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de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. EPIGENOMES 2023; 8:2. [PMID: 38247729 PMCID: PMC10801548 DOI: 10.3390/epigenomes8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.
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Affiliation(s)
| | - Carlos M. Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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2
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Merkulov P, Gvaramiya S, Dudnikov M, Komakhin R, Omarov M, Kocheshkova A, Konstantinov Z, Soloviev A, Karlov G, Divashuk M, Kirov I. Cas9-targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2242-2261. [PMID: 37555565 DOI: 10.1111/jipb.13555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
Transposable element insertions (TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large, complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that reflect mobilome dynamics are difficult to track using short reads. To address these challenges, we combined Cas9-targeted Nanopore sequencing (CANS) with the novel pipeline NanoCasTE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of the EVADÉ (EVD) retrotransposon in wild-type Arabidopsis thaliana and rapidly obtained up to 40× sequence coverage. Analysis of hemizygous T-DNA insertion sites and genetically inherited insertions of the EVD transposon in the ddm1 (decrease in DNA methylation 1) genome uncovered the crucial role of DNA methylation in shaping EVD insertion preference. We also investigated somatic transposition events of the ONSEN transposon family, finding that genes that are downregulated during heat stress are preferentially targeted by ONSENs. Finally, we detected hypomethylation of novel somatic insertions for two ONSENs. CANS and NanoCasTE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T-DNA insertion mutants and transgenic plants.
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Affiliation(s)
- Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Sofya Gvaramiya
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Roman Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Murad Omarov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Alina Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Zakhar Konstantinov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- All-Russia Center for Plant Quarantine, Ramenski, 140150, Russia
- N.V. Tsitsin Main Botanical Garden of the Russian Academy of Sciences, Moscow, 127276, Russia
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Mikhail Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
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Pinky, Jain R, Yadav A, Sharma R, Dhaka N. Emerging roles of long non-coding RNAs in regulating agriculturally important seed traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108019. [PMID: 37714026 DOI: 10.1016/j.plaphy.2023.108019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
Seeds have enormous economic importance as source of calories, nutrition, edible oil, and biofuels. Therefore, seed traits like seed size and shape, weight, micronutrient content, oil content, quality, post-harvest sprouting, etc., are some of the main targets in crop improvement. Designing the strategies for their improvement benefits heavily from understanding the regulatory aspects of seed development. Recent studies indicate that long non-coding RNAs (lncRNAs) are one of the important regulators of seed development. They played a significant role in crop domestication by influencing seed traits. LncRNAs are conventionally defined as non-coding RNAs greater than 200 bp in length but lacking protein coding potential. Here we highlight the emerging pieces of evidence of lncRNA-mediated regulation of seed development through diverse mechanisms, for instance, by acting as target mimics or precursors of regulatory small RNAs or through chromatin remodeling and post-transcriptional repression. We also enumerate the insights from high-throughput transcriptomic studies from developing seeds of cereal, oilseed, biofuel, and pulse crops. We highlight the lncRNA candidates and lncRNA-mediated regulatory networks regulating seed development and related agronomic traits. Further, we discuss the potential of lncRNAs for improvement of agriculturally important seed traits through marker-assisted breeding and/or transgenic approaches.
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Affiliation(s)
- Pinky
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhinandan Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
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Orozco-Arias S, Lopez-Murillo LH, Piña JS, Valencia-Castrillon E, Tabares-Soto R, Castillo-Ossa L, Isaza G, Guyot R. Genomic object detection: An improved approach for transposable elements detection and classification using convolutional neural networks. PLoS One 2023; 18:e0291925. [PMID: 37733731 PMCID: PMC10513252 DOI: 10.1371/journal.pone.0291925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
Analysis of eukaryotic genomes requires the detection and classification of transposable elements (TEs), a crucial but complex and time-consuming task. To improve the performance of tools that accomplish these tasks, Machine Learning approaches (ML) that leverage computer resources, such as GPUs (Graphical Processing Unit) and multiple CPU (Central Processing Unit) cores, have been adopted. However, until now, the use of ML techniques has mostly been limited to classification of TEs. Herein, a detection-classification strategy (named YORO) based on convolutional neural networks is adapted from computer vision (YOLO) to genomics. This approach enables the detection of genomic objects through the prediction of the position, length, and classification in large DNA sequences such as fully sequenced genomes. As a proof of concept, the internal protein-coding domains of LTR-retrotransposons are used to train the proposed neural network. Precision, recall, accuracy, F1-score, execution times and time ratios, as well as several graphical representations were used as metrics to measure performance. These promising results open the door for a new generation of Deep Learning tools for genomics. YORO architecture is available at https://github.com/simonorozcoarias/YORO.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Colombia
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
| | | | - Johan S. Piña
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Colombia
| | | | - Reinel Tabares-Soto
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Luis Castillo-Ossa
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
| | - Gustavo Isaza
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
| | - Romain Guyot
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
- Institut de Recherche pour le Développement, CIRAD, Univ. Montpellier, Montpellier, France
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Palos K, Yu L, Railey CE, Nelson Dittrich AC, Nelson ADL. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs. THE PLANT CELL 2023; 35:1762-1786. [PMID: 36738093 PMCID: PMC10226578 DOI: 10.1093/plcell/koad027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 05/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
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Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Li’ang Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Caylyn E Railey
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Graduate Field, Cornell University, Ithaca, NY 14853, USA
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Zou Y, Guo Q, Chang Y, Zhong Y, Cheng L, Wei W. Effects of Maternal High-Fructose Diet on Long Non-Coding RNAs and Anxiety-like Behaviors in Offspring. Int J Mol Sci 2023; 24:ijms24054460. [PMID: 36901891 PMCID: PMC10003385 DOI: 10.3390/ijms24054460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
Increased fructose intake is an international issue. A maternal high-fructose diet during gestation and lactation could affect nervous system development in offspring. Long non-coding RNA (lncRNA) plays an important role in brain biology. However, the mechanism whereby maternal high-fructose diets influence offspring brain development by affecting lncRNAs is still unclear. Here, we administered 13% and 40% fructose water to establish a maternal high-fructose diet model during gestation and lactation. To determine lncRNAs and their target genes, full-length RNA sequencing was performed using the Oxford Nanopore Technologies platform, and 882 lncRNAs were identified. Moreover, the 13% fructose group and the 40% fructose group had differentially expressed lncRNA genes compared with the control group. Enrichment analyses and co-expression analyses were performed to investigate the changes in biological function. Furthermore, enrichment analyses, behavioral science experiments, and molecular biology experiments all indicated that the fructose group offspring showed anxiety-like behaviors. In summary, this study provides insight into the molecular mechanisms underlying maternal high-fructose diet-induced lncRNA expression and co-expression of lncRNA and mRNA.
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Kirov I, Merkulov P, Polkhovskaya E, Konstantinov Z, Kazancev M, Saenko K, Polkhovskiy A, Dudnikov M, Garibyan T, Demurin Y, Soloviev A. Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower ( Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11243579. [PMID: 36559691 PMCID: PMC9784723 DOI: 10.3390/plants11243579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 06/12/2023]
Abstract
Transposable elements (TEs) contribute not only to genome diversity but also to transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts in sunflower, we exploited a recently developed transposon activation method ('TEgenesis') along with long-read cDNA Nanopore sequencing. This approach allows for the identification of 56 RTE transcripts from different genomic loci including full-length and non-autonomous RTEs. Using the mobilome analysis, we provided a new set of expressed and transpositional active sunflower RTEs for future studies. Among them, a Ty3/Gypsy RTE called SUNTY3 exhibited ongoing transposition activity, as detected by eccDNA analysis. We showed that the sunflower genome contains a diverse set of non-autonomous RTEs encoding a single RTE protein, including the previously described TR-GAG (terminal repeat with the GAG domain) as well as new categories, TR-RT-RH, TR-RH, and TR-INT-RT. Our results demonstrate that 40% of the loci for RTE-related transcripts (nonLTR-RTEs) lack their LTR sequences and resemble conventional eucaryotic genes encoding RTE-related proteins with unknown functions. It was evident based on phylogenetic analysis that three nonLTR-RTEs encode GAG (HadGAG1-3) fused to a host protein. These HadGAG proteins have homologs found in other plant species, potentially indicating GAG domestication. Ultimately, we found that the sunflower retrotranscriptome originated from the transcription of active RTEs, non-autonomous RTEs, and gene-like RTE transcripts, including those encoding domesticated proteins.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Ekaterina Polkhovskaya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Zakhar Konstantinov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Mikhail Kazancev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Ksenia Saenko
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
- Federal Research Center of Biological Plant Protection, 350039 Krasnodar, Russia
| | - Alexander Polkhovskiy
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Tsovinar Garibyan
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Yakov Demurin
- Pustovoit All-Russia Research Institute of Oilseed Crops, Filatova St. 17, 350038 Krasnodar, Russia
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
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Peng H, Mirouze M, Bucher E. Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102263. [PMID: 35872391 DOI: 10.1016/j.pbi.2022.102263] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Throughout the years, most plant genomic studies were focused on nuclear chromosomes. Extrachromosomal circular DNA (eccDNA) has largely been neglected for decades since its discovery in 1965. While initial research showed that eccDNAs can originate from highly repetitive sequences, recent findings show that many regions of the genome can contribute to the eccDNA pool. Currently, the biological functions of eccDNAs, if any, are a mystery but recent studies have indicated that they can be regulated by different genomic loci and contribute to stress response and adaptation. In this review, we outline current relevant technological developments facilitating eccDNA identification and the latest discoveries about eccDNAs in plants. Finally, we explore the probable functions and future research directions that could be undertaken with respect to different eccDNA sources.
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Affiliation(s)
- Haoran Peng
- Crop Genome Dynamics Group, Agroscope Changins, 1260, Nyon, Switzerland; Department of Botany and Plant Biology, Section of Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Marie Mirouze
- Institut de Recherche pour le Développement (IRD), EMR269 MANGO, Université de Perpignan, 66860 Perpignan, France; Laboratory of Plant Genome and Development, Université de Perpignan, 66860, Perpignan, France.
| | - Etienne Bucher
- Crop Genome Dynamics Group, Agroscope Changins, 1260, Nyon, Switzerland.
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Lee Y, Ha U, Moon S. Ongoing endeavors to detect mobilization of transposable elements. BMB Rep 2022. [PMID: 35725016 PMCID: PMC9340088 DOI: 10.5483/bmbrep.2022.55.7.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of ‘Dissociation (Dc) locus’ by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.
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Affiliation(s)
- Yujeong Lee
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Una Ha
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
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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.
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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.)
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Javaran VJ, Moffett P, Lemoyne P, Xu D, Adkar-Purushothama CR, Fall ML. Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112355. [PMID: 34834718 PMCID: PMC8623739 DOI: 10.3390/plants10112355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 05/30/2023]
Abstract
Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus-plant interactions, as well as the characterization of viral RNA modifications.
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Affiliation(s)
- Vahid Jalali Javaran
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Peter Moffett
- Département de Biologie, Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
| | - Pierre Lemoyne
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
| | - Dong Xu
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
| | - Charith Raj Adkar-Purushothama
- Département de Biochimie, Faculté de Médecine des Sciences de la Santé, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada;
| | - Mamadou Lamine Fall
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada; (V.J.J.); (P.L.); (D.X.)
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Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
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Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
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13
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Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, Ziganshin R, Kovalchuk S, Kharlampieva D, Lazarev V, Taliansky M, Koonin EV. A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic Acids Res 2021; 49:10328-10346. [PMID: 34570232 DOI: 10.1093/nar/gkab816] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/17/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Pervasive transcription of eukaryotic genomes results in expression of long non-coding RNAs (lncRNAs) most of which are poorly conserved in evolution and appear to be non-functional. However, some lncRNAs have been shown to perform specific functions, in particular, transcription regulation. Thousands of small open reading frames (smORFs, <100 codons) located on lncRNAs potentially might be translated into peptides or microproteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of lncRNAs-smORFs from the moss Physcomitrium patens across transcriptomes of 479 plant species. Although thousands of smORFs are subject to substantial purifying selection, the majority of the smORFs appear to be evolutionary young and could represent a major pool for functional innovation. Using nanopore RNA sequencing, we show that, on average, the transcriptional level of conserved smORFs is higher than that of non-conserved smORFs. Proteomic analysis confirmed translation of 82 novel species-specific smORFs. Numerous conserved smORFs containing low complexity regions (LCRs) or transmembrane domains were identified, the biological functions of a selected LCR-smORF were demonstrated experimentally. Thus, microproteins encoded by smORFs are a major, functionally diverse component of the plant proteome.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Andrey Knyazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Anna Glushkevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Rustam Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergey Kovalchuk
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Daria Kharlampieva
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation
| | - Vassili Lazarev
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region, 141701, Russian Federation
| | - Michael Taliansky
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation.,The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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14
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Loskutov IG. Advances in Cereal Crops Breeding. PLANTS 2021; 10:plants10081705. [PMID: 34451750 PMCID: PMC8399613 DOI: 10.3390/plants10081705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 01/14/2023]
Affiliation(s)
- Igor G Loskutov
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
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