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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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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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Azizi P, Hanafi MM, Sahebi M, Harikrishna JA, Taheri S, Yassoralipour A, Nasehi A. Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:508-523. [PMID: 32349860 DOI: 10.1071/fp19077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 02/23/2020] [Indexed: 06/11/2023]
Abstract
Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.
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Affiliation(s)
- Parisa Azizi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamed M Hanafi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; and Corresponding author.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Jennifer A Harikrishna
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sima Taheri
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ali Yassoralipour
- Department of Agricultural and Food Science, Faculty of Science (Kampar Campus), Universiti Tunku Abdul Rahman (UTAR), Jalan Universiti, Bandar Barat, 31900 Kampar, Perak, Malaysia
| | - Abbas Nasehi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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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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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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6
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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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7
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Paszkowski J. Controlled activation of retrotransposition for plant breeding. Curr Opin Biotechnol 2015; 32:200-206. [PMID: 25615932 DOI: 10.1016/j.copbio.2015.01.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 12/16/2022]
Abstract
Plant genomes consist to a large extent of transposable elements (TEs), predominantly retrotransposons. Their accumulation through periodic transposition bursts has shaped the structure and regulatory organization of plant genomes, often contributing to phenotypic traits. Transposon-generated phenotypes selected by humans during plant domestication have been maintained under strict selection during subsequent plant breeding. Our knowledge of the epigenetic, environmental, and developmental regulation of TE activity has advanced considerably in recent years. Here I will consider TEs as an attractive endogenous source of genetic variation that can be liberated in a controlled fashion and thus offer novel phenotypic diversity to be selected for crop improvement.
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Affiliation(s)
- Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom.
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8
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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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9
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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: 76] [Impact Index Per Article: 6.3] [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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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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Tadege M, Wang TL, Wen J, Ratet P, Mysore KS. Mutagenesis and beyond! Tools for understanding legume biology. PLANT PHYSIOLOGY 2009; 151:978-84. [PMID: 19741047 PMCID: PMC2773078 DOI: 10.1104/pp.109.144097] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 09/03/2009] [Indexed: 05/18/2023]
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14
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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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15
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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: 118] [Impact Index Per Article: 7.9] [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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16
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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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