpoolit software. Complementing the high-throughput approach, we describe a simplified sequence-specific amplification polymorphism (SSAP) protocol well suited for quick identification of insertion sites in a limited number of lines. Both the FSTpoolit and simplified SSAP protocols are generally applicable to insertion site identification in any insertional mutagenesis setup.
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Affiliation(s)
- Dorian Fabian Urbański
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus, Denmark
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Pislariu CI, D. Murray J, Wen J, Cosson V, Muni RRD, Wang M, A. Benedito V, Andriankaja A, Cheng X, Jerez IT, Mondy S, Zhang S, Taylor ME, Tadege M, Ratet P, Mysore KS, Chen R, Udvardi MK. A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation. PLANT PHYSIOLOGY 2012; 159:1686-99. [PMID: 22679222 PMCID: PMC3425206 DOI: 10.1104/pp.112.197061] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/01/2012] [Indexed: 05/20/2023]
Abstract
A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.
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Affiliation(s)
| | | | - JiangQi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Viviane Cosson
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - RajaSekhara Reddy Duvvuru Muni
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Mingyi Wang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Vagner A. Benedito
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Andry Andriankaja
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Xiaofei Cheng
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Ivone Torres Jerez
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Samuel Mondy
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Shulan Zhang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Mark E. Taylor
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Million Tadege
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Pascal Ratet
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Kirankumar S. Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Rujin Chen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Michael K. Udvardi
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
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Tsukahara S, Kawabe A, Kobayashi A, Ito T, Aizu T, Shin-i T, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T. Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata. Genes Dev 2012; 26:705-13. [PMID: 22431508 DOI: 10.1101/gad.183871.111] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The plant genome evolves with rapid proliferation of LTR-type retrotransposons, which is associated with their clustered accumulation in gene-poor regions, such as centromeres. Despite their major role for plant genome evolution, no mobile LTR element with targeted integration into gene-poor regions has been identified in plants. Here, we report such targeted integrations de novo. We and others have previously shown that an ATCOPIA93 family retrotransposon in Arabidopsis thaliana is mobilized when the DNA methylation machinery is compromised. Although ATCOPIA93 family elements are low copy number in the wild-type A. thaliana genome, high-copy-number related elements are found in the wild-type Arabidopsis lyrata genome, and they show centromere-specific localization. To understand the mechanisms for the clustered accumulation of the A. lyrata elements directly, we introduced one of them, named Tal1 (Transposon of Arabidopsis lyrata 1), into A. thaliana by transformation. The introduced Tal1 was retrotransposed in A. thaliana, and most of the retrotransposed copies were found in centromeric repeats of A. thaliana, suggesting targeted integration. The targeted integration is especially surprising because the centromeric repeat sequences differ considerably between A. lyrata and A. thaliana. Our results revealed unexpectedly dynamic controls for evolution of the transposon-rich heterochromatic regions.
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Affiliation(s)
- Sayuri Tsukahara
- Department of Integrated Genetics, National Institute of Genetics, Shizuoka 411-8540, Japan
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Fukai E, Soyano T, Umehara Y, Nakayama S, Hirakawa H, Tabata S, Sato S, Hayashi M. Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:720-30. [PMID: 22014259 DOI: 10.1111/j.1365-313x.2011.04826.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recovered by pyrosequencing. The two-dimensional arrangement of the plant population, together with the use of multiple identifier sequences in the primers used to amplify the flanking regions, made it possible to trace insertions back to the original plant lines. The large-scale detection of new LORE1 insertion sites revealed a preference for genic regions, especially in exons of protein-coding genes, which is an interesting feature to consider in the interaction between host genomes and chromoviruses, to which LORE1 belongs, a class of retrotransposon widely distributed among plants. Forward screening of the symbiotic mutants from the population succeeded to identify five symbiotic mutants of known genes. These data suggest that LORE1 is robust as a genetic tool.
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Affiliation(s)
- Eigo Fukai
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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Urbański DF, Małolepszy A, Stougaard J, Andersen SU. Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:731-41. [PMID: 22014280 DOI: 10.1111/j.1365-313x.2011.04827.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Use of insertion mutants facilitates functional analysis of genes, but it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics in most plant species. The main challenge is developing efficient high-throughput procedures for both mutagenesis and identification of insertion sites. To date, only floral-dip T-DNA transformation of Arabidopsis has produced independent germinal insertions, thereby allowing generation of mutant populations from seeds of single plants. In addition, advances in insertion detection have been hampered by a lack of protocols, including software for automated data analysis, that take full advantage of high-throughput next-generation sequencing. We have addressed these challenges by developing the FSTpoolit protocol and software package, and here we demonstrate its efficacy by detecting 8935 LORE1 insertions in 3744 Lotus japonicus plants. The identified insertions show that the endogenous LORE1 retrotransposon is well suited for insertion mutagenesis due to homogenous gene targeting and exonic insertion preference. As LORE1 transposition occurs in the germline, harvesting seeds from a single founder line and cultivating progeny generates a complete mutant population. This ease of LORE1 mutagenesis, combined with the efficient FSTpoolit protocol, which exploits 2D pooling, Illumina sequencing and automated data analysis, allows highly cost-efficient development of a comprehensive reverse genetic resource.
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Affiliation(s)
- Dorian Fabian Urbański
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
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26
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Fukai E, Umehara Y, Sato S, Endo M, Kouchi H, Hayashi M, Stougaard J, Hirochika H. Derepression of the plant Chromovirus LORE1 induces germline transposition in regenerated plants. PLoS Genet 2010; 6:e1000868. [PMID: 20221264 PMCID: PMC2832683 DOI: 10.1371/journal.pgen.1000868] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 02/01/2010] [Indexed: 12/13/2022] Open
Abstract
Transposable elements represent a large proportion of the eukaryotic genomes. Long Terminal Repeat (LTR) retrotransposons are very abundant and constitute the predominant family of transposable elements in plants. Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements. These elements contain chromodomains in their integrases, which suggests a preference for insertion into heterochromatin. In turn, this preference might have contributed to the patterning of heterochromatin observed in host genomes. Despite their potential importance for our understanding of plant genome dynamics and evolution, the regulatory mechanisms governing the behavior of chromoviruses and their activities remain largely uncharacterized. Here, we report a detailed analysis of the spatio-temporal activity of a plant chromovirus in the endogenous host. We examined LORE1a, a member of the endogenous chromovirus LORE1 family from the model legume Lotus japonicus. We found that this chromovirus is stochastically de-repressed in plant populations regenerated from de-differentiated cells and that LORE1a transposes in the male germline. Bisulfite sequencing of the 5′ LTR and its surrounding region suggests that tissue culture induces a loss of epigenetic silencing of LORE1a. Since LTR promoter activity is pollen specific, as shown by the analysis of transgenic plants containing an LTR::GUS fusion, we conclude that male germline-specific LORE1a transposition in pollen grains is controlled transcriptionally by its own cis-elements. New insertion sites of LORE1a copies were frequently found in genic regions and show no strong insertional preferences. These distinctive novel features of LORE1 indicate that this chromovirus has considerable potential for generating genetic and epigenetic diversity in the host plant population. Our results also define conditions for the use of LORE1a as a genetic tool. In contrast to animals, where germline differentiation initiates early in embryogenesis, germline differentiation in plants starts in the adult phase during reproductive development. Transpositions of transposable elements in both somatic and gametic cells can be transmitted to the next generation. As a result, plant genomes may contain transposable elements exhibiting a variety of tissue-specific activities. Thus far, the spatio-temporal activity of LTR retrotransposons, the most abundant class of transposable elements in plants, has not been well characterized. Here, we report a detailed analysis of the spatio-temporal transposition pattern of a plant LTR retrotransposon in the endogenous system. Using the model legume Lotus japonicus, we found that LORE1a, a member of the chromovirus LORE1 family that belongs to the Gypsy superfamily, was epigenetically de-repressed via tissue culture. Activation was stochastic and derepression was maintained in regenerated plants. This feature made it possible to trace the original spatio-temporal activity of the retrotransposon in the intact plants. We determined that the plant chromovirus retrotransposes mainly in the male germline, without obvious insertional preferences for chromosomal regions. This finding suggests that the tissue specificity of transposable elements should be taken into account when considering their impact on the host genome dynamics and evolution.
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Affiliation(s)
- Eigo Fukai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
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FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut. Chromosome Res 2010; 18:227-46. [PMID: 20127167 PMCID: PMC2844528 DOI: 10.1007/s10577-009-9109-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 12/16/2009] [Indexed: 12/26/2022]
Abstract
In this paper, we describe a Ty3-gypsy retrotransposon from allotetraploid peanut (Arachis hypogaea) and its putative diploid ancestors Arachis duranensis (A-genome) and Arachis ipaënsis (B-genome). The consensus sequence is 11,223 bp. The element, named FIDEL (Fairly long Inter-Dispersed Euchromatic LTR retrotransposon), is more frequent in the A- than in the B-genome, with copy numbers of about 3,000 (±950, A. duranensis), 820 (±480, A. ipaënsis), and 3,900 (±1,500, A. hypogaea) per haploid genome. Phylogenetic analysis of reverse transcriptase sequences showed distinct evolution of FIDEL in the ancestor species. Fluorescent in situ hybridization revealed disperse distribution in euchromatin and absence from centromeres, telomeric regions, and the nucleolar organizer region. Using paired sequences from bacterial artificial chromosomes, we showed that elements appear less likely to insert near conserved ancestral genes than near the fast evolving disease resistance gene homologs. Within the Ty3-gypsy elements, FIDEL is most closely related with the Athila/Calypso group of retrovirus-like retrotransposons. Putative transmembrane domains were identified, supporting the presence of a vestigial envelope gene. The results emphasize the importance of FIDEL in the evolution and divergence of different Arachis genomes and also may serve as an example of the role of retrotransposons in the evolution of legume genomes in general.
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Rakocevic A, Mondy S, Tirichine L, Cosson V, Brocard L, Iantcheva A, Cayrel A, Devier B, Abu El-Heba GA, Ratet P. MERE1, a low-copy-number copia-type retroelement in Medicago truncatula active during tissue culture. PLANT PHYSIOLOGY 2009; 151:1250-63. [PMID: 19656907 PMCID: PMC2773106 DOI: 10.1104/pp.109.138024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 07/29/2009] [Indexed: 05/18/2023]
Abstract
We have identified an active Medicago truncatula copia-like retroelement called Medicago RetroElement1-1 (MERE1-1) as an insertion in the symbiotic NSP2 gene. MERE1-1 belongs to a low-copy-number family in the sequenced Medicago genome. These copies are highly related, but only three of them have a complete coding region and polymorphism exists between the long terminal repeats of these different copies. This retroelement family is present in all M. truncatula ecotypes tested but also in other legume species like Lotus japonicus. It is active only during tissue culture in both R108 and Jemalong Medicago accessions and inserts preferentially in genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pascal Ratet
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France (A.R., S.M., L.T., V.C., L.B., A.C., B.D., G.A.A.E.-H., P.R.); and AgroBioinstitute, 1164 Sofia, Bulgaria (A.I.)
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Høgslund N, Radutoiu S, Krusell L, Voroshilova V, Hannah MA, Goffard N, Sanchez DH, Lippold F, Ott T, Sato S, Tabata S, Liboriussen P, Lohmann GV, Schauser L, Weiller GF, Udvardi MK, Stougaard J. Dissection of symbiosis and organ development by integrated transcriptome analysis of lotus japonicus mutant and wild-type plants. PLoS One 2009; 4:e6556. [PMID: 19662091 PMCID: PMC2717213 DOI: 10.1371/journal.pone.0006556] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 06/18/2009] [Indexed: 01/06/2023] Open
Abstract
Genetic analyses of plant symbiotic mutants has led to the identification of key genes involved in Rhizobium-legume communication as well as in development and function of nitrogen fixing root nodules. However, the impact of these genes in coordinating the transcriptional programs of nodule development has only been studied in limited and isolated studies. Here, we present an integrated genome-wide analysis of transcriptome landscapes in Lotus japonicus wild-type and symbiotic mutant plants. Encompassing five different organs, five stages of the sequentially developed determinate Lotus root nodules, and eight mutants impaired at different stages of the symbiotic interaction, our data set integrates an unprecedented combination of organ- or tissue-specific profiles with mutant transcript profiles. In total, 38 different conditions sampled under the same well-defined growth regimes were included. This comprehensive analysis unravelled new and unexpected patterns of transcriptional regulation during symbiosis and organ development. Contrary to expectations, none of the previously characterized nodulins were among the 37 genes specifically expressed in nodules. Another surprise was the extensive transcriptional response in whole root compared to the susceptible root zone where the cellular response is most pronounced. A large number of transcripts predicted to encode transcriptional regulators, receptors and proteins involved in signal transduction, as well as many genes with unknown function, were found to be regulated during nodule organogenesis and rhizobial infection. Combining wild type and mutant profiles of these transcripts demonstrates the activation of a complex genetic program that delineates symbiotic nitrogen fixation. The complete data set was organized into an indexed expression directory that is accessible from a resource database, and here we present selected examples of biological questions that can be addressed with this comprehensive and powerful gene expression data set.
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Affiliation(s)
- Niels Høgslund
- Centre for Carbohydrate Recognition and Signalling, MBI, Aarhus University, Aarhus C, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus C, Denmark
| | - Simona Radutoiu
- Centre for Carbohydrate Recognition and Signalling, MBI, Aarhus University, Aarhus C, Denmark
| | - Lene Krusell
- Centre for Carbohydrate Recognition and Signalling, MBI, Aarhus University, Aarhus C, Denmark
| | - Vera Voroshilova
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Matthew A. Hannah
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Nicolas Goffard
- ARC Centre of Excellence for Integrative Legume Research, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Diego H. Sanchez
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Felix Lippold
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Thomas Ott
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | | | - Poul Liboriussen
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus C, Denmark
| | - Gitte V. Lohmann
- Centre for Carbohydrate Recognition and Signalling, MBI, Aarhus University, Aarhus C, Denmark
| | - Leif Schauser
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus C, Denmark
| | - Georg F. Weiller
- ARC Centre of Excellence for Integrative Legume Research, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael K. Udvardi
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, MBI, Aarhus University, Aarhus C, Denmark
- * E-mail:
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Huo H, Conner JA, Ozias-Akins P. Genetic mapping of the apospory-specific genomic region in Pennisetum squamulatum using retrotransposon-based molecular markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:199-212. [PMID: 19370319 DOI: 10.1007/s00122-009-1029-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 03/25/2009] [Indexed: 05/21/2023]
Abstract
Pennisetum squamulatum reproduces by apomixis, a type of asexual reproduction through seeds. Apomixis in P. squamulatum is transmitted as a dominant Mendelian trait, and a genomic region, the apospory-specific genomic region (ASGR), is sufficient for inheritance of the trait. The ASGR is physically large (>50 Mb), highly heterochromatic, hemizygous, and recombinationally suppressed. These characteristics have hindered high-resolution genetic mapping and map-based cloning of apomixis genes. In this study, the long terminal repeat (LTR) regions of ASGR-abundant retrotransposons in the genome of P. squamulatum and ASGR-linked bacterial artificial chromosome clones were identified and sequenced for designing LTR-specific primers. Two hundred and ninety single-dose sequence specific amplified polymorphism (SSAP) markers were generated from 38 primer combinations. The SSAP markers combined with two previous ASGR-mapped markers were used for genetic linkage analysis and construction of a genetic map resulting in the formation of 27 linkage groups at LOD 10, one of which contained >60% of the SSAP markers. After removing identical markers (identical band scoring) on the largest linkage group, 46 markers were finally used for genetic mapping at LOD 10. The markers distributed across 10 different loci covering 19 cM; however, 45 markers were distributed within 9 cM. Six markers were recovered and sequenced. Five markers were successfully converted into sequence characterized amplified regions (SCARs). Segregation of SCAR markers was not always consistent with the SSAP markers of origin suggesting a greater level of error in the SSAP map resulting in an inflated map distance for the ASGR. One SCAR marker (Pst 56-1205-400) detected expression of an ASGR retrotransposon in root, anther, leaf and ovary of P. squamulatum, although sequencing of the RT-PCR product failed to find a functional open reading frame for the transcript.
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Affiliation(s)
- Heqiang Huo
- Department of Horticulture, University of Georgia Tifton Campus, Tifton, GA 31793, USA
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31
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CARE1, a TY3-gypsy like LTR-retrotransposon in the food legume chickpea (Cicer arietinum L.). Genetica 2009; 136:429-37. [DOI: 10.1007/s10709-008-9343-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Accepted: 12/06/2008] [Indexed: 02/02/2023]
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Yokota K, Fukai E, Madsen LH, Jurkiewicz A, Rueda P, Radutoiu S, Held M, Hossain MS, Szczyglowski K, Morieri G, Oldroyd GED, Downie JA, Nielsen MW, Rusek AM, Sato S, Tabata S, James EK, Oyaizu H, Sandal N, Stougaard J. Rearrangement of actin cytoskeleton mediates invasion of Lotus japonicus roots by Mesorhizobium loti. THE PLANT CELL 2009; 21:267-84. [PMID: 19136645 PMCID: PMC2648097 DOI: 10.1105/tpc.108.063693] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 12/03/2008] [Accepted: 12/18/2008] [Indexed: 05/18/2023]
Abstract
Infection thread-dependent invasion of legume roots by rhizobia leads to internalization of bacteria into the plant cells, which is one of the salient features of root nodule symbiosis. We found that two genes, Nap1 (for Nck-associated protein 1) and Pir1 (for 121F-specific p53 inducible RNA), involved in actin rearrangements were essential for infection thread formation and colonization of Lotus japonicus roots by its natural microsymbiont, Mesorhizobium loti. nap1 and pir1 mutants developed an excess of uncolonized nodule primordia, indicating that these two genes were not essential for the initiation of nodule organogenesis per se. However, both the formation and subsequent progression of infection threads into the root cortex were significantly impaired in these mutants. We demonstrate that these infection defects were due to disturbed actin cytoskeleton organization. Short root hairs of the mutants had mostly transverse or web-like actin filaments, while bundles of actin filaments in wild-type root hairs were predominantly longitudinal. Corroborating these observations, temporal and spatial differences in actin filament organization between wild-type and mutant root hairs were also observed after Nod factor treatment, while calcium influx and spiking appeared unperturbed. Together with various effects on plant growth and seed formation, the nap1 and pir1 alleles also conferred a characteristic distorted trichome phenotype, suggesting a more general role for Nap1 and Pir1 in processes establishing cell polarity or polar growth in L. japonicus.
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Affiliation(s)
- Keisuke Yokota
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology, University of Aarhus, 8000 Aarhus C, Denmark
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Fukai E, Dobrowolska AD, Madsen LH, Madsen EB, Umehara Y, Kouchi H, Hirochika H, Stougaard J. Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus. PLANT MOLECULAR BIOLOGY 2008; 68:653-63. [PMID: 18802778 DOI: 10.1007/s11103-008-9397-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 09/01/2008] [Indexed: 05/08/2023]
Abstract
We have identified a new Ty3-gypsy retrotransposon family named LORE2 (Lotus retrotransposon 2) and documented its activity in the model legume Lotus japonicus. Three new LORE2 insertions were found in symbiotic mutant alleles isolated from a plant population, established by tissue culture mediated transformation of the L. japonicus Gifu accession. Low transcriptional and transpositional activities of LORE2 in cultured cells suggested that the LORE2 transpositions identified in the three symbiotic mutants occurred in intact plants, not in callus. Tracing of the transpositional events identified two active LORE2 members in Gifu. One of them named LORE2A possesses a deletion in its coding region and polymorphisms between intraelemental LTRs. LORE2A is thus an aged element, estimated as 600 thousand years old. Our findings indicate that plant genomes carry more cryptic LTR retrotransposons, i.e., aged yet active, than estimated before, and that these cryptic elements may have contributed to plant genome dynamics, for example, the burst of transpositions reported in several plant species.
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Affiliation(s)
- Eigo Fukai
- National Institute of Agrobiological Science, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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Fujimoto R, Takuno S, Sasaki T, Nishio T. The pattern of amplification and differentiation of Ty1-copia and Ty3-gypsy retrotransposons in Brassicaceae species. Genes Genet Syst 2008; 83:13-22. [PMID: 18379130 DOI: 10.1266/ggs.83.13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
One of the causes of genome size expansion is considered to be amplification of retrotransposons. We determined nucleotide sequences of 24 PCR products for each of six retrotransposons in Brassica rapa and Brassica oleracea. Phylogenetic trees of these sequences showed species-specific clades. We also sequenced STF7a homologs and Tto1 homologs, 24 PCR products each, in nine diploids and three allopolyploids, and constructed phylogenetic trees. In these phylogenetic trees, species-specific clades of diploid species were also formed, but retrotransposons of allopolyploids were clustered into the clades of their original genomes, indicating that these two retrotransposons amplified after speciation of the nine diploids. Genetic variation in these retrotransposons may have arisen before emergence of allopolyploid species. There was a positive correlation between the genome size and the average number of substitutions of STF7a and Tto1 homologs in at least seven diploids. The implications of these results in the genome evolution of Brassicaceae are herein discussed.
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Affiliation(s)
- Ryo Fujimoto
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
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Benlloch R, d'Erfurth I, Ferrandiz C, Cosson V, Beltrán JP, Cañas LA, Kondorosi A, Madueño F, Ratet P. Isolation of mtpim proves Tnt1 a useful reverse genetics tool in Medicago truncatula and uncovers new aspects of AP1-like functions in legumes. PLANT PHYSIOLOGY 2006; 142:972-83. [PMID: 16963524 PMCID: PMC1630737 DOI: 10.1104/pp.106.083543] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Comparative studies help shed light on how the huge diversity in plant forms found in nature has been produced. We use legume species to study developmental differences in inflorescence architecture and flower ontogeny with classical models such as Arabidopsis thaliana or Antirrhinum majus. Whereas genetic control of these processes has been analyzed mostly in pea (Pisum sativum), Medicago truncatula is emerging as a promising alternative system for these studies due to the availability of a range of genetic tools. To assess the use of the retrotransposon Tnt1 for reverse genetics in M. truncatula, we screened a small Tnt1-mutagenized population using degenerate primers for MADS-box genes, known controllers of plant development. We describe here the characterization of mtpim, a new mutant caused by the insertion of Tnt1 in a homolog to the PROLIFERATING INFLORESCENCE MERISTEM (PIM)/APETALA1 (AP1)/SQUAMOSA genes. mtpim shows flower-to-inflorescence conversion and altered flowers with sepals transformed into leaves, indicating that MtPIM controls floral meristem identity and flower development. Although more extreme, this phenotype resembles the pea pim mutants, supporting the idea that M. truncatula could be used to complement analysis of reproductive development already initiated in pea. In fact, our study reveals aspects not shown by analysis of pea mutants: that the mutation in the AP1 homolog interferes with the specification of floral organs from common primordia and causes conversion of sepals into leaves, in addition to true conversion of flowers into inflorescences. The isolation of mtpim represents a proof of concept demonstrating that Tnt1 populations can be efficiently used in reverse genetics screenings in M. truncatula.
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Affiliation(s)
- Reyes Benlloch
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
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Acquadro A, Portis E, Moglia A, Magurno F, Lanteri S. Retrotransposon-based S-SAP as a platform for the analysis of genetic variation and linkage in globe artichoke. Genome 2006; 49:1149-59. [PMID: 17110995 DOI: 10.1139/g06-074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A high copy number of retrotransposon sequences are present and widely dispersed in plant genomes. Their activity generates a considerable degree of sequence polymorphism. Here, we report the cloning of CYRE-5, a long-terminal repeat carrying retrotransposon-like sequence in Cynara cardunculus L., and its exploitation to develop a DNA fingerprinting assay across 22 accessions, including both cultivated (globe artichoke and cultivated cardoon) and wild (wild cardoon) types. The effectiveness of the sequence-specific amplified polymorphism (S-SAP) platform is compared with that of amplified fragment length polymorphism (AFLP). A genetic linkage analysis, based on a hybrid population between 2 globe artichoke varietal types, resulted in the inclusion of 29 S-SAP loci in the core genetic map, confirming their dispersed distribution across the globe artichoke genome.
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Affiliation(s)
- Alberto Acquadro
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Turin, via L. da Vinci 44, I-10095 Grugliasco (Turin), Italy
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