1
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Merkulov P, Serganova M, Petrov G, Mityukov V, Kirov I. Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions. BMC Genomics 2024; 25:404. [PMID: 38658857 PMCID: PMC11044480 DOI: 10.1186/s12864-024-10314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Interspecific hybridization, a widely employed technique in tomato breeding, results in the creation of novel combinations of TEs from distinct species. The implications of this process for TE transposition activity have not been studied in modern cultivars. In this study, we used nanopore sequencing of extrachromosomal circular DNA (eccDNA) and identified two highly active Ty1/Copia LTR retrotransposon families of tomato (Solanum lycopersicum), called Salsa and Ketchup. Elements of these families produce thousands of eccDNAs under controlled conditions and epigenetic stress. EccDNA sequence analysis revealed that the major parts of eccDNA produced by Ketchup and Salsa exhibited low similarity to the S. lycopersicum genomic sequence. To trace the origin of these TEs, whole-genome nanopore sequencing and de novo genome assembly were performed. We found that these TEs occurred in a tomato breeding line via interspecific introgression from S. peruvianum. Our findings collectively show that interspecific introgressions can contribute to both genetic and phenotypic diversity not only by introducing novel genetic variants, but also by importing active transposable elements from other species.
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Affiliation(s)
- Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Melania Serganova
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Georgy Petrov
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Vladislav Mityukov
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051, Moscow, Russia
| | - Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550, Moscow, Russia.
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia.
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2
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Wong DCJ, Wang Z, Perkins J, Jin X, Marsh GE, John EG, Peakall R. The road less taken: Dihydroflavonol 4-reductase inactivation and delphinidin anthocyanin loss underpins a natural intraspecific flower colour variation. Mol Ecol 2024:e17334. [PMID: 38651763 DOI: 10.1111/mec.17334] [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: 11/14/2023] [Revised: 02/22/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Visual cues are of critical importance for the attraction of animal pollinators, however, little is known about the molecular mechanisms underpinning intraspecific floral colour variation. Here, we combined comparative spectral analysis, targeted metabolite profiling, multi-tissue transcriptomics, differential gene expression, sequence analysis and functional analysis to investigate a bee-pollinated orchid species, Glossodia major with common purple- and infrequent white-flowered morphs. We found uncommon and previously unreported delphinidin-based anthocyanins responsible for the conspicuous and pollinator-perceivable colour of the purple morph and three genetic changes underpinning the loss of colour in the white morph - (1) a loss-of-function (LOF; frameshift) mutation affecting dihydroflavonol 4-reductase (DFR1) coding sequence due to a unique 4-bp insertion, (2) specific downregulation of functional DFR1 expression and (3) the unexpected discovery of chimeric Gypsy transposable element (TE)-gene (DFR) transcripts with potential consequences to the genomic stability and post-transcriptional or epigenetic regulation of DFR. This is one of few known cases where regulatory changes and LOF mutation in an anthocyanin structural gene, rather than transcription factors, are important. Furthermore, if TEs prove to be a frequent source of mutation, the interplay between environmental stress-induced TE evolution and pollinator-mediated selection for adaptive colour variation may be an overlooked mechanism maintaining floral colour polymorphism in nature.
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Zemin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - James Perkins
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xin Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Grace Emma Marsh
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Emma Grace John
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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3
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Horvath R, Minadakis N, Bourgeois Y, Roulin AC. The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role. eLife 2024; 12:RP93284. [PMID: 38606833 PMCID: PMC11014726 DOI: 10.7554/elife.93284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.
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Affiliation(s)
- Robert Horvath
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRDMontpellierFrance
- University of PortsmouthPortsmouthUnited Kingdom
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
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4
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Li W, Chu C, Li H, Zhang H, Sun H, Wang S, Wang Z, Li Y, Foster TM, López-Girona E, Yu J, Li Y, Ma Y, Zhang K, Han Y, Zhou B, Fan X, Xiong Y, Deng CH, Wang Y, Xu X, Han Z. Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing. Nat Genet 2024; 56:505-516. [PMID: 38347217 DOI: 10.1038/s41588-024-01657-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/08/2024] [Indexed: 03/16/2024]
Abstract
Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock 'M9', the semi-vigorous rootstock 'MM106' and 'Fuji', one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of 'M9', the major locus for rootstock-induced dwarfing. Comparing 'M9' and 'MM106' genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees.
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Affiliation(s)
- Wei Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Hui Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Hengtao Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Haochen Sun
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Shiyao Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Zijun Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Yuqi Li
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Toshi M Foster
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Motueka, New Zealand
| | - Elena López-Girona
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Jiaxin Yu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, USA
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yongming Han
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Bowen Zhou
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Xingqiang Fan
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Yao Xiong
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Auckland, New Zealand.
| | - Yi Wang
- Institute for Horticultural Plants, China Agricultural University, Beijing, China.
| | - Xuefeng Xu
- Institute for Horticultural Plants, China Agricultural University, Beijing, China
| | - Zhenhai Han
- Institute for Horticultural Plants, China Agricultural University, Beijing, China.
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5
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Thieme M, Minadakis N, Himber C, Keller B, Xu W, Rutowicz K, Matteoli C, Böhrer M, Rymen B, Laudencia-Chingcuanco D, Vogel JP, Sibout R, Stritt C, Blevins T, Roulin AC. Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon. PLoS Genet 2024; 20:e1011200. [PMID: 38470914 PMCID: PMC10959353 DOI: 10.1371/journal.pgen.1011200] [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: 10/30/2023] [Revised: 03/22/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers of evolution. Yet, the uncontrolled and potentially selfish proliferation of LTR-RTs can lead to deleterious mutations and genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, the understanding of their dual role in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grass Brachypodium distachyon to characterize how genetic and environmental factors influence plant LTR-RT dynamics in the wild. When combining a coverage-based approach to estimate global LTR-RT copy number variations with mobilome-sequencing of nine accessions exposed to eight different stresses, we find little evidence for a major role of environmental factors in LTR-RT accumulations in B. distachyon natural accessions. Instead, we show that loss of RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation in plants, results in high transcriptional and transpositional activities of RLC_BdisC024 (HOPPLA) LTR-RT family elements, and that these effects are not stress-specific. This work supports findings indicating an ongoing mobility in B. distachyon and reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.
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Affiliation(s)
- Michael Thieme
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christophe Himber
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Bettina Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Wenbo Xu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Kinga Rutowicz
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Calvin Matteoli
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Marcel Böhrer
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Bart Rymen
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Debbie Laudencia-Chingcuanco
- United States Department of Agriculture Agricultural Research Service Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Richard Sibout
- Institut National de la Recherche Agronomique Unité BIA- 1268 Biopolymères Interactions Assemblages Equipe Paroi Végétale et Polymères Pariétaux (PVPP), Nantes, France
| | - Christoph Stritt
- Swiss Tropical and Public Health Institute (Swiss TPH), Allschwil, Switzerland
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Anne C. Roulin
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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6
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Badet T, Tralamazza SM, Feurtey A, Croll D. Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen. Nucleic Acids Res 2024; 52:1226-1242. [PMID: 38142443 PMCID: PMC10853768 DOI: 10.1093/nar/gkad1214] [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: 04/09/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/26/2023] Open
Abstract
Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate the spread of the pathogenicity-associated Styx element across five species that last diverged ∼11 000 years ago. We show that the element likely originated in the Zymoseptoria fungal pathogen genus and underwent multiple independent reactivation events. Using a global 900-genome panel of the wheat pathogen Zymoseptoria tritici, we assess Styx copy number variation and identify renewed transposition activity in Oceania and South America. We show that the element can mobilize to create additional Styx copies in a four-generation pedigree. Importantly, we find that new copies of the element are not affected by genomic defenses suggesting minimal control against the element. Styx copies are preferentially located in recombination breakpoints and likely triggered multiple types of large chromosomal rearrangements. Taken together, we establish the origin, diversification and reactivation of a highly active TE with likely major consequences for chromosomal integrity and the expression of disease.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
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7
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Ma X, Vanneste S, Chang J, Ambrosino L, Barry K, Bayer T, Bobrov AA, Boston L, Campbell JE, Chen H, Chiusano ML, Dattolo E, Grimwood J, He G, Jenkins J, Khachaturyan M, Marín-Guirao L, Mesterházy A, Muhd DD, Pazzaglia J, Plott C, Rajasekar S, Rombauts S, Ruocco M, Scott A, Tan MP, Van de Velde J, Vanholme B, Webber J, Wong LL, Yan M, Sung YY, Novikova P, Schmutz J, Reusch TBH, Procaccini G, Olsen JL, Van de Peer Y. Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment. NATURE PLANTS 2024; 10:240-255. [PMID: 38278954 PMCID: PMC7615686 DOI: 10.1038/s41477-023-01608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/05/2023] [Indexed: 01/28/2024]
Abstract
We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.
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Affiliation(s)
- Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jiyang Chang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Luca Ambrosino
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Till Bayer
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | | | - LoriBeth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Justin E Campbell
- Coastlines and Oceans Division, Institute of Environment, Florida International University-Biscayne Bay Campus, Miami, FL, USA
| | - Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria Luisa Chiusano
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Agricultural Sciences, University Federico II of Naples, Naples, Italy
| | - Emanuela Dattolo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Guifen He
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marina Khachaturyan
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
- Institute of General Microbiology, University of Kiel, Kiel, Germany
| | - Lázaro Marín-Guirao
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain
| | - Attila Mesterházy
- Centre for Ecological Research, Wetland Ecology Research Group, Debrecen, Hungary
| | - Danish-Daniel Muhd
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jessica Pazzaglia
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Miriam Ruocco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Fano Marine Center, Fano, Italy
| | - Alison Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Min Pau Tan
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jozefien Van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Li Lian Wong
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Mi Yan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yeong Yik Sung
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Polina Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany.
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
- National Biodiversity Future Centre, Palermo, Italy.
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
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8
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Xiao Y, Xi Z, Wang F, Wang J. Genomic asymmetric epigenetic modification of transposable elements is involved in gene expression regulation of allopolyploid Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:226-241. [PMID: 37797206 DOI: 10.1111/tpj.16491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Polyploids are common and have a wide geographical distribution and environmental adaptability. Allopolyploidy may lead to the activation of transposable elements (TE). However, the mechanism of epigenetic modification of TEs in the establishment and evolution of allopolyploids remains to be explored. We focused on the TEs of model allopolyploid Brassica napus (An An Cn Cn ), exploring the TE characteristics of the genome, epigenetic modifications of TEs during allopolyploidization, and regulation of gene expression by TE methylation. In B. napus, approximately 50% of the genome was composed of TEs. TEs increased with proximity to genes, especially DNA transposons. TE methylation levels were negatively correlated with gene expression, and changes in TE methylation levels were able to regulate the expression of neighboring genes related to responses to light intensity and stress, which promoted powerful adaptation of allopolyploids to new environments. TEs can be synergistically regulated by RNA-directed DNA methylation pathways and histone modifications. The epigenetic modification levels of TEs tended to be similar to those of the diploid parents during the genome evolution of B. napus. The TEs of the An subgenome were more likely to be modified, and the imbalance in TE number and epigenetic modification level in the An and Cn subgenomes may lead to the establishment of subgenome dominance. Our study analyzed the characteristics of TE location, DNA methylation, siRNA, and histone modification in B. napus and highlighted the importance of TE epigenetic modifications during the allopolyploidy process, providing support for revealing the mechanism of allopolyploid formation and evolution.
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Affiliation(s)
- Yafang Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zengde Xi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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9
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Brasileiro ACM, Gimenes MA, Pereira BM, Mota APZ, Aguiar MN, Martins ACQ, Passos MAS, Guimaraes PM. The Stilbene Synthase Family in Arachis: A Genome-Wide Study and Functional Characterization in Response to Stress. Genes (Basel) 2023; 14:2181. [PMID: 38137003 PMCID: PMC10742623 DOI: 10.3390/genes14122181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Peanut (Arachis hypogaea) and its wild relatives are among the few species that naturally synthesize resveratrol, a well-known stilbenoid phytoalexin that plays a crucial role in plant defense against biotic and abiotic stresses. Resveratrol has received considerable attention due to its health benefits, such as preventing and treating various human diseases and disorders. Chalcone (CHS) and Stilbene (STS) Synthases are plant-specific type III Polyketide Synthases (PKSs) that share the same substrates and are key branch enzymes in the biosynthesis of flavonoids and stilbenoids, respectively. Although resveratrol accumulation in response to external stimulus has been described in peanut, there are no comprehensive studies of the CHS and STS gene families in the genus Arachis. In the present study, we identified and characterized 6 CHS and 46 STS genes in the tetraploid peanut and an average of 4 CHS and 22 STS genes in three diploid wild species (Arachis duranensis, Arachis ipaënsis and Arachis stenosperma). The CHS and STS gene and protein structures, chromosomal distributions, phylogenetic relationships, conserved amino acid domains, and cis-acting elements in the promoter regions were described for all Arachis species studied. Based on gene expression patterns of wild A. stenosperma STS genes in response to different biotic and abiotic stresses, we selected the candidate AsSTS4 gene, which is strongly induced by ultraviolet (UV) light exposure, for further functional investigation. The AsSTS4 overexpression in peanut hairy roots significantly reduced (47%) root-knot nematode infection, confirming that stilbene synthesis activation in transgenic plants can increase resistance to pathogens. These findings contribute to understanding the role of resveratrol in stress responses in Arachis species and provide the basis for genetic engineering for improved production of valuable secondary metabolites in plants.
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Affiliation(s)
- Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
| | - Marcos Aparecido Gimenes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Bruna Medeiros Pereira
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Ana Paula Zotta Mota
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Matheus Nascimento Aguiar
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Andressa Cunha Quintana Martins
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Mario Alfredo Saraiva Passos
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
| | - Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
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10
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Kirov I. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding. Int J Mol Sci 2023; 24:17054. [PMID: 38069377 PMCID: PMC10706983 DOI: 10.3390/ijms242317054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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11
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Kreiner JM, Hnatovska S, Stinchcombe JR, Wright SI. Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus. PLoS Genet 2023; 19:e1010865. [PMID: 38150485 PMCID: PMC10775983 DOI: 10.1371/journal.pgen.1010865] [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: 07/12/2023] [Revised: 01/09/2024] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
Genome size variation, largely driven by repeat content, is poorly understood within and among populations, limiting our understanding of its significance for adaptation. Here we characterize intraspecific variation in genome size and repeat content across 186 individuals of Amaranthus tuberculatus, a ubiquitous native weed that shows flowering time adaptation to climate across its range and in response to agriculture. Sequence-based genome size estimates vary by up to 20% across individuals, consistent with the considerable variability in the abundance of transposable elements, unknown repeats, and rDNAs across individuals. The additive effect of this variation has important phenotypic consequences-individuals with more repeats, and thus larger genomes, show slower flowering times and growth rates. However, compared to newly-characterized gene copy number and polygenic nucleotide changes underlying variation in flowering time, we show that genome size is a marginal contributor. Differences in flowering time are reflected by genome size variation across sexes and marginally, habitats, while polygenic variation and a gene copy number variant within the ATP synthesis pathway show consistently stronger environmental clines than genome size. Repeat content nonetheless shows non-neutral distributions across the genome, and across latitudinal and environmental gradients, demonstrating the numerous governing processes that in turn influence quantitative genetic variation for phenotypes key to plant adaptation.
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Affiliation(s)
- Julia M. Kreiner
- Department of Botany, Biodiversity Research Centre, University of British Columbia
- Department of Ecology & Evolutionary Biology, University of Toronto
| | - Solomiya Hnatovska
- Department of Ecology & Evolutionary Biology, University of Toronto
- Department of Molecular Genetics, University of Toronto
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12
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Dionisio JF, Pezenti LF, de Souza RF, Sosa-Gómez DR, da Rosa R. Annotation of transposable elements in the transcriptome of the Neotropical brown stink bug Euschistus heros and its chromosomal distribution. Mol Genet Genomics 2023; 298:1377-1388. [PMID: 37646857 DOI: 10.1007/s00438-023-02063-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
Transposable elements (TEs) are DNA sequences capable of moving within the genome. Their distribution is very dynamic among organisms, and despite advances, there are still gaps in the understanding of the diversity and evolution of TEs in many insect species. In the case of Euschistus heros, considered the main stink bug in the soybean crop in Brazil, little is known about the participation of these elements. Therefore, the objective of the current work was to identify the different groups of transposable elements present in the E. heros transcriptome, evidencing their chromosomal distribution. Through RNA-Seq and de novo assembly, 60,009 transcripts were obtained, which were annotated locally via Blastn against specific databases. Of the 367 transcripts identified as TEs, 202 belong to Class II, with emphasis on the TIR order. Among Class I elements or retrotransposons, most were characterized as LINE. Phylogenetic analyses were performed with the protein domains, evidencing differences between Tc1-mariner sequences, which may be related to possible horizontal transfer events. The transposable elements that stood out in the transcriptome were selected for fluorescent in situ hybridization. DNA transposon probes hAT, Helitron, and Tc1-mariner showed mostly scattered signals, with the presence of some blocks. Retrotransposon probes Copia, Gypsy, Jockey, and RTE showed a more pulverized hybridization pattern, with the presence of small interstitial and/or terminal blocks. Studies like this one, integrating functional genomics and molecular cytogenetic tools, are essential to expanding knowledge about transcriptionally active mobile elements, and their behavior in the chromosomes.
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Affiliation(s)
- Jaqueline Fernanda Dionisio
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Larissa Forim Pezenti
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Caixa Postal: 4006, Londrina, PR, CEP: 86085-981, Brazil
| | - Renata da Rosa
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil.
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13
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Gorbenko IV, Petrushin IS, Shcherban AB, Orlov YL, Konstantinov YM. Short Interrupted Repeat Cassette (SIRC)-Novel Type of Repetitive DNA Element Found in Arabidopsis thaliana. Int J Mol Sci 2023; 24:11116. [PMID: 37446293 DOI: 10.3390/ijms241311116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Short interrupted repeat cassette (SIRC)-a novel DNA element found throughout the A. thaliana nuclear genome. SIRCs are represented by short direct repeats interrupted by diverse DNA sequences. The maxima of SIRC's distribution are located within pericentromeric regions. We suggest that originally SIRC was a special case of the complex internal structure of the miniature inverted repeat transposable element (MITE), and further MITE amplification, transposition, and loss of terminal inverted repeats gave rise to SIRC as an independent DNA element. SIRC sites were significantly enriched with several histone modifications associated with constitutive heterochromatin and mobile genetic elements. The majority of DNA-binding proteins, strongly associated with SIRC, are related to histone modifications for transcription repression. A part of SIRC was found to overlap highly inducible protein-coding genes, suggesting a possible regulatory role for these elements, yet their definitive functions need further investigation.
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Affiliation(s)
- Igor V Gorbenko
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
| | - Ivan S Petrushin
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
- Department of Business Communications and Informatics, Irkutsk State University, Irkutsk 664033, Russia
| | - Andrey B Shcherban
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Kurchatov Genomic Center ICG SB RAS, Novosibirsk 630090, Russia
| | - Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
- Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow 117198, Russia
| | - Yuri M Konstantinov
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
- Biosoil Department, Irkutsk State University, Irkutsk 664003, Russia
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14
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Walker MG, Klompe S, Zhang D, Sternberg S. Novel molecular requirements for CRISPR RNA-guided transposition. Nucleic Acids Res 2023; 51:4519-4535. [PMID: 37078593 PMCID: PMC10201428 DOI: 10.1093/nar/gkad270] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
CRISPR-associated transposases (CASTs) direct DNA integration downstream of target sites using the RNA-guided DNA binding activity of nuclease-deficient CRISPR-Cas systems. Transposition relies on several key protein-protein and protein-DNA interactions, but little is known about the explicit sequence requirements governing efficient transposon DNA integration activity. Here, we exploit pooled library screening and high-throughput sequencing to reveal novel sequence determinants during transposition by the Type I-F Vibrio cholerae CAST system (VchCAST). On the donor DNA, large transposon end libraries revealed binding site nucleotide preferences for the TnsB transposase, as well as an additional conserved region that encoded a consensus binding site for integration host factor (IHF). Remarkably, we found that VchCAST requires IHF for efficient transposition, thus revealing a novel cellular factor involved in CRISPR-associated transpososome assembly. On the target DNA, we uncovered preferred sequence motifs at the integration site that explained previously observed heterogeneity with single-base pair resolution. Finally, we exploited our library data to design modified transposon variants that enable in-frame protein tagging. Collectively, our results provide new clues about the assembly and architecture of the paired-end complex formed between TnsB and the transposon DNA, and inform the design of custom payload sequences for genome engineering applications with CAST systems.
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Affiliation(s)
- Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Dennis J Zhang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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15
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Guo Z, Guo L, Bai Y, Kang S, Sun D, Qin J, Ye F, Wang S, Wu Q, Xie W, Yang X, Crickmore N, Zhou X, Zhang Y. Retrotransposon-mediated evolutionary rewiring of a pathogen response orchestrates a resistance phenotype in an insect host. Proc Natl Acad Sci U S A 2023; 120:e2300439120. [PMID: 36996102 PMCID: PMC10083559 DOI: 10.1073/pnas.2300439120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/23/2023] [Indexed: 03/31/2023] Open
Abstract
Ongoing host-pathogen interactions can trigger a coevolutionary arms race, while genetic diversity within the host can facilitate its adaptation to pathogens. Here, we used the diamondback moth (Plutella xylostella) and its pathogen Bacillus thuringiensis (Bt) as a model for exploring an adaptive evolutionary mechanism. We found that insect host adaptation to the primary Bt virulence factors was tightly associated with a short interspersed nuclear element (SINE - named SE2) insertion into the promoter of the transcriptionally activated MAP4K4 gene. This retrotransposon insertion coopts and potentiates the effect of the transcription factor forkhead box O (FOXO) in inducing a hormone-modulated Mitogen-activated protein kinase (MAPK) signaling cascade, leading to an enhancement of a host defense mechanism against the pathogen. This work demonstrates that reconstructing a cis-trans interaction can escalate a host response mechanism into a more stringent resistance phenotype to resist pathogen infection, providing a new insight into the coevolutionary mechanism of host organisms and their microbial pathogens.
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Affiliation(s)
- Zhaojiang Guo
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Le Guo
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Yang Bai
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Shi Kang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Dan Sun
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jianying Qin
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Fan Ye
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Shaoli Wang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Qingjun Wu
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Wen Xie
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Xin Yang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, BrightonBN1 9QG, UK
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY40546-0091
| | - Youjun Zhang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
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16
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Mérot C, Stenløkk KSR, Venney C, Laporte M, Moser M, Normandeau E, Árnyasi M, Kent M, Rougeux C, Flynn JM, Lien S, Bernatchez L. Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads. Mol Ecol 2023; 32:1458-1477. [PMID: 35416336 DOI: 10.1111/mec.16468] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022]
Abstract
Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the lake whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements and analysed the genomes in the light of related coregonid species. Next, we used a combination of long- and short-read sequencing to characterize SVs and genotype them at the population scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transposable elements (TEs), suggesting that TE accumulation may represent a key component of genetic divergence between the Dwarf and Normal species. Together, our results suggest that SVs may play an important role in speciation and that, by combining second- and third-generation sequencing, we now have the ability to integrate SVs into speciation genomics.
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Affiliation(s)
- Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Kristina S R Stenløkk
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Clare Venney
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,Ministère des Forêts, de la Faune et des Parcs (MFFP) du Québec, Québec, Québec, Canada
| | - Michel Moser
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Clément Rougeux
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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17
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Almer J, Resl P, Gudmundsson H, Warshan D, Andrésson ÓS, Werth S. Symbiont-specific responses to environmental cues in a threesome lichen symbiosis. Mol Ecol 2023; 32:1045-1061. [PMID: 36478478 DOI: 10.1111/mec.16814] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We compared gene expression of thallus sectors of the photosymbiodeme-forming lichen Peltigera britannica containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts and investigated differential gene expression at different temperatures representing mild and putatively stressful conditions. First, we quantified photobiont-mediated differences in fungal gene expression. Second, because of known ecological differences between photomorphs, we investigated symbiont-specific responses in gene expression to temperature increases. Photobiont-mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression. Furthermore, high temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data and to an increased expression of genes involved in photosynthesis in both photobiont types at 15 and 25°C. The fungus and the cyanobacteria exhibited thermal stress responses already at 15°C, the green algae mainly at 25°C, demonstrating symbiont-specific responses to environmental cues and symbiont-specific ecological optima.
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Affiliation(s)
- Jasmin Almer
- Systematics, Biodiversity and Evolution of Plants, LMU Munich, Munich, Germany.,Institute of Biology, University of Graz, Graz, Austria
| | - Philipp Resl
- Systematics, Biodiversity and Evolution of Plants, LMU Munich, Munich, Germany.,Institute of Biology, University of Graz, Graz, Austria
| | - Hörður Gudmundsson
- Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Denis Warshan
- Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Ólafur S Andrésson
- Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Silke Werth
- Systematics, Biodiversity and Evolution of Plants, LMU Munich, Munich, Germany
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18
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Wang H, Lu Y, Zhang T, Liu Z, Cao L, Chang Q, Liu Y, Lu X, Yu S, Li H, Jiang J, Liu G, Sederoff HW, Sederoff RR, Zhang Q, Zheng Z. The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion. PLANT PHYSIOLOGY 2023; 191:1122-1137. [PMID: 36494195 PMCID: PMC9922402 DOI: 10.1093/plphys/kiac571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
As essential organs of reproduction in angiosperms, flowers, and the genetic mechanisms of their development have been well characterized in many plant species but not in the woody tree yellowhorn (Xanthoceras sorbifolium). Here, we focused on the double flower phenotype in yellowhorn, which has high ornamental value. We found a candidate C-class gene, AGAMOUS1 (XsAG1), through bovine serum albumin sequencing and genetics analysis with a Long Interpersed Nuclear Elements 1 (LINE1) transposable element fragment (Xsag1-LINE1-1) inserted into its second intron that caused a loss-of-C-function and therefore the double flower phenotype. In situ hybridization of XsAG1 and analysis of the expression levels of other ABC genes were used to identify differences between single- and double-flower development processes. These findings enrich our understanding of double flower formation in yellowhorn and provide evidence that transposon insertions into genes can reshape plant traits in forest trees.
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dos Santos LB, Aono AH, Francisco FR, da Silva CC, Souza LM, de Souza AP. The rubber tree kinome: Genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1068202. [PMID: 36824205 PMCID: PMC9941580 DOI: 10.3389/fpls.2023.1068202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, with the aim of providing novel inferences about the mechanisms associated with the stress response developed by PKs and retained throughout evolution, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species Manihot esculenta and Ricinus communis. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.
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Affiliation(s)
- Lucas Borges dos Santos
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Felipe Roberto Francisco
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
| | - Livia Moura Souza
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
- São Francisco University (USF), Itatiba, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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20
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Ventimiglia M, Marturano G, Vangelisti A, Usai G, Simoni S, Cavallini A, Giordani T, Natali L, Zuccolo A, Mascagni F. Genome-wide identification and characterization of exapted transposable elements in the large genome of sunflower (Helianthus annuus L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:734-748. [PMID: 36573648 DOI: 10.1111/tpj.16078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/07/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Transposable elements (TEs) are an important source of genome variability, playing many roles in the evolution of eukaryotic species. Besides well-known phenomena, TEs may undergo the exaptation process and generate the so-called exapted transposable element genes (ETEs). Here we present a genome-wide survey of ETEs in the large genome of sunflower (Helianthus annuus L.), in which the massive amount of TEs, provides a significant source for exaptation. A library of sunflower TEs was used to build TE-specific Hidden Markov Model profiles, to search for all available sunflower gene products. In doing so, 20 016 putative ETEs were identified and further investigated for the characteristics that distinguish TEs from genes, leading to the validation of 3530 ETEs. The analysis of ETEs transcription patterns under different stress conditions showed a differential regulation triggered by treatments mimicking biotic and abiotic stress; furthermore, the distribution of functional domains of differentially regulated ETEs revealed a relevant presence of domains involved in many aspects of cellular functions. A comparative genomic investigation was performed including species representative of Asterids and appropriate outgroups: the bulk of ETEs that resulted were specific to the sunflower, while few ETEs presented orthologues in the genome of all analyzed species, making the hypothesis of a conserved function. This study highlights the crucial role played by exaptation, actively contributing to species evolution.
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Affiliation(s)
- Maria Ventimiglia
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Giovanni Marturano
- Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Samuel Simoni
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Zuccolo
- Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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21
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Faro TAS, de Oliveira EHC. Canine transmissible venereal tumor - From general to molecular characteristics: A review. Anim Genet 2023; 54:82-89. [PMID: 36259378 DOI: 10.1111/age.13260] [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: 05/23/2022] [Revised: 08/07/2022] [Accepted: 08/23/2022] [Indexed: 01/07/2023]
Abstract
Cancer is a group of complex diseases resulting from the accumulation of genetic and epigenetic changes affecting control and activity of several genes, especially those involved in cell differentiation and growth processes, leading to an abnormal proliferation. When the disease reaches an advanced stage, cancer can lead to metastasis in other organs. Interestingly, recent studies have shown that some types of cancer spread not only through the body, but also can be transmitted among individuals. Therefore, these cancers are known as transmissible tumors. Among the three types of transmissible tumors that occur in nature, the canine transmissible venereal tumor (CTVT) is known as the oldest cancer in the world, since it was originated from a single individual 11 000 years ago. The disease has a worldwide distribution, and its occurrence has been documented since 1810. The CTVT presents three types of cytomorphological classification: lymphocytoid type, mixed type, and plasmacytoid type, the latter being chemoresistant due to overexpression of the ABCB1 gene, and consequently increase of the P-glycoprotein. More knowledge about the epidemiology and evolution of CTVT may help to elucidate the pathway and form of the global spread of the disease.
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Affiliation(s)
- Thamirys A S Faro
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, SEAMB, Instituto Evandro Chagas Ananindeua, Belém, Pará, Brazil
| | - Edivaldo H C de Oliveira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Citogenômica e Mutagênese Ambiental, SEAMB, Instituto Evandro Chagas Ananindeua, Belém, Pará, Brazil
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22
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Arce AL, Mencia R, Cambiagno DA, Lang PL, Liu C, Burbano HA, Weigel D, Manavella PA. Polymorphic inverted repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana. Cell Rep 2023; 42:112029. [PMID: 36689329 DOI: 10.1016/j.celrep.2023.112029] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/03/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023] Open
Abstract
Transposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable element (TE)-derived inverted repeats (IRs) are commonly found near genes, where they affect host gene expression. However, the molecular mechanisms of such regulation are unclear in most cases. Expression of these IRs is associated with production of 24-nt small RNAs, methylation of the IRs, and drastic changes in local 3D chromatin organization. Notably, many of these IRs differ between Arabidopsis thaliana accessions, causing variation in short-range chromatin interactions and gene expression. CRISPR-Cas9-mediated disruption of two IRs leads to a switch in genome topology and gene expression with phenotypic consequences. Our data show that insertion of an IR near a gene provides an anchor point for chromatin interactions that profoundly impact the activity of neighboring loci. This turns IRs into powerful evolutionary agents that can contribute to rapid adaptation.
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Affiliation(s)
- Agustín L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Regina Mencia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Patricia L Lang
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany
| | - Hernán A Burbano
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany; Centre for Life's Origins and Evolution, University College London, London, UK
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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23
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Walker MW, Klompe SE, Zhang DJ, Sternberg SH. Transposon mutagenesis libraries reveal novel molecular requirements during CRISPR RNA-guided DNA integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524723. [PMID: 36711804 PMCID: PMC9882353 DOI: 10.1101/2023.01.19.524723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
CRISPR-associated transposons (CASTs) direct DNA integration downstream of target sites using the RNA-guided DNA binding activity of nuclease-deficient CRISPR-Cas systems. Transposition relies on several key protein-protein and protein-DNA interactions, but little is known about the explicit sequence requirements governing efficient transposon DNA integration activity. Here, we exploit pooled library screening and high-throughput sequencing to reveal novel sequence determinants during transposition by the Type I-F Vibrio cholerae CAST system. On the donor DNA, large mutagenic libraries identified core binding sites recognized by the TnsB transposase, as well as an additional conserved region that encoded a consensus binding site for integration host factor (IHF). Remarkably, we found that VchCAST requires IHF for efficient transposition, thus revealing a novel cellular factor involved in CRISPR-associated transpososome assembly. On the target DNA, we uncovered preferred sequence motifs at the integration site that explained previously observed heterogeneity with single-base pair resolution. Finally, we exploited our library data to design modified transposon variants that enable in-frame protein tagging. Collectively, our results provide new clues about the assembly and architecture of the paired-end complex formed between TnsB and the transposon DNA, and inform the design of custom payload sequences for genome engineering applications of CAST systems.
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Affiliation(s)
- Matt W.G. Walker
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Sanne E. Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Dennis J. Zhang
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
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24
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Bariah I, Gribun L, Kashkush K. Transposable elements are associated with genome-specific gene expression in bread wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1072232. [PMID: 36714723 PMCID: PMC9878150 DOI: 10.3389/fpls.2022.1072232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Recent studies in wheat emphasized the importance of TEs, which occupy ~85% of the wheat genome, as a major source of intraspecific genetic variation due to their recent activity and involvement in genomic rearrangements. The contribution of TEs to structural and functional variations in bread wheat genes is not fully understood. METHODS Here, publicly available RNA-Seq databases of bread wheat were integrated to identify TE insertions within gene bodies (exons\ introns) and assess the impact of TE insertions on gene expression variations of homoeologs gene groups. Overall, 70,818 homoeologs genes were analyzed: 55,170 genes appeared in each one of the three subgenomes (termed ABD), named triads; 12,640 genes appeared in two of the three subgenomes (in A and B only, termed AB; or in A and D only, termed AD; or in B and D only, termed BD);, named dyads; and 3,008 genes underwent duplication in one of the three subgenomes (two copies in: subgenome A, termed AABD; subgenome B, termed ABBD; or subgenome D, termed ABDD), named tetrads. RESULTS To this end, we found that ~36% of the 70,818 genes contained at least one TE insertion within the gene body, mostly in triads. Analysis of 14,258 triads revealed that the presence of TE insertion in at least one of the triad genes (7,439 triads) was associated with balanced expression (similar expression levels) between the homoeolog genes. TE insertions within the exon or in the untranslated regions (UTRs) of one or more of the homoeologs in a triad were significantly associated with homoeolog expression bias. Furthermore, we found a statistically significant correlation between the presence\absence of TEs insertions belonging to six TE superfamilies and 17 TE subfamilies and the suppression of a single homoeolog gene. A significant association was observed between the presence of TE insertions from specific superfamilies and the expression of genes that are associated with biotic and abiotic stress responses. CONCLUSION Our data strongly indicate that TEs might play a prominent role in controlling gene expression in a genome-specific manner in bread wheat.
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25
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Merenciano M, Coronado-Zamora M, González J. Experimental Validation of Transposable Element Insertions Using the Polymerase Chain Reaction (PCR). Methods Mol Biol 2023; 2607:95-114. [PMID: 36449160 DOI: 10.1007/978-1-0716-2883-6_6] [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] [Indexed: 06/17/2023]
Abstract
Transposable elements (TEs), also known as transposons, are repetitive DNA sequences, present in virtually all organisms, that can move from one genomic position to another. TEs can be a source of mutations with important consequences for organisms. Despite their interest, its repetitive nature has made their study very challenging. However, the emergence of new sequencing technologies that allow obtaining long-read sequences, has improved the in silico de novo detection and annotation of TEs. The de novo annotation of TEs has already been performed in several organisms including the fruit fly Drosophila melanogaster. Yet, experimental validation can be used to confirm the presence of TEs in specific D. melanogaster natural populations. Here, we present a step-by-step protocol to experimentally validate by polymerase chain reaction (PCR) the presence and/or absence of TEs in natural populations of D. melanogaster. This detailed protocol has been implemented in the participant high schools of the Citizen Fly Lab activity that is part of the international citizen science project Melanogaster: Catch the Fly! ( https://melanogaster.eu ). Specifically, the students collaborate with the scientists of the European Drosophila Population Genomics Consortium (DrosEU) in the experimental validation of new genetic variants, previously identified using bioinformatic techniques.
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Affiliation(s)
| | | | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain.
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26
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Monshi FI, Katsube-Tanaka T. 2S albumin g13 polypeptide, less related to Fag e 2, can be eliminated in common buckwheat (Fagopyrum esculentum Moench) seeds. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 5:100138. [PMID: 36187231 PMCID: PMC9523277 DOI: 10.1016/j.fochms.2022.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022]
Abstract
2S albumin (g11, g13, g14, and g28) is an important allergen in common buckwheat. g13 is hydrophobic, scarce, and less related to g14 than g11/g28 is related to g14. g13_null allele homozygote produced no g13 protein in seeds. Insert-like sequence of g13_null allele resided frequently in buckwheat genome. g13_null homozygote lowered allergenicity in common buckwheat.
2S albumin (g11, g13, g14, and g28) is an important allergen in common buckwheat (Fagopyrum esculentum). g13 is hydrophobic, rare in seeds, and may show distinct allergenicity from the others; therefore, we tried to eliminate this protein. Phylogenetic and property distance analyses indicated g13 is less related to g14 (Fag e 2) than g11/g28 is related to g14, particularly in the second domain containing the II and III α-helices. A null allele with a 531 bp insertion in the coding region was found for g13 at an allele frequency of 2 % in natural populations of common buckwheat. The g13_null allele homozygote accumulated no g13 protein. A BLAST search for the 531 bp insertion suggested the insert-like sequence resided frequently in the buckwheat genome, including the self-incompatibility responsible gene ELF3 in Fagopyrum tataricum. The g13_null insert-like sequence could, therefore, help in producing hypoallergenic cultivars, and expand the genetic diversity of buckwheat.
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27
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De Kort H, Legrand S, Honnay O, Buckley J. Transposable elements maintain genome-wide heterozygosity in inbred populations. Nat Commun 2022; 13:7022. [PMID: 36396660 PMCID: PMC9672359 DOI: 10.1038/s41467-022-34795-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding. Capitalizing on the mixed mating system of Arabidopsis lyrata, we assess genome-wide heterozygosity and signatures of selection at single nucleotide polymorphisms near transposable elements across an inbreeding gradient. Under intense inbreeding, we find systematically elevated heterozygosity downstream of several TE superfamilies, associated with signatures of balancing selection. In addition, we demonstrate increased heterozygosity in stress-responsive genes that consistently occur downstream of TEs. We finally reveal that TE superfamilies are associated with specific signatures of selection that are reproducible across independent evolutionary lineages of A. lyrata. Together, our study provides an important hypothesis for the success of self-fertilizing species.
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Affiliation(s)
- Hanne De Kort
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - Sylvain Legrand
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Olivier Honnay
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - James Buckley
- grid.11201.330000 0001 2219 0747School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL1 2BT UK
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28
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Chumová Z, Belyayev A, Mandáková T, Zeisek V, Hodková E, Šemberová K, Euston-Brown D, Trávníček P. The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae). FRONTIERS IN PLANT SCIENCE 2022; 13:982852. [PMID: 36247607 PMCID: PMC9559566 DOI: 10.3389/fpls.2022.982852] [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: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, Masaryk University, Brno, Czechia
| | - Vojtěch Zeisek
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Eva Hodková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | | | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
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29
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Kim WR, Park EG, Lee YJ, Bae WH, Lee DH, Kim HS. Integration of TE Induces Cancer Specific Alternative Splicing Events. Int J Mol Sci 2022; 23:ijms231810918. [PMID: 36142830 PMCID: PMC9502224 DOI: 10.3390/ijms231810918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing of messenger RNA (mRNA) precursors contributes to genetic diversity by generating structurally and functionally distinct transcripts. In a disease state, alternative splicing promotes incidence and development of several cancer types through regulation of cancer-related biological processes. Transposable elements (TEs), having the genetic ability to jump to other regions of the genome, can bring about alternative splicing events in cancer. TEs can integrate into the genome, mostly in the intronic regions, and induce cancer-specific alternative splicing by adjusting various mechanisms, such as exonization, providing splicing donor/acceptor sites, alternative regulatory sequences or stop codons, and driving exon disruption or epigenetic regulation. Moreover, TEs can produce microRNAs (miRNAs) that control the proportion of transcripts by repressing translation or stimulating the degradation of transcripts at the post-transcriptional level. Notably, TE insertion creates a cancer-friendly environment by controlling the overall process of gene expression before and after transcription in cancer cells. This review emphasizes the correlative interaction between alternative splicing by TE integration and cancer-associated biological processes, suggesting a macroscopic mechanism controlling alternative splicing by TE insertion in cancer.
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Affiliation(s)
- Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
- Correspondence:
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Vourlaki IT, Castanera R, Ramos-Onsins SE, Casacuberta JM, Pérez-Enciso M. Transposable element polymorphisms improve prediction of complex agronomic traits in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3211-3222. [PMID: 35931838 PMCID: PMC9482605 DOI: 10.1007/s00122-022-04180-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Transposon insertion polymorphisms can improve prediction of complex agronomic traits in rice compared to using SNPs only, especially when accessions to be predicted are less related to the training set. Transposon insertion polymorphisms (TIPs) are significant sources of genetic variation. Previous work has shown that TIPs can improve detection of causative loci on agronomic traits in rice. Here, we quantify the fraction of variance explained by single nucleotide polymorphisms (SNPs) compared to TIPs, and we explore whether TIPs can improve prediction of traits when compared to using only SNPs. We used eleven traits of agronomic relevance from by five different rice population groups (Aus, Indica, Aromatic, Japonica, and Admixed), 738 accessions in total. We assess prediction by applying data split validation in two scenarios. In the within-population scenario, we predicted performance of improved Indica varieties using the rest of Indica accessions. In the across population scenario, we predicted all Aromatic and Admixed accessions using the rest of populations. In each scenario, Bayes C and a Bayesian reproducible kernel Hilbert space regression were compared. We find that TIPs can explain an important fraction of total genetic variance and that they also improve genomic prediction. In the across population prediction scenario, TIPs outperformed SNPs in nine out of the eleven traits analyzed. In some traits like leaf senescence or grain width, using TIPs increased predictive correlation by 30-50%. Our results evidence, for the first time, that TIPs genotyping can improve prediction on complex agronomic traits in rice, especially when accessions to be predicted are less related to training accessions.
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Affiliation(s)
- Ioanna-Theoni Vourlaki
- Universitat Autònoma de Barcelona, Department of Animal Production, 08193, Bellaterra, Barcelona, Spain.
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain.
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain
| | - Sebastián E Ramos-Onsins
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Universitat Autònoma de Barcelona, Department of Animal Production, 08193, Bellaterra, Barcelona, Spain.
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain.
- Catalan Institute for Research and Advanced studies, ICREA, 08010, Barcelona, Spain.
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31
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Gallo‐Franco JJ, Ghneim‐Herrera T, Tobar‐Tosse F, Romero M, Chaura J, Quimbaya M. Whole-genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response. PLANT DIRECT 2022; 6:e430. [PMID: 36051226 PMCID: PMC9414936 DOI: 10.1002/pld3.430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/25/2022] [Accepted: 07/06/2022] [Indexed: 05/05/2023]
Abstract
Epigenetic mechanisms in crops have emerged as a fundamental factor in plant adaptation and acclimation to biotic and abiotic stresses. Among described epigenetic mechanisms, DNA methylation has been defined as the most studied epigenetic modification involved in several developmental processes. It has been shown that contrasting methylation marks are associated with gene expression variations between cultivated and wild crop species. In this study, we analyzed single-base resolution methylome maps for Oryza sativa (a cultivated species) and Oryza glumaepatula (a wild species) genotypes grown under control conditions. Our results showed that overall, genome-wide methylation profiles are mainly conserved between both species, nevertheless, there are several differentially methylated regions with species-specific methylation patterns. In addition, we analyzed the association of identified DNA methylation marks in relation with Aluminum-tolerance levels of studied genotypes. We found several differentially methylated regions (DMRs) and DMR-associated genes (DAGs) that are linked with Al tolerance. Some of these DAGs have been previously reported as differentially expressed under Al exposure in O. sativa. Complementarily a Transposable Elements (TE) analysis revealed that specific aluminum related genes have associated-TEs potentially regulated by DNA methylation. Interestingly, the DMRs and DAGs between Al-tolerant and susceptible genotypes were different between O. sativa and O. glumaepatula, suggesting that methylation patterns related to Al responses are unique for each rice species. Our findings provide novel insights into DNA methylation patterns in wild and cultivated rice genotypes and their possible role in the regulation of plant stress responses.
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Affiliation(s)
| | | | - Fabian Tobar‐Tosse
- Departamento de Ciencias Básicas de la SaludPontificia Universidad Javeriana CaliCaliColombia
| | - Miguel Romero
- Departamento de Electrónica y Ciencias de la computaciónPontificia Universidad Javeriana CaliCaliColombia
| | - Juliana Chaura
- Departamento de Ciencias BiológicasUniversidad ICESICaliColombia
| | - Mauricio Quimbaya
- Departamento de Ciencias Naturales y MatemáticasPontificia Universidad Javeriana CaliCaliColombia
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32
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Chakraborty T, Trujillo JT, Kendall T, Mosher RA. A null allele of the pol IV second subunit impacts stature and reproductive development in Oryza sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:748-755. [PMID: 35635763 DOI: 10.1111/tpj.15848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
All eukaryotes possess three DNA-dependent RNA polymerases, Pols I-III, while land plants possess two additional polymerases, Pol IV and Pol V. Derived through duplication of Pol II subunits, Pol IV produces 24-nt short interfering RNAs that interact with Pol V transcripts to target de novo DNA methylation and silence transcription of transposons. Members of the grass family encode additional duplicated subunits of Pol IV and V, raising questions regarding the function of each paralog. In this study, we identify a null allele of the putative Pol IV second subunit, NRPD2, and demonstrate that NRPD2 is the sole subunit functioning with NRPD1 in small RNA production and CHH methylation in leaves. Homozygous nrpd2 mutants have neither gametophytic defects nor embryo lethality, although adult plants are dwarf and sterile.
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Affiliation(s)
- Tania Chakraborty
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Joshua T Trujillo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Timmy Kendall
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
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33
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Eriksson MC, Mandáková T, McCann J, Temsch EM, Chase MW, Hedrén M, Weiss-Schneeweiss H, Paun O. Repeat dynamics across timescales: a perspective from sibling allotetraploid marsh orchids (Dactylorhiza majalis s.l.). Mol Biol Evol 2022; 39:6651906. [PMID: 35904928 PMCID: PMC9366187 DOI: 10.1093/molbev/msac167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
To provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridization between diploids D. fuchsii and D. incarnata. Our results first reveal that the paternal D. incarnata genome shows a marked increased content of LTR retrotransposons compared to the maternal species, reflected in its larger genome size and consistent with a previously hypothesized bottleneck. With regard to the allopolyploids, in the youngest D. purpurella both genome size and TE composition appear to be largely additive with respect to parents, whereas for polyploids of intermediate ages we uncover rampant genome expansion on a magnitude of multiple entire genomes of some plants such as Arabidopsis. The oldest allopolyploids in the series are not larger than the intermediate ones. A putative tandem repeat, potentially derived from a non-autonomous miniature inverted-repeat TE (MITE) drives much of the genome dynamics in the allopolyploids. The highly dynamic MITE-like element is found in higher proportions in the maternal diploid, D. fuchsii, but is observed to increase in copy number in both subgenomes of the allopolyploids. Altogether, the fate of repeats appears strongly regulated and therefore predictable across multiple independent allopolyploidization events in this system. Apart from the MITE-like element, we consistently document a mild genomic shock following the allopolyploidizations investigated here, which may be linked to their relatively large genome sizes, possibly associated with strong selection against further genome expansions.
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Affiliation(s)
- Mimmi C Eriksson
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.,Vienna Graduate School of Population Genetics, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Terezie Mandáková
- Plant Cytogenomics Research Group, CEITEC-Central - European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Jamie McCann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Mark W Chase
- Royal Botanic Gardens Kew, London TW9 3AE, United Kingdom.,Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Mikael Hedrén
- Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Tian Y, Thrimawithana A, Ding T, Guo J, Gleave A, Chagné D, Ampomah‐Dwamena C, Ireland HS, Schaffer RJ, Luo Z, Wang M, An X, Wang D, Gao Y, Wang K, Zhang H, Zhang R, Zhou Z, Yan Z, Zhang L, Zhang C, Cong P, Deng CH, Yao J. Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1285-1297. [PMID: 35258172 PMCID: PMC9241373 DOI: 10.1111/pbi.13806] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Allele-specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar 'Royal Gala' (RG). A high quality chromosome-level genome was assembled using a homozygous tetra-haploid RG plant, derived from anther cultures. Using RNA-sequencing (RNA-seq) data from RG flower and fruit tissues, we identified 2091 ASE genes. Compared with the haploid genome of 'Golden Delicious' (GD), a parent of RG, we distinguished the genomic sequences between the two alleles of 817 ASE genes, and further identified allele-specific presence of a transposable element (TE) in the upstream region of 354 ASE genes. These included MYB110a that encodes a transcription factor regulating anthocyanin biosynthesis. Interestingly, another ASE gene, MYB10 also showed an allele-specific TE insertion and was identified using genome data of other apple cultivars. The presence of the TE insertion in both MYB genes was positively associated with ASE and anthocyanin accumulation in apple petals through analysis of 231 apple accessions, and thus underpins apple flower colour evolution. Our study demonstrated the importance of TEs in regulating ASE on a genome-wide scale and presents a novel method for rapid identification of ASE genes and their regulatory elements in plants.
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Affiliation(s)
- Yi Tian
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Amali Thrimawithana
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Tiyu Ding
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Jian Guo
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Andrew Gleave
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - David Chagné
- PFRPalmerston North Research CentrePalmerston NorthNew Zealand
| | - Charles Ampomah‐Dwamena
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Hilary S. Ireland
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- School of Biological SciencesAuckland Mail CentreThe University of AucklandAucklandNew Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Meili Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Xiuhong An
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
- Present address:
Hebei Agricultural UniversityBaodingChina
| | - Dajiang Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Yuan Gao
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Kun Wang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Hengtao Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Ruiping Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhe Zhou
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Zhenli Yan
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Liyi Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Caixia Zhang
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Peihua Cong
- Research Institute of PomologyChinese Academy of Agricultural SciencesXinchengChina
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
| | - Jia‐Long Yao
- The New Zealand Institute for Plant and Food Research Limited (PFR)Mount Albert Research CentreAucklandNew Zealand
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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35
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Simoni S, Clemente C, Usai G, Vangelisti A, Natali L, Tavarini S, Angelini LG, Cavallini A, Mascagni F, Giordani T. Characterisation of LTR-Retrotransposons of Stevia rebaudiana and Their Use for the Analysis of Genetic Variability. Int J Mol Sci 2022; 23:ijms23116220. [PMID: 35682899 PMCID: PMC9181549 DOI: 10.3390/ijms23116220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
Stevia rebaudiana is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The Gypsy retrotransposons were twice as abundant as the Copia ones. A disproportionate abundance of elements belonging to the Chromovirus/Tekay lineage was observed among the Gypsy elements. Only the SIRE and Angela lineages represented significant portions of the genome among the Copia elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage Angela was used to analyse the genetic variability in 25 accessions of S. rebaudiana using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding.
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36
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Kwolek K, Kędzierska P, Hankiewicz M, Mirouze M, Panaud O, Grzebelus D, Macko‐Podgórni A. Diverse and mobile: eccDNA-based identification of carrot low-copy-number LTR retrotransposons active in callus cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1811-1828. [PMID: 35426957 PMCID: PMC9324142 DOI: 10.1111/tpj.15773] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR-RTs) are mobilized via an RNA intermediate using a 'copy and paste' mechanism, and account for the majority of repetitive DNA in plant genomes. As a side effect of mobilization, the formation of LTR-RT-derived extrachromosomal circular DNAs (eccDNAs) occurs. Thus, high-throughput sequencing of eccDNA can be used to identify active LTR-RTs in plant genomes. Despite the release of a reference genome assembly, carrot LTR-RTs have not yet been thoroughly characterized. LTR-RTs are abundant and diverse in the carrot genome. We identified 5976 carrot LTR-RTs, 2053 and 1660 of which were attributed to Copia and Gypsy superfamilies, respectively. They were further classified into lineages, families and subfamilies. More diverse LTR-RT lineages, i.e. lineages comprising many low-copy-number subfamilies, were more frequently associated with genic regions. Certain LTR-RT lineages have been recently active in Daucus carota. In particular, low-copy-number LTR-RT subfamilies, e.g. those belonging to the DcAle lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. We utilized eccDNA sequencing to identify and characterize two DcAle subfamilies, Alex1 and Alex3, active in carrot callus. We documented 14 and 32 de novo insertions of Alex1 and Alex3, respectively, which were positioned in non-repetitive regions.
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Affiliation(s)
- Kornelia Kwolek
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Patrycja Kędzierska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Magdalena Hankiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Marie Mirouze
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
- IRD, EMR IRD‐CNRS‐UPVD ‘MANGO’Université de PerpignanPerpignanFrance
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Alicja Macko‐Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
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37
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The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. Int J Mol Sci 2022; 23:ijms23105847. [PMID: 35628657 PMCID: PMC9148063 DOI: 10.3390/ijms23105847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) have been extensively studied for decades. In recent years, the introduction of whole-genome and whole-transcriptome approaches, as well as single-cell resolution techniques, provided a breakthrough that uncovered TE involvement in host gene expression regulation underlying multiple normal and pathological processes. Of particular interest is increased TE activity in neuronal tissue, and specifically in the hippocampus, that was repeatedly demonstrated in multiple experiments. On the other hand, numerous neuropathologies are associated with TE dysregulation. Here, we provide a comprehensive review of literature about the role of TEs in neurons published over the last three decades. The first chapter of the present review describes known mechanisms of TE interaction with host genomes in general, with the focus on mammalian and human TEs; the second chapter provides examples of TE exaptation in normal neuronal tissue, including TE involvement in neuronal differentiation and plasticity; and the last chapter lists TE-related neuropathologies. We sought to provide specific molecular mechanisms of TE involvement in neuron-specific processes whenever possible; however, in many cases, only phenomenological reports were available. This underscores the importance of further studies in this area.
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38
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Lata D, Coates BS, Walden KKO, Robertson HM, Miller NJ. Genome size evolution in the beetle genus Diabrotica. G3 (BETHESDA, MD.) 2022; 12:jkac052. [PMID: 35234880 PMCID: PMC8982398 DOI: 10.1093/g3journal/jkac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/22/2022] [Indexed: 11/20/2022]
Abstract
Diabrocite corn rootworms are one of the most economically significant pests of maize in the United States and Europe and an emerging model for insect-plant interactions. Genome sizes of several species in the genus Diabrotica were estimated using flow cytometry along with that of Acalymma vittatum as an outgroup. Genome sizes ranged between 1.56 and 1.64 gigabase pairs and between 2.26 and 2.59 Gb, respectively, for the Diabrotica subgroups fucata and virgifera; the Acalymma vittatum genome size was around 1.65 Gb. This result indicated that a substantial increase in genome size occurred in the ancestor of the virgifera group. Further analysis of the fucata group and the virgifera group genome sequencing reads indicated that the genome size difference between the Diabrotica subgroups could be attributed to a higher content of transposable elements, mostly miniature inverted-transposable elements and gypsy-like long terminal repeat retroelements.
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Affiliation(s)
- Dimpal Lata
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Nicholas J Miller
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
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39
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Mascagni F, Barghini E, Ceccarelli M, Baldoni L, Trapero C, Díez CM, Natali L, Cavallini A, Giordani T. The Singular Evolution of Olea Genome Structure. FRONTIERS IN PLANT SCIENCE 2022; 13:869048. [PMID: 35432417 PMCID: PMC9009077 DOI: 10.3389/fpls.2022.869048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The current view of plant genome evolution proposes that genome size has mainly been determined by polyploidisation and amplification/loss of transposons, with a minor role played by other repeated sequences, such as tandem repeats. In cultivated olive (Olea europaea subsp. europaea var. europaea), available data suggest a singular model of genome evolution, in which a massive expansion of tandem-repeated sequences accompanied changes in nuclear architecture. This peculiar scenario highlights the importance of focusing on Olea genus evolution, to shed light on mechanisms that led to its present genomic structure. Next-generation sequencing technologies, bioinformatics and in situ hybridisation were applied to study the genomic structure of five related Olea taxa, which originated at different times from their last common ancestor. On average, repetitive DNA in the Olea taxa ranged from ~59% to ~73% of the total genome, showing remarkable differences in terms of composition. Among repeats, we identified 11 major families of tandem repeats, with different abundances in the analysed taxa, five of which were novel discoveries. Interestingly, overall tandem repeat abundance was inversely correlated to that of retrotransposons. This trend might imply a competition in the proliferation of these repeat classes. Indeed, O. paniculata, the species closest to the Olea common ancestor, showed very few tandem-repeated sequences, while it was rich in long terminal repeat retrotransposons, suggesting that the amplification of tandem repeats occurred after its divergence from the Olea ancestor. Furthermore, some tandem repeats were physically localised in closely related O. europaea subspecies (i.e., cultivated olive and O. europaea subsp. cuspidata), which showed a significant difference in tandem repeats abundance. For 4 tandem repeats families, a similar number of hybridisation signals were observed in both subspecies, apparently indicating that, after their dissemination throughout the olive genome, these tandem repeats families differentially amplified maintaining the same positions in each genome. Overall, our research identified the temporal dynamics shaping genome structure during Olea speciation, which represented a singular model of genome evolution in higher plants.
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Affiliation(s)
- Flavia Mascagni
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Elena Barghini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Luciana Baldoni
- CNR, Institute of Biosciences and BioResources, Perugia, Italy
| | - Carlos Trapero
- CSIRO Agriculture & Food, Narrabri, NSW, Australia
- Agronomy Department, University of Cordoba, Cordoba, Spain
| | | | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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40
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Specificities and Dynamics of Transposable Elements in Land Plants. BIOLOGY 2022; 11:biology11040488. [PMID: 35453688 PMCID: PMC9033089 DOI: 10.3390/biology11040488] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Transposable elements are dynamic components of plant genomes, and display a high diversity of lineages and distribution as the result of evolutionary driving forces and overlapping mechanisms of genetic and epigenetic regulation. They are now regarded as main contributors for genome evolution and function, and important regulators of endogenous gene expression. In this review, we survey recent progress and current challenges in the identification and classification of transposon lineages in complex plant genomes, highlighting the molecular specificities that may explain the expansion and diversification of mobile genetic elements in land plants. Abstract Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature.
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Stalder L, Oggenfuss U, Mohd‐Assaad N, Croll D. The population genetics of adaptation through copy‐number variation in a fungal plant pathogen. Mol Ecol 2022; 32:2443-2460. [PMID: 35313056 DOI: 10.1111/mec.16435] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022]
Abstract
Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwide set of populations and identify a total of 7,879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. Although CNVs are generally under negative selection, we find that genes affected by CNVs are enriched in functions related to host exploitation (i.e., effectors and cell-wall-degrading enzymes). We perform genome-wide association studies (GWAS) and identify a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We show that the adaptive CNVs were probably created by recently active transposable element families. Moreover, we find that specific transposable element families are important drivers of recent gene CNV. Finally, we use a genome-wide single nucleotide polymorphism data set to replicate the GWAS and contrast it with the CNV-focused analysis. Together, our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.
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Affiliation(s)
- Luzia Stalder
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| | - Norfarhan Mohd‐Assaad
- Plant Pathology Institute of Integrative Biology ETH, Zurich 8092 Zurich Switzerland
- Department of Applied Physics Faculty of Science and Technology Universiti Kebangsaan Malaysia 43600 Bangi Selangor Malaysia
| | - Daniel Croll
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
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Signor S, Yocum G, Bowsher J. Life stage and the environment as effectors of transposable element activity in two bee species. JOURNAL OF INSECT PHYSIOLOGY 2022; 137:104361. [PMID: 35063439 DOI: 10.1016/j.jinsphys.2022.104361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Diapause is a complex physiological phenomenon that allows insects to weather stressful environmental conditions. The regulation of diapause is accordingly complex, including signaling pathways that involve both small RNA and mRNA and affect the cell cycle, stress resistance, and developmental timing. Transposable elements, mobile genetic elements that replicate within the genome, are also thought to be stress responsive and regulated by the small RNA pathway. Therefore, we asked what the relationship was between environmental stress, diapause status, and transposable element expression in two species of agriculturally important bees, Megachile rotundata and Osmia lignaria. We characterized the TE content of the genomes of both species, then evaluated the expression of TE families during temperature stress, general environmental stress, and diapause stage. We found that the genomic TE content of the two species was very different, and M. rotundata has a larger number of annotated TEs compared to O. lignaria. We also found that both diapause stage and temperature stress had large effects on TE expression. The fold change of TE famlies tended to be larger in those expressed during diapause, however there was only a small majority that were upregulated during diapause. This suggests that stress and diapause do not break down to a simple up-regulation or down-regulation of TEs, but rather that the TE family, the genomic position of its insertions, and the exact heterochromatin formation of the organism at any given environmental state or life stage may affect overall expression of TEs.
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Affiliation(s)
- Sarah Signor
- North Dakota State University, Department of Biological Sciences, United States.
| | - George Yocum
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Service, United States
| | - Julia Bowsher
- North Dakota State University, Department of Biological Sciences, United States
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Fan W, Wang L, Chu J, Li H, Kim EY, Cho J. Tracing Mobile DNAs: From Molecular to Population Scales. FRONTIERS IN PLANT SCIENCE 2022; 13:837378. [PMID: 35178063 PMCID: PMC8843828 DOI: 10.3389/fpls.2022.837378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs, transposons) are mobile DNAs that are prevalent in most eukaryotic genomes. In plants, their mobility has vastly contributed to genetic diversity which is essential for adaptive changes and evolution of a species. Such mobile nature of transposon has been also actively exploited in plant science research by generating genetic mutants in non-model plant systems. On the other hand, transposon mobilization can bring about detrimental effects to host genomes and they are therefore mostly silenced by the epigenetic mechanisms. TEs have been studied as major silencing targets and acted a main feature in the remarkable growth of the plant epigenetics field. Despite the importance of transposon in plant biology and biotechnology, their mobilization and the underlying mechanisms are largely left unanswered. This is mainly because of the sequence repetitiveness of transposons, which makes their detection and analyses difficult and complicated. Recently, some attempts have been made to develop new experimental methods detecting active transposons and their mobilization behavior. These techniques reveal TE mobility in various levels, including the molecular, cellular, organismal and population scales. In this review, we will highlight the novel technical approaches in the study of mobile genetic elements and discuss how these techniques impacted on the advancement of transposon research and broadened our understanding of plant genome plasticity.
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Affiliation(s)
- Wenwen Fan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Chu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai, China
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Pradhan RK, Ramakrishna W. Transposons: Unexpected players in cancer. Gene 2022; 808:145975. [PMID: 34592349 DOI: 10.1016/j.gene.2021.145975] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.
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Deneweth J, Van de Peer Y, Vermeirssen V. Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum. BMC Genomics 2022; 23:18. [PMID: 34983397 PMCID: PMC8725346 DOI: 10.1186/s12864-021-08215-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum. RESULTS We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato. CONCLUSIONS Overall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.
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Affiliation(s)
- Jan Deneweth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Vanessa Vermeirssen
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium. .,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. .,Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. BIOLOGY 2021; 11:biology11010024. [PMID: 35053022 PMCID: PMC8773270 DOI: 10.3390/biology11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)69-7542-1856
| | - Véronique Jamilloux
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Nathalie Choisne
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Gregor Rolshausen
- Senckenberg Center for Wildlife Genetics, Clamecystrasse 12, 63571 Gelnhausen, Germany;
| | - Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany;
| | - Meike Schulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Strasse. 9, 60438 Frankfurt am Main, Germany
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Zenda T, Liu S, Dong A, Li J, Wang Y, Liu X, Wang N, Duan H. Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value. FRONTIERS IN PLANT SCIENCE 2021; 12:774994. [PMID: 34925418 PMCID: PMC8672198 DOI: 10.3389/fpls.2021.774994] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Songtao Liu
- Academy of Agriculture and Forestry Sciences, Hebei North University, Zhangjiakou, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yafei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinyue Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
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Zhang Y, Li Z, Zhang Y, Lin K, Peng Y, Ye L, Zhuang Y, Wang M, Xie Y, Guo J, Teng W, Tong Y, Zhang W, Xue Y, Lang Z, Zhang Y. Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. Genome Res 2021; 31:2276-2289. [PMID: 34503979 PMCID: PMC8647832 DOI: 10.1101/gr.275658.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023]
Abstract
More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.
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Affiliation(s)
- Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu'e Zhang
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Kande Lin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuan Peng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyu Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Henan University, School of Life Science, Kaifeng, Henan 457000, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongbiao Xue
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and National Centre for Bioinformation, Beijing 100101 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhaobo Lang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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Muller H, Loiseau V, Guillier S, Cordaux R, Gilbert C. Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni). Genome Biol Evol 2021; 13:evab231. [PMID: 34613390 PMCID: PMC8634313 DOI: 10.1093/gbe/evab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Most studies of stress-induced transposable element (TE) expression have so far focused on abiotic sources of stress. Here, we analyzed the impact of an infection by the AcMNPV baculovirus on TE expression in a cell line (Tnms42) and midgut tissues of the cabbage looper moth (Trichoplusia ni). We find that a large fraction of TE families (576/636 in Tnms42 cells and 503/612 in midgut) is lowly expressed or not expressed at all [≤ 4 transcripts per million (TPM)] in the uninfected condition (median TPM of 0.37 in Tnms42 and 0.46 in midgut cells). In the infected condition, a total of 62 and 187 TE families were differentially expressed (DE) in midgut and Tnms42 cells, respectively, with more up- (46) than downregulated (16) TE families in the former and as many up- (91) as downregulated (96) TE families in the latter. Expression log2 fold changes of DE TE families varied from -4.95 to 9.11 in Tnms42 cells and from -4.28 to 7.66 in midgut. Large variations in expression profiles of DE TEs were observed depending on the type of cells and on time after infection. Overall, the impact of AcMNPV on TE expression in T. ni is moderate but potentially sufficient to affect TE activity and genome architecture. Interestingly, one host-derived TE integrated into AcMNPV genomes is highly expressed in infected Tnms42 cells. This result shows that virus-borne TEs can be expressed, further suggesting that they may be able to transpose and that viruses may act as vectors of horizontal transfer of TEs in insects.
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Affiliation(s)
- Héloïse Muller
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Vincent Loiseau
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Sandra Guillier
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Universite de Poitiers, CNRS, France
| | - Clément Gilbert
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
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Viviani A, Ventimiglia M, Fambrini M, Vangelisti A, Mascagni F, Pugliesi C, Usai G. Impact of transposable elements on the evolution of complex living systems and their epigenetic control. Biosystems 2021; 210:104566. [PMID: 34718084 DOI: 10.1016/j.biosystems.2021.104566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy.
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
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