1
|
Sun Y, Chen J, Yuan Y, Jiang N, Liu C, Zhang Y, Mao X, Zhang Q, Fang Y, Sun Z, Gai S. Auxin efflux carrier PsPIN4 identified through genome-wide analysis as vital factor of petal abscission. FRONTIERS IN PLANT SCIENCE 2024; 15:1380417. [PMID: 38799094 PMCID: PMC11116700 DOI: 10.3389/fpls.2024.1380417] [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: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024]
Abstract
PIN-FORMED (PIN) proteins, which function as efflux transporters, play many crucial roles in the polar transportation of auxin within plants. In this study, the exogenous applications of auxin IAA and TIBA were found to significantly prolong and shorten the florescence of tree peony (Paeonia suffruticosa Andr.) flowers. This finding suggests that auxin has some regulatory influence in petal senescence and abscission. Further analysis revealed a total of 8 PsPINs distributed across three chromosomes, which could be categorized into two classes based on phylogenetic and structural analysis. PsPIN1, PsPIN2a-b, and PsPIN4 were separated into the "long" PIN category, while PsPIN5, PsPIN6a-b, and PsPIN8 belonged to the "short" one. Additionally, the cis-regulatory elements of PsPIN promoters were associated with plant development, phytohormones, and environmental stress. These genes displayed tissue-specific expression, and phosphorylation sites were abundant throughout the protein family. Notably, PsPIN4 displayed distinct and elevated expression levels in roots, leaves, and flower organs. Expression patterns among the abscission zone (AZ) and adjacent areas during various flowering stages and IAA treatment indicate that PsPIN4 likely influences the initiation of peony petal abscission. The PsPIN4 protein was observed to be co-localized on both the plasma membrane and the cell nucleus. The ectopic expression of PsPIN4 reversed the premature flower organs abscission in the Atpin4 and significantly protracted florescence when introduced to Col Arabidopsis. Our findings established a strong basis for further investigation of PIN gene biological functions, particularly concerning intrinsic relationship between PIN-mediated auxin polar.
Collapse
Affiliation(s)
- Yin Sun
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Junqiang Chen
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Yanchao Yuan
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Nannan Jiang
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Chunying Liu
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yuxi Zhang
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiuhong Mao
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Qian Zhang
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Yifu Fang
- Shandong Provincial Key Laboratory of Forest Genetic Improvement, Yellow River delta forest ecosystem positioning research station, Shandong Provincial Academy of Forestry, Jinan, China
| | - Zhenyuan Sun
- State Key Laboratory of Efficient Production of Forest Resources, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shupeng Gai
- University Key Laboratory of Plant Biotechnology in Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
2
|
Somaclonal Variation-Advantage or Disadvantage in Micropropagation of the Medicinal Plants. Int J Mol Sci 2023; 24:ijms24010838. [PMID: 36614275 PMCID: PMC9821087 DOI: 10.3390/ijms24010838] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/08/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
Cell and tissue plant cultures are used either to save vulnerable species from extinction or to multiply valuable genotypes, or both, and are widely applied for economically important plant species. For medicinal plants, the use of in vitro technologies for the production of secondary metabolites and pathogen-free plants has been greatly developed. Two opposite aspects characterize the in vitro micropropagation of medicinal plants: maintaining genetic fidelity for the perpetuation and preservation of elites, and the identification and exploitation of somaclonal variations associated with new, useful traits. A balance between what is advantageous and what is undesirable is necessary, and this implies the identification of somaclonal variability at all levels, from the phenotypic to molecular ones. This review addresses the somaclonal variation arising from the in vitro multiplication of medicinal plants from three perspectives: cytogenetics, genetics, and epigenetics. The possible causes of the appearance of somaclones, the methods for their identification, and the extent to which they are desirable are presented comparatively for different plant species with therapeutic properties. The emphasis is on the subtle changes at the genetic and epigenetic level, as it results from the application of methods based on DNA markers.
Collapse
|
3
|
Koo H, Kim S, Park HS, Lee SJ, Paek NC, Cho J, Yang TJ. Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin. Mob DNA 2022; 13:18. [PMID: 35698176 PMCID: PMC9190103 DOI: 10.1186/s13100-022-00274-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022] Open
Abstract
Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, amplification LTRs of eclDNAs followed by sequencing (ALE-seq) uncover the current transpositional potential of the LTR-RTs. The ALE-seq protocol was validated by identification of Tos17 in callus of Nipponbare cultivar. Here, we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in rice cultivar Dongjin callus based on the ALE-seq technology. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.
Collapse
Affiliation(s)
- Hyunjin Koo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Soomin Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Sang-Ji Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea
| | - Jungnam Cho
- CAS-JIC Centre of Excellence for Plant and Microbial Science, 200032, Shanghai, China
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826, Seoul, Republic of Korea.
| |
Collapse
|
4
|
Kirov I, Merkulov P, Dudnikov M, Polkhovskaya E, Komakhin RA, Konstantinov Z, Gvaramiya S, Ermolaev A, Kudryavtseva N, Gilyok M, Divashuk MG, Karlov GI, Soloviev A. Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline. PLANTS (BASEL, SWITZERLAND) 2021; 10:2681. [PMID: 34961152 PMCID: PMC8704663 DOI: 10.3390/plants10122681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/12/2023]
Abstract
Long-read data is a great tool to discover new active transposable elements (TEs). However, no ready-to-use tools were available to gather this information from low coverage ONT datasets. Here, we developed a novel pipeline, nanotei, that allows detection of TE-contained structural variants, including individual TE transpositions. We exploited this pipeline to identify TE insertion in the Arabidopsis thaliana genome. Using nanotei, we identified tens of TE copies, including ones for the well-characterized ONSEN retrotransposon family that were hidden in genome assembly gaps. The results demonstrate that some TEs are inaccessible for analysis with the current A. thaliana (TAIR10.1) genome assembly. We further explored the mobilome of the ddm1 mutant with elevated TE activity. Nanotei captured all TEs previously known to be active in ddm1 and also identified transposition of non-autonomous TEs. Of them, one non-autonomous TE derived from (AT5TE33540) belongs to TR-GAG retrotransposons with a single open reading frame (ORF) encoding the GAG protein. These results provide the first direct evidence that TR-GAGs and other non-autonomous LTR retrotransposons can transpose in the plant genome, albeit in the absence of most of the encoded proteins. In summary, nanotei is a useful tool to detect active TEs and their insertions in plant genomes using low-coverage data from Nanopore genome sequencing.
Collapse
Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Ekaterina Polkhovskaya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Roman A. Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Zakhar Konstantinov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Sofya Gvaramiya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Aleksey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia; (A.E.); (N.K.)
| | - Natalya Kudryavtseva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia; (A.E.); (N.K.)
| | - Marina Gilyok
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| |
Collapse
|
5
|
Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
Collapse
Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | | | | | | |
Collapse
|
6
|
Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
Collapse
Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| |
Collapse
|
7
|
Debladis E, Lee TF, Huang YJ, Lu JH, Mathioni SM, Carpentier MC, Llauro C, Pierron D, Mieulet D, Guiderdoni E, Chen PY, Meyers BC, Panaud O, Lasserre E. Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice ( Oryza sativa ssp japonica cv Nipponbare). Philos Trans R Soc Lond B Biol Sci 2020; 375:20190338. [PMID: 32075556 DOI: 10.1098/rstb.2019.0338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of osnrpd1, a knock-down RNA interference line of OsNRPD1 gene that encodes the largest subunit of Pol IV in rice (Oryza sativa ssp japonica cv Nipponbare). We show that osnrpd1 displays a lower accumulation of OsNRPD1 transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons Tos17 and Lullaby and the long interspersed nuclear element-type retrotransposon Karma. However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of in planta global reactivation of transposition. This knock-down of OsNRPD1 likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of OsNRPD1 would cause sterility in rice. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
Collapse
Affiliation(s)
- Emilie Debladis
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Tzuu-Fen Lee
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Yan-Jiun Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | - Davy Pierron
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| | | | | | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA.,Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Institut Universitaire de France, Paris, France
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, Université de Perpignan Via Domitia, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France.,Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, 52, Avenue Paul alduy, 66860 Perpignan Cedex, France
| |
Collapse
|
8
|
Park D, Choi IY, Kim NS. Detection of mPing mobilization in transgenic rice plants. Genes Genomics 2019; 42:47-54. [PMID: 31721104 DOI: 10.1007/s13258-019-00877-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/18/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Various kinds of transposable elements (TEs) constitute high proportions of eukaryotic genomes. Although most of these TEs are not actively mobile, genome stress can induce mobilization of dormant TEs. Transgenic plants undergo tissue culture and subsequent whole-plant regeneration, which can cause genomic stress and in turn induce mobilization of inactive TEs. OBJECTIVES To investigate the activation of transposable elements on the genome wide of the GM plant. METHODS Transposon activities were analyzed in three transgenic rice plants carrying the insect resistance gene Cry1Ac and an herbicide resistance gene by the transposon display technique. These three transgenic plants were derived from a leading Korean rice variety, Illmi. RESULTS We detected seven mobile activities in the mPing element, which is a MITE family transposon. The identity of the novel fragments in the gel display was confirmed by checking TAA target site duplication via sequence analysis. The genomic integration sites were all on different chromosomes, and the integrations were specific to either one or two T1 transgenic lines, except for one common integration on chromosome 4. One integration was in the 5'-UTR of the Glycerol-3-phosphate acyltransferase 8 gene, two integrations were in introns of expressed genes, and the other four integrations were in intergenic regions. CONCLUSION Thus, novel mobilization of dormant TEs occurs in transgenic plants, which must be considered in the generation of genetically modified crops (GM crops).
Collapse
Affiliation(s)
- Doori Park
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Ik-Young Choi
- Department of Molecular Bioscience, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea.
| | - Nam-Soo Kim
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea.
| |
Collapse
|
9
|
Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nat Commun 2019; 10:24. [PMID: 30604755 PMCID: PMC6318337 DOI: 10.1038/s41467-018-07974-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
Collapse
Affiliation(s)
- Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Ernandes Manfroi
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, 305-8687, Ibaraki, Japan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Emilie Debladis
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France.
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France.
| |
Collapse
|
10
|
Cho J, Benoit M, Catoni M, Drost HG, Brestovitsky A, Oosterbeek M, Paszkowski J. Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. NATURE PLANTS 2019; 5:26-33. [PMID: 30531940 PMCID: PMC6366555 DOI: 10.1038/s41477-018-0320-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 11/07/2018] [Indexed: 05/02/2023]
Abstract
Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2. Such studies provide important 'snapshots' reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis3. However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALE-seq reveals sequences of 5' LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality.
Collapse
Affiliation(s)
- Jungnam Cho
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai, China.
| | - Matthias Benoit
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Hajk-Georg Drost
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Matthijs Oosterbeek
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Laboratory of Nematology, Wageningen University, Wageningen, the Netherlands
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- Radachowka 37, Kolbiel, Poland.
| |
Collapse
|
11
|
Michno JM, Stupar RM. The importance of genotype identity, genetic heterogeneity, and bioinformatic handling for properly assessing genomic variation in transgenic plants. BMC Biotechnol 2018; 18:38. [PMID: 29859067 PMCID: PMC5984819 DOI: 10.1186/s12896-018-0447-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The advent of -omics technologies has enabled the resolution of fine molecular differences among individuals within a species. DNA sequence variations, such as single nucleotide polymorphisms or small deletions, can be tabulated for many kinds of genotype comparisons. However, experimental designs and analytical approaches are replete with ways to overestimate the level of variation present within a given sample. Analytical pipelines that do not apply proper thresholds nor assess reproducibility among samples are susceptible to calling false-positive variants. Furthermore, issues with sample genotype identity or failing to account for heterogeneity in reference genotypes may lead to misinterpretations of standing variants as polymorphisms derived de novo. RESULTS A recent publication that featured the analysis of RNA-sequencing data in three transgenic soybean event series appeared to overestimate the number of sequence variants identified in plants that were exposed to a tissue culture based transformation process. We reanalyzed these data with a stringent set of criteria and demonstrate three different factors that lead to variant overestimation, including issues related to the genetic identity of the background genotype, unaccounted genetic heterogeneity in the reference genome, and insufficient bioinformatics filtering. CONCLUSIONS This study serves as a cautionary tale to users of genomic and transcriptomic data that wish to assess the molecular variation attributable to tissue culture and transformation processes. Moreover, accounting for the factors that lead to sequence variant overestimation is equally applicable to samples derived from other germplasm sources, including chemical or irradiation mutagenesis and genome engineering (e.g., CRISPR) processes.
Collapse
Affiliation(s)
- Jean-Michel Michno
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| | - Robert M. Stupar
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN USA
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN 55108 USA
| |
Collapse
|
12
|
Debladis E, Llauro C, Carpentier MC, Mirouze M, Panaud O. Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology. BMC Genomics 2017; 18:537. [PMID: 28715998 PMCID: PMC5513335 DOI: 10.1186/s12864-017-3753-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV). However, these have relied on Illumina platform that generates short reads (up to 350 nucleotides). This limitation in size of sequence reads can cause high false discovery rate (FDR) and therefore limit the power of detection of TEASVs, especially in the case of large, complex genomes. The newest sequencing technologies, such as Oxford Nanopore Technologies (ONT) can generate kilobases-long reads thus representing a promising tool for TEASV detection in plant and animals. RESULTS We present the results of a pilot experiment for TEASV detection on the model plant species Arabidopsis thaliana using ONT sequencing and show that it can be used efficiently to detect TE movements. We generated a ~0.8X genome coverage of a met1-derived epigenetic recombinant inbred line (epiRIL) using a MinIon device with R7 chemistry. We were able to detect nine new copies of the LTR-retrotransposon Evadé (EVD). We also evidenced the activity of the DNA transposon CACTA, CAC1. CONCLUSIONS Even at a low sequence coverage (0.8X), ONT sequencing allowed us to reliably detect several TE insertions in Arabidopsis thaliana genome. The long read length allowed a precise and un-ambiguous mapping of the structural variations caused by the activity of TEs. This suggests that the trade-off between read length and genome coverage for TEASV detection may be in favor of the former. Should the technology be further improved both in terms of lower error rate and operation costs, it could be efficiently used in diversity studies at population level.
Collapse
Affiliation(s)
- Emilie Debladis
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France.,Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France
| | - Christel Llauro
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France.,Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France
| | - Marie-Christine Carpentier
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France.,Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France
| | - Marie Mirouze
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France.,Institut de Recherche pour le Développement, UMR232 DIADE Diversité Adaptation et Développement des Plantes, Perpignan, France
| | - Olivier Panaud
- Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France. .,Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, 52, avenue Paul alduy, 66860, Perpignan cedex, France. .,Institut Universitaire de France, Paris, France.
| |
Collapse
|
13
|
Goubert C, Henri H, Minard G, Valiente Moro C, Mavingui P, Vieira C, Boulesteix M. High-throughput sequencing of transposable element insertions suggests adaptive evolution of the invasive Asian tiger mosquito towards temperate environments. Mol Ecol 2017; 26:3968-3981. [DOI: 10.1111/mec.14184] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 05/06/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Clement Goubert
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
- Department of Human Genetics; University of Utah; Salt Lake City UT USA
| | - Helene Henri
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
| | - Guillaume Minard
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Ecologie Microbienne; UMR CNRS 5557; UMR INRA 1418; Villeurbanne France
- Department of Biosciences; Metapopulation Research Center; University of Helsinki; Helsinki Finland
| | - Claire Valiente Moro
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Ecologie Microbienne; UMR CNRS 5557; UMR INRA 1418; Villeurbanne France
| | - Patrick Mavingui
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Ecologie Microbienne; UMR CNRS 5557; UMR INRA 1418; Villeurbanne France
- UMR PIMIT; INSERM 1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI; Universite de La Reunion; Sainte-Clotilde Reunion
| | - Cristina Vieira
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
| | - Matthieu Boulesteix
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
| |
Collapse
|
14
|
Li WX, Wu SL, Liu YH, Jin GL, Zhao HJ, Fan LJ, Shu QY. Genome-wide profiling of genetic variation in Agrobacterium-transformed rice plants. J Zhejiang Univ Sci B 2017; 17:992-996. [PMID: 27921404 DOI: 10.1631/jzus.b1600301] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate "transgene-clean" targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed. To reveal the genome-wide variation in transformed plants, we sequenced the genomes of five independent T0 rice plants using next-generation sequencing (NGS) techniques. Bioinformatics analyses followed by experimental validation revealed the following: (1) in addition to transfer-DNA (T-DNA) insertions, three transformed plants carried heritable plasmid backbone DNA of variable sizes (855-5216 bp) and in different configurations with the T-DNA insertions (linked or apart); (2) each transgenic plant contained an estimated 338-1774 independent genetic variations (single nucleotide variations (SNVs) or small insertion/deletions); and (3) 2-6 new Tos17 insertions were detected in each transformed plant, but no other transposable elements or bacterial genomic DNA.
Collapse
Affiliation(s)
- Wen-Xu Li
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Institute for Wheat Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - San-Ling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan-Hua Liu
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Gu-Lei Jin
- Hangzhou Guhe Information and Technology Co., Ltd., Hangzhou 310058, China
| | - Hai-Jun Zhao
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Long-Jiang Fan
- IBM Biocomputational Laboratory, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qing-Yao Shu
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
15
|
Schouten HJ, Vande Geest H, Papadimitriou S, Bemer M, Schaart JG, Smulders MJM, Perez GS, Schijlen E. Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere. PLANT CELL REPORTS 2017; 36:493-504. [PMID: 28155116 PMCID: PMC5316556 DOI: 10.1007/s00299-017-2098-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/02/2017] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE Transformation resulted in deletions and translocations at T-DNA inserts, but not in genome-wide small mutations. A tiny T-DNA splinter was detected that probably would remain undetected by conventional techniques. We investigated to which extent Agrobacterium tumefaciens-mediated transformation is mutagenic, on top of inserting T-DNA. To prevent mutations due to in vitro propagation, we applied floral dip transformation of Arabidopsis thaliana. We re-sequenced the genomes of five primary transformants, and compared these to genomic sequences derived from a pool of four wild-type plants. By genome-wide comparisons, we identified ten small mutations in the genomes of the five transgenic plants, not correlated to the positions or number of T-DNA inserts. This mutation frequency is within the range of spontaneous mutations occurring during seed propagation in A. thaliana, as determined earlier. In addition, we detected small as well as large deletions specifically at the T-DNA insert sites. Furthermore, we detected partial T-DNA inserts, one of these a tiny 50-bp fragment originating from a central part of the T-DNA construct used, inserted into the plant genome without flanking other T-DNA. Because of its small size, we named this fragment a T-DNA splinter. As far as we know this is the first report of such a small T-DNA fragment insert in absence of any T-DNA border sequence. Finally, we found evidence for translocations from other chromosomes, flanking T-DNA inserts. In this study, we showed that next-generation sequencing (NGS) is a highly sensitive approach to detect T-DNA inserts in transgenic plants.
Collapse
Affiliation(s)
- Henk J Schouten
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Henri Vande Geest
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sofia Papadimitriou
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan G Schaart
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
16
|
Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLoS Genet 2017; 13:e1006630. [PMID: 28212378 PMCID: PMC5338827 DOI: 10.1371/journal.pgen.1006630] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/06/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
Collapse
|
17
|
Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation. G3-GENES GENOMES GENETICS 2017; 7:203-219. [PMID: 27852012 PMCID: PMC5217110 DOI: 10.1534/g3.116.036020] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5′ untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.
Collapse
|
18
|
Anderson JE, Michno JM, Kono TJY, Stec AO, Campbell BW, Curtin SJ, Stupar RM. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol 2016; 16:41. [PMID: 27176220 PMCID: PMC4866027 DOI: 10.1186/s12896-016-0271-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.
Collapse
Affiliation(s)
- Justin E Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Adrian O Stec
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Benjamin W Campbell
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Robert M Stupar
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA.
| |
Collapse
|
19
|
Wei FJ, Kuang LY, Oung HM, Cheng SY, Wu HP, Huang LT, Tseng YT, Chiou WY, Hsieh-Feng V, Chung CH, Yu SM, Lee LY, Gelvin SB, Hsing YIC. Somaclonal variation does not preclude the use of rice transformants for genetic screening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:648-59. [PMID: 26833589 DOI: 10.1111/tpj.13132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/21/2015] [Accepted: 01/20/2016] [Indexed: 05/07/2023]
Abstract
Rice (Oryza sativa) is one of the world's most important crops. Rice researchers make extensive use of insertional mutants for the study of gene function. Approximately half a million flanking sequence tags from rice insertional mutant libraries are publicly available. However, the relationship between genotype and phenotype is very weak. Transgenic plant assays have been used frequently for complementation, overexpression or antisense analysis, but sequence changes caused by callus growth, Agrobacterium incubation medium, virulence genes, transformation and selection conditions are unknown. We used high-throughput sequencing of DNA from rice lines derived from Tainung 67 to analyze non-transformed and transgenic rice plants for mutations caused by these parameters. For comparison, we also analyzed sequence changes for two additional rice varieties and four T-DNA tagged transformants from the Taiwan Rice Insertional Mutant resource. We identified single-nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromosome translocations in these lines. Using standard rice regeneration/transformation procedures, the mutation rates of regenerants and transformants were relatively low, with no significant differences among eight tested treatments in the Tainung 67 background and in the cultivars Taikeng 9 and IR64. Thus, we could not conclusively detect sequence changes resulting from Agrobacterium-mediated transformation in addition to those caused by tissue culture-induced somaclonal variation. However, the mutation frequencies within the two publically available tagged mutant populations, including TRIM transformants or Tos17 lines, were about 10-fold higher than the frequency of standard transformants, probably because mass production of embryogenic calli and longer callus growth periods were required to generate these large libraries.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Lin-Yun Kuang
- Transgenic Plant Core Facility, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Hui-Min Oung
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Sin-Yuan Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Yi-Tzu Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
- Institute of Plant Biology, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Wan-Yi Chiou
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Vicki Hsieh-Feng
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd, Taipei, 10617, Taiwan
| | - Cheng-Han Chung
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| | - Lan-Ying Lee
- Department of Biological Sciences, Purdue University, 201 South University St., West Lafayette, IN, 47907-1392, USA
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, 201 South University St., West Lafayette, IN, 47907-1392, USA
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Yien-Chu-Yuan Road, Taipei, 11529, Taiwan
| |
Collapse
|
20
|
Dubrovina AS, Kiselev KV. Age-associated alterations in the somatic mutation and DNA methylation levels in plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:185-196. [PMID: 26211365 DOI: 10.1111/plb.12375] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/21/2015] [Indexed: 05/18/2023]
Abstract
Somatic mutations of the nuclear and mitochondrial DNA and alterations in DNA methylation levels in mammals are well known to play important roles in ageing and various diseases, yet their specific contributions await further investigation. For plants, it has also been proposed that unrepaired DNA damage and DNA polymerase errors accumulate in plant cells and lead to increased somatic mutation rate and alterations in transcription, which eventually contribute to plant ageing. A number of studies also show that DNA methylation levels vary depending on the age of plant tissue and chronological age of a whole plant. Recent studies reveal that prolonged cultivation of plant cells in vitro induces single nucleotide substitutions and increases global DNA methylation level in a time-dependent fashion. Changes in DNA methylation are known to influence DNA repair and can lead to altered mutation rates, and, therefore, it is interesting to investigate both the genetic and epigenetic integrity in relationship to ageing in plants. This review will summarise and discuss the current studies investigating somatic DNA mutation and DNA methylation levels in relation to plant ageing and senescence. The analysis has shown that there still remains a lack of clarity concerning plant biological ageing and the role of the genetic and epigenetic instabilities in this process.
Collapse
Affiliation(s)
- A S Dubrovina
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - K V Kiselev
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia
- Department of Biochemistry, Microbiology and Biotechnology, The School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russia
| |
Collapse
|
21
|
Dievart A, Perin C, Hirsch J, Bettembourg M, Lanau N, Artus F, Bureau C, Noel N, Droc G, Peyramard M, Pereira S, Courtois B, Morel JB, Guiderdoni E. The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:240-249. [PMID: 26566841 DOI: 10.1016/j.plantsci.2015.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/17/2015] [Accepted: 06/22/2015] [Indexed: 05/08/2023]
Abstract
Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.
Collapse
Affiliation(s)
- Anne Dievart
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France.
| | | | - Judith Hirsch
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | | | - Nadège Lanau
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | | | | | - Nicolas Noel
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | - Gaétan Droc
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | | | - Serge Pereira
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | | | - Jean-Benoit Morel
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | | |
Collapse
|
22
|
Hénaff E, Zapata L, Casacuberta JM, Ossowski S. Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution. BMC Genomics 2015; 16:768. [PMID: 26459856 PMCID: PMC4603299 DOI: 10.1186/s12864-015-1975-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 10/02/2015] [Indexed: 11/20/2022] Open
Abstract
Background Transposable elements are major players in genome evolution. Transposon insertion polymorphisms can translate into phenotypic differences in plants and animals and are linked to different diseases including human cancer, making their characterization highly relevant to the study of genome evolution and genetic diseases. Results Here we present Jitterbug, a novel tool that identifies transposable element insertion sites at single-nucleotide resolution based on the pairedend mapping and clipped-read signatures produced by NGS alignments. Jitterbug can be easily integrated into existing NGS analysis pipelines, using the standard BAM format produced by frequently applied alignment tools (e.g. bwa, bowtie2), with no need to realign reads to a set of consensus transposon sequences. Jitterbug is highly sensitive and able to recall transposon insertions with a very high specificity, as demonstrated by benchmarks in the human and Arabidopsis genomes, and validation using long PacBio reads. In addition, Jitterbug estimates the zygosity of transposon insertions with high accuracy and can also identify somatic insertions. Conclusions We demonstrate that Jitterbug can identify mosaic somatic transposon movement using sequenced tumor-normal sample pairs and allows for estimating the cancer cell fraction of clones containing a somatic TE insertion. We suggest that the independent methods we use to evaluate performance are a step towards creating a gold standard dataset for benchmarking structural variant prediction tools. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1975-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elizabeth Hénaff
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain. .,current address: Weill Cornell Medical College, Institute for Computational Biomedicine, 1305 York Avenue, New York, NY, 10021, USA.
| | - Luís Zapata
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain.
| | - Stephan Ossowski
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
23
|
El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA. A new approach for annotation of transposable elements using small RNA mapping. Nucleic Acids Res 2015; 43:e84. [PMID: 25813049 PMCID: PMC4513842 DOI: 10.1093/nar/gkv257] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 03/10/2015] [Accepted: 03/15/2015] [Indexed: 12/31/2022] Open
Abstract
Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants.Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/.
Collapse
Affiliation(s)
- Moaine El Baidouri
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
| | - Siwaret Arikit
- Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Olivier Panaud
- Université de Perpignan Via Domitia. Laboratoire Génome et Développement des Plantes. UMR5096 CNRS/UPVD., 52, avenue Paul Alduy. 66860 Perpignan Cedex, France
| | - Blake C Meyers
- Delaware Biotechnology Institute and Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA
| |
Collapse
|
24
|
Roffler S, Wicker T. Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons. Mob DNA 2015; 6:8. [PMID: 25954322 PMCID: PMC4423477 DOI: 10.1186/s13100-015-0040-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/16/2015] [Indexed: 12/18/2022] Open
Abstract
Background DNA (Class II) transposons are ubiquitous in plant genomes. However, unlike for (Class I) retrotransposons, only little is known about their proliferation mechanisms, activity, and impact on genomes. Asian and African rice (Oryza sativa and O. glaberrima) diverged approximately 600,000 years ago. Their fully sequenced genomes therefore provide an excellent opportunity to study polymorphisms introduced from recent transposon activity. Results We manually analyzed 1,821 transposon related polymorphisms among which we identified 487 loci which clearly resulted from DNA transposon insertions and excisions. In total, we estimate about 4,000 (3.5% of all DNA transposons) to be polymorphic between the two species, indicating a high level of transposable element (TE) activity. The vast majority of the recently active elements are non-autonomous. Nevertheless, we identified multiple potentially functional autonomous elements. Furthermore, we quantified the impacts of insertions and excisions on the adjacent sequences. Transposon insertions were found to be generally precise, creating simple target site duplications. In contrast, excisions almost always go along with the deletion of flanking sequences and/or the insertion of foreign ‘filler’ segments. Some of the excision-triggered deletions ranged from hundreds to thousands of bp flanking the excision site. Furthermore, we found in some superfamilies unexpectedly low numbers of excisions. This suggests that some excisions might cause such large-scale rearrangements so that they cannot be detected anymore. Conclusions We conclude that the activity of DNA transposons (particularly the excision process) is a major evolutionary force driving the generation of genetic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0040-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Stefan Roffler
- Institute for Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Thomas Wicker
- Institute for Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| |
Collapse
|
25
|
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]
|
26
|
Finatto T, de Oliveira AC, Chaparro C, da Maia LC, Farias DR, Woyann LG, Mistura CC, Soares-Bresolin AP, Llauro C, Panaud O, Picault N. Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. RICE (NEW YORK, N.Y.) 2015; 8:13. [PMID: 25844118 PMCID: PMC4385019 DOI: 10.1186/s12284-015-0045-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Iron toxicity is a root related abiotic stress, occurring frequently in flooded soils. It can affect the yield of rice in lowland production systems. This toxicity is associated with high concentrations of reduced iron (Fe(2+)) in the soil solution. Although the first interface of the element is in the roots, the consequences of an excessive uptake can be observed in several rice tissues. In an original attempt to find both genes and transposable elements involved in the response to an iron toxicity stress, we used a microarray approach to study the transcriptional responses of rice leaves of cv. Nipponbare (Oryza sativa L. ssp. japonica) to iron excess in nutrient solution. RESULTS A large number of genes were significantly up- or down-regulated in leaves under the treatment. We analyzed the gene ontology and metabolic pathways of genes involved in the response to this stress and the cis-regulatory elements (CREs) present in the promoter region of up-regulated genes. The majority of genes act in the pathways of lipid metabolic process, carbohydrate metabolism, biosynthesis of secondary metabolites and plant hormones. We also found genes involved in iron acquisition and mobilization, transport of cations and regulatory mechanisms for iron responses, and in oxidative stress and reactive oxygen species detoxification. Promoter regions of 27% of genes up-regulated present at least one significant occurrence of an ABA-responsive CRE. Furthermore, and for the first time, we were able to show that iron stress triggers the up-regulation of many LTR-retrotransposons. We have established a complete inventory of transposable elements transcriptionally activated under iron excess and the CREs which are present in their LTRs. CONCLUSION The short-term response of Nipponbare seedlings to iron excess, includes activation of genes involved in iron homeostasis, in particular transporters, transcription factors and ROS detoxification in the leaves, but also many transposable elements. Our data led to the identification of CREs which are associated with both genes and LTR-retrotransposons up-regulated under iron excess. Our results strengthen the idea that LTR-retrotransposons participate in the transcriptional response to stress and could thus confer an adaptive advantage for the plant.
Collapse
Affiliation(s)
- Taciane Finatto
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
- />Present address: Universidade Tecnológica Federal do Paraná, Campus Pato Branco, 85503-390 Pato Branco, PR Brazil
| | - Antonio Costa de Oliveira
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Cristian Chaparro
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
- />Present address: Laboratoire Ecologie et Evolution des Interactions, UMR 5244, F-66860, Université de Perpignan Via Domitia, Perpignan, France
| | - Luciano C da Maia
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Daniel R Farias
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Leomar G Woyann
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Claudete C Mistura
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Adriana P Soares-Bresolin
- />Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, 96010-610 Pelotas, RS Brazil
| | - Christel Llauro
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Olivier Panaud
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Nathalie Picault
- />Laboratoire Génome et Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, F-66860 Perpignan, France
- />CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| |
Collapse
|
27
|
Zhang D, Wang Z, Wang N, Gao Y, Liu Y, Wu Y, Bai Y, Zhang Z, Lin X, Dong Y, Ou X, Xu C, Liu B. Tissue culture-induced heritable genomic variation in rice, and their phenotypic implications. PLoS One 2014; 9:e96879. [PMID: 24804838 PMCID: PMC4013045 DOI: 10.1371/journal.pone.0096879] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/12/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Somaclonal variation generally occurs in plants regenerated from tissue culture. However, fundamental issues regarding molecular characteristics, mutation rates and mutation spectra of plant somatic variation as well as their phenotypic relevance have been addressed only recently. Moreover, these studies have reported highly discrepant results in different plant species and even in the same plant genotype. METHODOLOGY/PRINCIPAL FINDINGS We investigated heritable genomic variation induced by tissue culture in rice by whole genome re-sequencing of an extensively selfed somaclonal line (TC-reg-2008) and its wild type (WT) donor (cv. Hitomebore). We computed the overall mutation rate, single nucleotide polymorphisms (SNPs), small scale insertions/deletions (Indels) and mobilization of transposable elements (TEs). We assessed chromosomal distribution of the various types of genomic variations, tested correlations between SNPs and Indels, and examined concomitancy between TE activity and its cytosine methylation states. We also performed gene ontology (GO) analysis of genes containing nonsynonymous mutations and large-effect mutations, and assayed effects of the genomic variations on phenotypes under both normal growing condition and several abiotic stresses. We found that heritable somaclonal genomic variation occurred extensively in rice. The genomic variations distributed non-randomly across each of the 12 rice chromosomes, and affected a large number of functional genes. The phenotypic penetrance of the genomic variations was condition-dependent. CONCLUSIONS/SIGNIFICANCE Tissue culture is a potent means to generate heritable genetic variations in rice, which bear distinct difference at least in space (chromosomal distribution) from those occurred under natural settings. Our findings have provided new information regarding the mutation rate and spectrum as well as chromosomal distribution pattern of somaclonal variation in rice. Our data also suggest that rice possesses a strong capacity to canalize genetic variations under normal growing conditions to maintain phenotypic robustness, which however can be released by certain abiotic stresses to generate variable phenotypes.
Collapse
Affiliation(s)
- Di Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Yang Gao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuzhu Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiufang Ou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| |
Collapse
|
28
|
Abstract
Background Tos17 was the first LTR retrotransposon (Copia) described as active in cultivated rice, and is present in two copies in the genome of the sequenced Nipponbare variety. Only the chromosome 7 copy is active and able to retrotranspose, at least during in vitro culture, and this ability was widely used in insertional mutagenesis assays. Results Here the structure of the active Tos17 was thoroughly annotated using a set of bioinformatic analyses. Conclusions Unexpectedly, Tos17 appears to be a non-autonomous LTR retrotransposon, lacking the gag sequence and thus unable to transpose by itself.
Collapse
Affiliation(s)
- Francois Sabot
- UMR DIADE IRD/UM2, 911 Avenue Agropolis BP64503, F-34394 Montpellier Cedex 5, France.
| |
Collapse
|
29
|
Vitte C, Fustier MA, Alix K, Tenaillon MI. The bright side of transposons in crop evolution. Brief Funct Genomics 2014; 13:276-95. [PMID: 24681749 DOI: 10.1093/bfgp/elu002] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The past decades have revealed an unexpected yet prominent role of so-called 'junk DNA' in the regulation of gene expression, thereby challenging our view of the mechanisms underlying phenotypic evolution. In particular, several mechanisms through which transposable elements (TEs) participate in functional genome diversity have been depicted, bringing to light the 'TEs bright side'. However, the relative contribution of those mechanisms and, more generally, the importance of TE-based polymorphisms on past and present phenotypic variation in crops species remain poorly understood. Here, we review current knowledge on both issues, and discuss how analyses of massively parallel sequencing data combined with statistical methodologies and functional validations will help unravelling the impact of TEs on crop evolution in a near future.
Collapse
|
30
|
Arai-Kichise Y, Shiwa Y, Ebana K, Shibata-Hatta M, Yoshikawa H, Yano M, Wakasa K. Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. PLoS One 2014; 9:e86312. [PMID: 24466017 PMCID: PMC3897683 DOI: 10.1371/journal.pone.0086312] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 12/09/2013] [Indexed: 01/04/2023] Open
Abstract
Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html).
Collapse
Affiliation(s)
- Yuko Arai-Kichise
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- * E-mail:
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Kaworu Ebana
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Mari Shibata-Hatta
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Kyo Wakasa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| |
Collapse
|
31
|
Wei FJ, Droc G, Guiderdoni E, Hsing YIC. International Consortium of Rice Mutagenesis: resources and beyond. RICE (NEW YORK, N.Y.) 2013; 6:39. [PMID: 24341871 PMCID: PMC3946042 DOI: 10.1186/1939-8433-6-39] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/04/2013] [Indexed: 05/20/2023]
Abstract
Rice is one of the most important crops in the world. The rice community needs to cooperate and share efforts and resources so that we can understand the functions of rice genes, especially those with a role in important agronomical traits, for application in agricultural production. Mutation is a major source of genetic variation that can be used for studying gene function. We will present here the status of mutant collections affected in a random manner by physical/chemical and insertion mutageneses.As of early September 2013, a total of 447, 919 flanking sequence tags from rice mutant libraries with T-DNA, Ac/Ds, En/Spm, Tos17, nDART/aDART insertions have been collected and publicly available. From these, 336,262 sequences are precisely positioned on the japonica rice chromosomes, and 67.5% are in gene interval. We discuss the genome coverage and preference of the insertion, issues limiting the exchange and use of the current collections, as well as new and improved resources. We propose a call to renew all mutant populations as soon as possible. We also suggest that a common web portal should be established for ordering seeds.
Collapse
Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Hsing: Rm312, IPMB, Academia Sinica, Nankang District, Taipei 11529 Taiwan
| | - Gaëtan Droc
- CIRAD, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Cirad - av. Agropolis -TA A-108/03, 34398 Montpellier Cedex 5, France
| | - Emmanuel Guiderdoni
- CIRAD, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Cirad - av. Agropolis -TA A-108/03, 34398 Montpellier Cedex 5, France
| | - Yue-ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Hsing: Rm312, IPMB, Academia Sinica, Nankang District, Taipei 11529 Taiwan
| |
Collapse
|
32
|
Wang ZH, Zhang D, Bai Y, Zhang YH, Liu Y, Wu Y, Lin XY, Wen JW, Xu CM, Li LF, Liu B. Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing. PLoS One 2013; 8:e74479. [PMID: 24058573 PMCID: PMC3776793 DOI: 10.1371/journal.pone.0074479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp) paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs) and 17,839 homozygous insertions/deletions (indels) were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs) was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q) RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a sexually incompatible species may represent a potent means to generate novel genetic diversities, and which may have played relevant roles in plant evolution and can be manipulated for crop improvements.
Collapse
Affiliation(s)
- Zhen-Hui Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Di Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yun-Hong Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Ying Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiu-Yun Lin
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jia-Wei Wen
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chun-Ming Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- * E-mail: (LL); (BL)
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- * E-mail: (LL); (BL)
| |
Collapse
|
33
|
Kawakatsu T, Kawahara Y, Itoh T, Takaiwa F. A whole-genome analysis of a transgenic rice seed-based edible vaccine against cedar pollen allergy. DNA Res 2013; 20:623-31. [PMID: 23956243 PMCID: PMC3859328 DOI: 10.1093/dnares/dst036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genetic modification (GM) by Agrobacterium-mediated transformation is a robust and widely employed method to confer new traits to crops. In this process, a transfer DNA is delivered into the host genome, but it is still unclear how the host genome is altered by this event at single-base resolution. To decipher genomic discrepancy between GM crops and their host, we conducted whole-genome sequencing of a transgenic rice line OSCR11. This rice line expresses a seed-based edible vaccine containing two major pollen allergens, Cry j 1 and Cry j 2, against Japanese cedar pollinosis. We revealed that genetic differences between OSCR11 and its host a123 were significantly less than those between a123 and its precedent cultivar Koshihikari. The pattern of nucleotide base substitution in OSCR11, relative to a123, was consistent with somaclonal variation. Mutations in OSCR11 probably occurred during the cell culture steps. In addition, strand-specific mRNA-Seq revealed similar transcriptomes of a123 and OSCR11, supporting genomic integrity between them.
Collapse
Affiliation(s)
- Taiji Kawakatsu
- 1Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kan-nondai, Tsukuba, Ibaraki 305-8602, Japan
| | | | | | | |
Collapse
|
34
|
Sveinsson S, Gill N, Kane NC, Cronk Q. Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species. BMC Genomics 2013; 14:502. [PMID: 23883295 PMCID: PMC3726317 DOI: 10.1186/1471-2164-14-502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/19/2013] [Indexed: 01/24/2023] Open
Abstract
Background Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. Results (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. Conclusions (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a “fingerprint” to identify and characterize cacao accessions.
Collapse
Affiliation(s)
- Saemundur Sveinsson
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
| | | | | | | |
Collapse
|
35
|
Bleykasten-Grosshans C, Friedrich A, Schacherer J. Genome-wide analysis of intraspecific transposon diversity in yeast. BMC Genomics 2013; 14:399. [PMID: 23768249 PMCID: PMC4022208 DOI: 10.1186/1471-2164-14-399] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 06/06/2013] [Indexed: 02/02/2023] Open
Abstract
Background In the model organism Saccharomyces cerevisiae, the transposable elements (TEs) consist of LTR (Long Terminal Repeat) retrotransposons called Ty elements belonging to five families, Ty1 to Ty5. They take the form of either full-length coding elements or non-coding solo-LTRs corresponding to remnants of former transposition events. Although the biological features of Ty elements have been studied in detail in S. cerevisiae and the Ty content of the reference strain (S288c) was accurately annotated, the Ty-related intra-specific diversity has not been closely investigated so far. Results In this study, we investigated the Ty contents of 41 available genomes of isolated S. cerevisiae strains of diverse geographical and ecological origins. The strains were compared in terms of the number of Ty copies, the content of the potential transpositionally active elements and the genomic insertion maps. The strain repertoires were also investigated in the closely related Ty1 and Ty2 families and subfamilies. Conclusions This is the first genome-wide analysis of the diversity associated to the Ty elements, carried out for a large set of S. cerevisiae strains. The results of the present analyses suggest that the current Ty-related polymorphism has resulted from multiple causes such as differences between strains, between Ty families and over time, in the recent transpositional activity of Ty elements. Some new Ty1 variants were also identified, and we have established that Ty1 variants have different patterns of distribution among strains, which further contributes to the strain diversity.
Collapse
Affiliation(s)
- Claudine Bleykasten-Grosshans
- CNRS, Department of Genetics, Genomics and Microbiology, University of Strasbourg, UMR 7156, 28, rue Goethe, Strasbourg, 67083, France.
| | | | | |
Collapse
|
36
|
Wang X, Wu R, Lin X, Bai Y, Song C, Yu X, Xu C, Zhao N, Dong Y, Liu B. Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids. BMC PLANT BIOLOGY 2013; 13:77. [PMID: 23642214 PMCID: PMC3648424 DOI: 10.1186/1471-2229-13-77] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 04/26/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-induced genomic alterations, the issue of whether and to what extent distinct plant genotypes, e.g., pure-lines, hybrids and polyploids, may respond differentially to the tissue culture condition remains poorly understood. RESULTS We investigated tissue culture-induced genetic and epigenetic alterations in a set of rice genotypes including two pure-lines (different subspecies), a pair of reciprocal F1 hybrids parented by the two pure-lines, and a pair of reciprocal tetraploids resulted from the hybrids. Using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), both genetic and DNA methylation alterations were detected in calli and regenerants from all six genotypes, but genetic alteration is more prominent than epigenetic alteration. While significant genotypic difference was observed in frequencies of both types of alterations, only genetic alteration showed distinctive features among the three types of genomes, with one hybrid (N/9) being exceptionally labile. Surprisingly, difference in genetic alteration frequencies between the pair of reciprocal F1 hybrids is much greater than that between the two pure-line subspecies. Difference also exists in the pair of reciprocal tetraploids, but is to a less extent than that between the hybrids. The steady-state transcript abundance of genes involved in DNA repair and DNA methylation was significantly altered in both calli and regenerants, and some of which were correlated with the genetic and/or epigenetic alterations. CONCLUSIONS Our results, based on molecular marker analysis of ca. 1,000 genomic loci, document that genetic alteration is the major cause of somaclonal variation in rice, which is concomitant with epigenetic alterations. Perturbed expression by tissue culture of a set of 41 genes encoding for enzymes involved in DNA repair and DNA methylation is associated with both genetic and epigenetic alterations. There exist fundamental differences among distinct genotypes, pure-lines, hybrids and tetraploids, in propensities of generating both genetic and epigenetic alterations under the tissue culture condition. Parent-of-origin has a conspicuous effect on the alteration frequencies.
Collapse
Affiliation(s)
- Xiaoran Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Rui Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Present address: Carnegie Institution for Science, Department of Plant Biology, Stanford University, Stanford, CA, 94305, USA
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Congdi Song
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Bioengineering, Jilin College of Agricultural Science & Technology, Jilin, 132301, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Na Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, 13118, China
| | - Yuzhu Dong
- School of Life Science, Changchun Normal University, Changchun, 130032, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| |
Collapse
|
37
|
Resequencing rice genomes: an emerging new era of rice genomics. Trends Genet 2013; 29:225-32. [DOI: 10.1016/j.tig.2012.12.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/27/2012] [Accepted: 12/07/2012] [Indexed: 11/19/2022]
|
38
|
Wang X, Weigel D, Smith LM. Transposon variants and their effects on gene expression in Arabidopsis. PLoS Genet 2013; 9:e1003255. [PMID: 23408902 PMCID: PMC3567156 DOI: 10.1371/journal.pgen.1003255] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 12/03/2012] [Indexed: 02/01/2023] Open
Abstract
Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants. Transposable elements (TEs) are selfish DNA sequences. Together with their immobilized derivatives, they account for a large fraction of eukaryotic genomes. TEs can affect nearby gene activity, either directly by disrupting regulatory sequences or indirectly through the host mechanisms used to prevent TE proliferation. A comparison of Arabidopsis thaliana genomes reveals rapid TE degeneration. We asked what drives TE degeneration and how often TE variation affects nearby gene expression. To answer these questions, we studied the interplay between TEs, DNA sequence variation, and short interfering RNAs (siRNAs) in three A. thaliana strains. We find sequence variation in genes and adjacent TEs to be correlated, from which we conclude either that TEs insert more often near polymorphic genes or that TEs next to polymorphic genes are less efficiently purged from the genome. We also noticed that processes that cause deletions within TEs and ones that silence TEs appear to be linked, because siRNA targeting is a predictor of sequence loss in accessions. Our work provides insight into the contribution of TEs to gene expression plasticity, and it links TE silencing mechanisms to the evolution of TE variation between genomes, thereby linking TE silencing mechanisms to expression plasticity.
Collapse
Affiliation(s)
- Xi Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail: (DW); (LMS)
| | - Lisa M. Smith
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail: (DW); (LMS)
| |
Collapse
|
39
|
Elbaidouri M, Chaparro C, Panaud O. Use of Next Generation Sequencing (NGS) technologies for the genome-wide detection of transposition. Methods Mol Biol 2013; 1057:265-74. [PMID: 23918435 DOI: 10.1007/978-1-62703-568-2_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plant transposable elements are ubiquitous in eukaryotes. Their propensity to densely populate the genomes of many plants and animal species has put them in the focus of both structural and functional genomics. Although a number of bioinformatic software have been recently developed for the annotation of TEs in sequenced genomes, there are very few computational tools strictly dedicated to the identification of active TEs using genome-wide approaches. In this paper, we describe SearchTESV, a pipeline that we have developed to detect Transposable Elements-associated structural variants (TEASVs) using Next Generation Sequencing (NGS) technologies.
Collapse
Affiliation(s)
- Moaine Elbaidouri
- Laboratoire Génome et développement des plantes, Université de Perpignan Via Domitia, Perpignan, Cedex, France
| | | | | |
Collapse
|
40
|
Lin C, Lin X, Hu L, Yang J, Zhou T, Long L, Xu C, Xing S, Qi B, Dong Y, Liu B. Dramatic genotypic difference in, and effect of genetic crossing on, tissue culture-induced mobility of retrotransposon Tos17 in rice. PLANT CELL REPORTS 2012; 31:2057-63. [PMID: 22945626 DOI: 10.1007/s00299-012-1316-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 07/09/2012] [Accepted: 07/13/2012] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE : We show for the first time that intraspecific crossing may impact mobility of the prominent endogenous retrotransposon Tos17 under tissue culture conditions in rice. Tos17, an endogenous copia retrotransposon of rice, is transpositionally active in tissue culture. To study whether there exists fundamental genotypic difference in the tissue culture-induced mobility of Tos17, and if so, whether the difference is under genetic and/or epigenetic control, we conducted this investigation. We show that dramatic difference in tissue culture-induced Tos17 mobility exists among different rice pure-line cultivars sharing the same maternal parent: of the three lines studied that harbor Tos17, two showed mobilization of Tos17, which accrued in proportion to subculture duration, while the third line showed total quiescence (immobility) of the element and the fourth line did not contain the element. In reciprocal F1 hybrids between Tos17-mobile and -immobile (or absence) parental lines, immobility was dominant over mobility. In reciprocal F1 hybrids between both Tos17-mobile parental lines, an additive or synergistic effect on mobility of the element was noticed. In both types of reciprocal F1 hybrids, clear difference in the extent of Tos17 mobility was noted between crossing directions. Given that all lines share the same maternal parent, this observation indicates the existence of epigenetic parent-of-origin effect. We conclude that the tissue culture-induced mobility of Tos17 in rice is under complex genetic and epigenetic control, which can be either enhanced or repressed by intraspecific genetic crossing.
Collapse
Affiliation(s)
- Chunjing Lin
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, 130024, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Lorieux M, Blein M, Lozano J, Bouniol M, Droc G, Diévart A, Périn C, Mieulet D, Lanau N, Bès M, Rouvière C, Gay C, Piffanelli P, Larmande P, Michel C, Barnola I, Biderre-Petit C, Sallaud C, Perez P, Bourgis F, Ghesquière A, Gantet P, Tohme J, Morel JB, Guiderdoni E. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:555-68. [PMID: 22369597 DOI: 10.1111/j.1467-7652.2012.00689.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions.
Collapse
Affiliation(s)
- Mathias Lorieux
- IRD, UMR DIADE, CIAT, Agrobiodiversity and Biotechnology Project, Cali, Colombia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Hernández-Pinzón I, Cifuentes M, Hénaff E, Santiago N, Espinás ML, Casacuberta JM. The Tnt1 retrotransposon escapes silencing in tobacco, its natural host. PLoS One 2012; 7:e33816. [PMID: 22479451 PMCID: PMC3316501 DOI: 10.1371/journal.pone.0033816] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/17/2012] [Indexed: 12/31/2022] Open
Abstract
Retrotransposons' high capacity for mutagenesis is a threat that genomes need to control tightly. Transcriptional gene silencing is a general and highly effective control of retrotransposon expression. Yet, some retrotransposons manage to transpose and proliferate in plant genomes, suggesting that, as shown for plant viruses, retrotransposons can escape silencing. However no evidence of retrotransposon silencing escape has been reported. Here we analyze the silencing control of the tobacco Tnt1 retrotransposon and report that even though constructs driven by the Tnt1 promoter become silenced when stably integrated in tobacco, the endogenous Tnt1 elements remain active. Silencing of Tnt1-containing transgenes correlates with high DNA methylation and the inability to incorporate H2A.Z into their promoters, whereas the endogenous Tnt1 elements remain partially methylated at asymmetrical positions and incorporate H2A.Z upon induction. Our results show that the promoter of Tnt1 is a target of silencing in tobacco, but also that endogenous Tnt1 elements can escape this control and be expressed in their natural host.
Collapse
Affiliation(s)
- Inmaculada Hernández-Pinzón
- Department of Molecular Genetics, Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB), Barcelona, Spain
| | - Marta Cifuentes
- Department of Molecular Genetics, Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB), Barcelona, Spain
| | - Elizabeth Hénaff
- Department of Molecular Genetics, Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB), Barcelona, Spain
| | - Néstor Santiago
- Department of Molecular Genetics, Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB), Barcelona, Spain
| | - M. Lluïsa Espinás
- Department of Molecular Genomics, Molecular Biology Institute of Barcelona (IBMB), CSIC, Barcelona, Spain
| | - Josep M. Casacuberta
- Department of Molecular Genetics, Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB), Barcelona, Spain
| |
Collapse
|
43
|
Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS One 2012; 7:e32973. [PMID: 22427919 PMCID: PMC3299709 DOI: 10.1371/journal.pone.0032973] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 02/06/2012] [Indexed: 12/22/2022] Open
Abstract
Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.
Collapse
Affiliation(s)
- Grégory Carrier
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Scientific opinion addressing the safety assessment of plants developed through cisgenesis and intragenesis. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2561] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
45
|
Genome-Wide Analysis of Transposition Using Next Generation Sequencing Technologies. PLANT TRANSPOSABLE ELEMENTS 2012. [DOI: 10.1007/978-3-642-31842-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
46
|
Abstract
The recent development of next-generation sequencing (NGS) technologies allowed various authors to imagine, test, and validate new approaches for TE analysis, in their nature, type, activity, or quantity. In this chapter, we describe briefly the technologies used, then the various approaches and methods used already, and finally some potential new methods. In contrast to the more molecular chapters of the book, the approaches described here are purely bioinformatics, and have a set of NGS data as a starting point. Moreover, as these analyses are quite recent in the field, most of them were only performed once, and we cannot be sure that they could be reused in other species or context than the original one. However, there are a lot of interesting approaches and results that NGS can provide in the TE field.
Collapse
Affiliation(s)
- Cristian Chaparro
- UMR LGDP, CNRS/UPVD, Université de Perpignan Via Domitia, Perpignan Cedex, France
| | | |
Collapse
|
47
|
Miyao A, Nakagome M, Ohnuma T, Yamagata H, Kanamori H, Katayose Y, Takahashi A, Matsumoto T, Hirochika H. Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. PLANT & CELL PHYSIOLOGY 2012; 53:256-64. [PMID: 22156226 DOI: 10.1093/pcp/pcr172] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Somaclonal variation is a phenomenon that results in the phenotypic variation of plants regenerated from cell culture. One of the causes of somaclonal variation in rice is the transposition of retrotransposons. However, many aspects of the mechanisms that result in somaclonal variation remain undefined. To detect genome-wide changes in regenerated rice, we analyzed the whole-genome sequences of three plants independently regenerated from cultured cells originating from a single seed stock. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were detected in the genomes of the regenerated plants. The transposition of only Tos17 among 43 transposons examined was detected in the regenerated plants. Therefore, the SNPs and indels contribute to the somaclonal variation in regenerated rice in addition to the transposition of Tos17. The observed molecular spectrum was similar to that of the spontaneous mutations in Arabidopsis thaliana. However, the base change ratio was estimated to be 1.74 × 10(-6) base substitutions per site per regeneration, which is 248-fold greater than the spontaneous mutation rate of A. thaliana.
Collapse
Affiliation(s)
- Akio Miyao
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|