1
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Choudhury RR, Neuhaus JM, Parisod C. Resolving fine-grained dynamics of retrotransposons: comparative analysis of inferential methods and genomic resources. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:979-993. [PMID: 28244250 DOI: 10.1111/tpj.13524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 02/15/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
Transposable elements support genome diversification, but comparison of their proliferation and genomic distribution within and among species is necessary to characterize their role in evolution. Such inferences are challenging because of potential bias with incomplete sampling of repetitive genome regions. Here, using the assembled genome as well as genome skimming datasets in Arabis alpina, we assessed the limits of current approaches inferring the biology of transposable elements. Long terminal repeat retrotransposons (LTR-RTs) identified in the assembled genome were classified into monophyletic lineages (here called tribes), including families of similar copies in Arabis along with elements from related Brassicaceae. Inference of their dynamics using divergence of LTRs in full-length copies and mismatch distribution of genetic variation among all copies congruently highlighted recent transposition bursts, although ancient proliferation events were apparent only with mismatch distribution. Similar inferences of LTR-RT dynamics based on random sequences from genome skimming were highly correlated with assembly-based estimates, supporting accurate analyses from shallow sequencing. Proportions of LTR-RT copies next to genes from both assembled genomes and genome skimming were congruent, pointing to tribes being over- or under-represented in the vicinity of genes. Finally, genome skimming at low coverage revealed accurate inferences of LTR-RT dynamics and distribution, although only the most abundant families appeared robustly analysed at 0.1X. Examining the pitfalls and benefits of approaches relying on different genomic resources, we highlight that random sequencing reads represent adequate data suitably complementing biased samples of LTR-RT copies retrieved from assembled genomes towards comprehensive surveys of the biology of transposable elements.
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Affiliation(s)
| | - Jean-Marc Neuhaus
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Christian Parisod
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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2
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Rocha DM, Marques A, Andrade CGTJ, Guyot R, Chaluvadi SR, Pedrosa-Harand A, Houben A, Bennetzen JL, Vanzela ALL. Developmental programmed cell death during asymmetric microsporogenesis in holocentric species of Rhynchospora (Cyperaceae). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5391-5401. [PMID: 27492982 PMCID: PMC5049389 DOI: 10.1093/jxb/erw300] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Members of the Cyperaceae family exhibit an asymmetric microsporogenesis that results in the degeneration of three out of four meiotic products. Efforts have been made previously to describe the resulting structure, named the pseudomonad, but mechanisms concerning the establishment of cell domains, nuclear development, and programmed cell death are largely unknown. Using the Rhynchospora genus as a model, evidence for cell asymmetry, cytoplasmic isolation, and programmed cell death was obtained by a combination of electron microscopic, cytochemical, immunocytochemical, in situ hybridization, and flow cytometric methods. Degenerative cells were identified at the abaxial region, with the cytoskeleton marking their delimitation from the functional domain after meiosis. After attempting to initiate cell division with an unreplicated genome and abnormal spindle assembly, these cells exhibited a gradual process of cytoplasmic contraction associated with hypermethylation of cytosines and differential loss of DNA. These results indicate that the asymmetric tetrad establishes a functional cell, where one nucleus is preferentially selected to survive. Degenerative haploid cells are then eliminated in a multistep process associated with mitotic disorder, non-random elimination of repetitive DNA, vacuolar cell death, and DNA fragmentation.
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Affiliation(s)
- Danilo M Rocha
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center of Biological Sciences, State University of Londrina, Londrina 86057-970, Paraná, Brazil
| | - André Marques
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Celia G T J Andrade
- Laboratory of Electron Microscopy and Microanalysis, Pro-PPG, State University of Londrina, 86051990, Londrina, Brazil
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394, Montpellier Cedex, France
| | | | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt Seeland, Germany
| | | | - André L L Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center of Biological Sciences, State University of Londrina, Londrina 86057-970, Paraná, Brazil
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3
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Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification. Genetica 2016; 144:577-589. [PMID: 27671023 DOI: 10.1007/s10709-016-9926-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/17/2016] [Indexed: 12/15/2022]
Abstract
Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.
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Abstract
Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of available software that can help biologists to look for these repeats and check some hypothetical models intended to characterize their structures. Since transposable elements are a major source of repeats in plants, many methods have been used or developed for this large class of sequences. They are representative of the range of tools available for other classes of repeats and we have provided a whole section on this topic as well as a selection of the main existing software. In order to better understand how they work and how repeats may be efficiently found in genomes, it is necessary to look at the technical issues involved in the large-scale search of these structures. Indeed, it may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of the search for repeats and more complex patterns. The second section introduces the key concepts that are useful for understanding the current state of the art in playing with words, applied to genomic sequences. This can be seen as the first stage of a very general approach called linguistic analysis that is interested in the analysis of natural or artificial texts. Words, the lexical level, correspond to simple repeated entities in texts or strings. In fact, biologists need to represent more complex entities where a repeat family is built on more abstract structures, including direct or inverted small repeats, motifs, composition constraints as well as ordering and distance constraints between these elementary blocks. In terms of linguistics, this corresponds to the syntactic level of a language. The last section introduces concepts and practical tools that can be used to reach this syntactic level in biological sequence analysis.
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Affiliation(s)
- Jacques Nicolas
- Dyliss Team, Irisa/Inria Centre de Rennes Bretagne Atlantique, Campus de Beaulieu, 35510, Rennes cedex, France.
| | - Pierre Peterlongo
- Irisa/Inria Centre de Rennes Bretagne Atlantique, Campus de Beaulieu, 35510, Rennes cedex, France
| | - Sébastien Tempel
- LCB, CNRS UMR 7283, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France
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5
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Dias ES, Hatt C, Hamon S, Hamon P, Rigoreau M, Crouzillat D, Carareto CMA, de Kochko A, Guyot R. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families. PLANT MOLECULAR BIOLOGY 2015; 89:83-97. [PMID: 26245353 DOI: 10.1007/s11103-015-0352-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 07/28/2015] [Indexed: 06/04/2023]
Abstract
Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer.
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Affiliation(s)
- Elaine Silva Dias
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
- Department of Biology, UNESP-Univ. Estadual Paulista, São José do Rio Preto, Araraquara, SP, Brazil.
| | - Clémence Hatt
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Serge Hamon
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Perla Hamon
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Michel Rigoreau
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France.
| | - Dominique Crouzillat
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France.
| | | | | | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394, Montpellier Cedex 5, France.
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Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E, Maumus F, Pollock DD, Quesneville H, Smit A, Wheeler TJ, Bureau TE, Blanchette M. A call for benchmarking transposable element annotation methods. Mob DNA 2015; 6:13. [PMID: 26244060 PMCID: PMC4524446 DOI: 10.1186/s13100-015-0044-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/22/2015] [Indexed: 12/31/2022] Open
Abstract
DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.
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Affiliation(s)
- Douglas R Hoen
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada
| | - Glenn Hickey
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec Canada ; McGill University and Génome Québec Innovation Center, Montréal, Québec Canada
| | - Josep Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), Equipe Evolution, Vecteurs, Adaptation et Symbiose, UMR5554 CNRS-Université Montpellier, Montpellier, 34090 cedex 05 France
| | - Aurélie Hua-Van
- Laboratoire Evolution, Génomes, Comportement Ecologie, CNRS-Université Paris-Sud (UMR 9191)-IRD (UMR 247)-Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Robert Hubley
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA 98109 USA
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Emmanuelle Lerat
- Laboratoire Biometrie et Biologie Evolutive, Universite Claude Bernard-Lyon 1, UMR-CNRS 5558-Bat. Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne cedex, France
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France
| | - David D Pollock
- University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Hadi Quesneville
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France
| | - Arian Smit
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA 98109 USA
| | - Travis J Wheeler
- Department of Computer Science, University of Montana, Missoula, MT 59812 USA
| | - Thomas E Bureau
- Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada
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7
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Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ON, Rakotomalala JJ, Nowak MD, Davis AP, de Kochko A. Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species. Mol Genet Genomics 2015; 291:155-68. [PMID: 26231981 DOI: 10.1007/s00438-015-1098-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/21/2015] [Indexed: 01/10/2023]
Abstract
The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.
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Affiliation(s)
- Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, A1B 3X9, Canada. .,UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France.
| | - Romain Guyot
- UMR IPME, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France
| | - Perla Hamon
- UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France
| | - Dominique Crouzillat
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France
| | - Michel Rigoreau
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France
| | | | | | - Michael D Nowak
- Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 17165, Solna, Sweden
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
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8
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Bardil A, Tayalé A, Parisod C. Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:621-31. [PMID: 25823965 DOI: 10.1111/tpj.12837] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 05/21/2023]
Abstract
Long terminal repeat retrotransposons (LTR-RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR-RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR-RTs and/or genetic redundancy supports the accumulation of active LTR-RTs through relaxation of selective constraints. Available evidence supports interspecific hybridization as the main trigger of genome dynamics, but few studies have addressed the consequences of intraspecific polyploidy (i.e. autopolyploidy), where the genome shock is expectedly minimized. The dynamics of LTR-RTs was thus here evaluated through low coverage 454 sequencing of three closely related diploid progenitors and three independent autotetraploids from the young Biscutella laevigata species complex. Genomes from this early diverging Brassicaceae lineage presented a minimum of 40% repeats and a large diversity of transposable elements. Differential abundances and patterns of sequence divergence among genomes for 37 LTR-RT families revealed contrasted dynamics during species diversification. Quiescent LTR-RT families with limited genetic variation among genomes were distinguished from active families (37.8%) having proliferated in specific taxa. Specific families proliferated in autopolyploids only, but most transpositionally active families in polyploids were also differentiated among diploids. Low expression levels of transpositionally active LTR-RT families in autopolyploids further supported that genome shock and redundancy are non-mutually exclusive triggers of LTR-RT proliferation. Although reputed stable, autopolyploid genomes show LTR-RT fractions presenting analogies with polyploids between widely divergent genomes.
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Affiliation(s)
- Amélie Bardil
- Laboratory of Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Alexandre Tayalé
- Laboratory of Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
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9
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Leslie T, Baucom RS. De novo assembly and annotation of the transcriptome of the agricultural weed Ipomoea purpurea uncovers gene expression changes associated with herbicide resistance. G3 (BETHESDA, MD.) 2014; 4:2035-47. [PMID: 25155274 PMCID: PMC4199709 DOI: 10.1534/g3.114.013508] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 08/21/2014] [Indexed: 12/22/2022]
Abstract
Human-mediated selection can lead to rapid evolution in very short time scales, and the evolution of herbicide resistance in agricultural weeds is an excellent example of this phenomenon. The common morning glory, Ipomoea purpurea, is resistant to the herbicide glyphosate, but genetic investigations of this trait have been hampered by the lack of genomic resources for this species. Here, we present the annotated transcriptome of the common morning glory, Ipomoea purpurea, along with an examination of whole genome expression profiling to assess potential gene expression differences between three artificially selected herbicide resistant lines and three susceptible lines. The assembled Ipomoea transcriptome reported in this work contains 65,459 assembled transcripts, ~28,000 of which were functionally annotated by assignment to Gene Ontology categories. Our RNA-seq survey using this reference transcriptome identified 19 differentially expressed genes associated with resistance-one of which, a cytochrome P450, belongs to a large plant family of genes involved in xenobiotic detoxification. The differentially expressed genes also broadly implicated receptor-like kinases, which were down-regulated in the resistant lines, and other growth and defense genes, which were up-regulated in resistant lines. Interestingly, the target of glyphosate-EPSP synthase-was not overexpressed in the resistant Ipomoea lines as in other glyphosate resistant weeds. Overall, this work identifies potential candidate resistance loci for future investigations and dramatically increases genomic resources for this species. The assembled transcriptome presented herein will also provide a valuable resource to the Ipomoea community, as well as to those interested in utilizing the close relationship between the Convolvulaceae and the Solanaceae for phylogenetic and comparative genomics examinations.
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Affiliation(s)
- Trent Leslie
- Department of Biological Sciences. University of Cincinnati, Cincinnati, Ohio 45221
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48103
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10
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Bonchev G, Parisod C. Transposable elements and microevolutionary changes in natural populations. Mol Ecol Resour 2013; 13:765-75. [DOI: 10.1111/1755-0998.12133] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Georgi Bonchev
- Laboratory of evolutionary botany Institute of biology University of Neuchâtel Rue Emile‐Argand 11 CH‐2000 Neuchâtel Switzerland
- Institute of plant physiology and genetics Bulgarian academy of sciences G. Bonchev Street, Bldg 24 Sofia 1113 Bulgaria
| | - Christian Parisod
- Laboratory of evolutionary botany Institute of biology University of Neuchâtel Rue Emile‐Argand 11 CH‐2000 Neuchâtel Switzerland
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11
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Hertweck KL. Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Genome 2013; 56:487-94. [PMID: 24168669 DOI: 10.1139/gen-2013-0042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a nonmodel system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from 11 exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that although some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.
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Affiliation(s)
- Kate L Hertweck
- National Evolutionary Synthesis Center, 2024 West Main Street, Suite A200, Durham, NC 27705, USA
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12
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Estep MC, DeBarry JD, Bennetzen JL. The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution. Heredity (Edinb) 2013; 110:194-204. [PMID: 23321774 PMCID: PMC3554455 DOI: 10.1038/hdy.2012.99] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 10/22/2012] [Accepted: 10/23/2012] [Indexed: 11/09/2022] Open
Abstract
Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with >5-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.
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Affiliation(s)
- M C Estep
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - J D DeBarry
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - J L Bennetzen
- Department of Genetics, University of Georgia, Athens, GA, USA
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13
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Senerchia N, Wicker T, Felber F, Parisod C. Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat. Genome Biol Evol 2013; 5:1010-20. [PMID: 23595021 PMCID: PMC4104650 DOI: 10.1093/gbe/evt064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2013] [Indexed: 12/23/2022] Open
Abstract
Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindrica and Ae. geniculata using 454 identified more than 70% of the sequences as known TEs, mainly long terminal repeat (LTR) retrotransposons. Comparing the abundance of reads as well as patterns of sequence diversity and divergence within and among genomes assessed the dynamics of 44 major LTR retrotransposon families of the 165 identified. In particular, molecular population genetics on individual TE copies distinguished recently active from quiescent families and highlighted different evolutionary trajectories of retrotransposons among related species. This work presents a suite of tools suitable for current sequencing data, allowing to address the genome-wide evolutionary dynamics of TEs at the family level and advancing our understanding of the evolution of nonmodel genomes.
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Affiliation(s)
- Natacha Senerchia
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Switzerland
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Switzerland
| | - François Felber
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Switzerland
- Musée et Jardins botaniques cantonaux, Lausanne, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Switzerland
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Xu HE, Zhang HH, Han MJ, Shen YH, Huang XZ, Xiang ZH, Zhang Z. [Computational approaches for identification and classification of transposable elements in eukaryotic genomes]. YI CHUAN = HEREDITAS 2012; 34:1009-1019. [PMID: 22917906 DOI: 10.3724/sp.j.1005.2012.01009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Repetitive sequences (repeats) represent a significant fraction of the eukaryotic genomes and can be divided into tandem repeats, segmental duplications, and interspersed repeats on the basis of their sequence characteristics and how they are formed. Most interspersed repeats are derived from transposable elements (TEs). Eukaryotic TEs have been subdivided into two major classes according to the intermediate they use to move. The transposition and amplification of TEs have a great impact on the evolution of genes and the stability of genomes. However, identification and classification of TEs are complex and difficult due to the fact that their structure and classification are complex and diverse compared with those of other types of repeats. Here, we briefly introduced the function and classification of TEs, and summarized three different steps for identification, classification and annotation of TEs in eukaryotic genomes: (1) assembly of a repeat library, (2) repeat correction and classification, and (3) genome annotation. The existing computational approaches for each step were summarized and the advantages and disadvantages of the approaches were also highlighted in this review. To accurately identify, classify, and annotate the TEs in eukaryotic genomes requires combined methods. This review provides useful information for biologists who are not familiar with these approaches to find their way through the forest of programs.
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Affiliation(s)
- Hong-En Xu
- The Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.
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Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS One 2012; 7:e32973. [PMID: 22427919 PMCID: PMC3299709 DOI: 10.1371/journal.pone.0032973] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 02/06/2012] [Indexed: 12/22/2022] Open
Abstract
Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.
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Affiliation(s)
- Grégory Carrier
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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Muñoz-Diez C, Vitte C, Ross-Ibarra J, Gaut BS, Tenaillon MI. Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content. PLANT TRANSPOSABLE ELEMENTS 2012. [DOI: 10.1007/978-3-642-31842-9_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Abstract
The recent development of next-generation sequencing (NGS) technologies allowed various authors to imagine, test, and validate new approaches for TE analysis, in their nature, type, activity, or quantity. In this chapter, we describe briefly the technologies used, then the various approaches and methods used already, and finally some potential new methods. In contrast to the more molecular chapters of the book, the approaches described here are purely bioinformatics, and have a set of NGS data as a starting point. Moreover, as these analyses are quite recent in the field, most of them were only performed once, and we cannot be sure that they could be reused in other species or context than the original one. However, there are a lot of interesting approaches and results that NGS can provide in the TE field.
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Affiliation(s)
- Cristian Chaparro
- UMR LGDP, CNRS/UPVD, Université de Perpignan Via Domitia, Perpignan Cedex, France
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Abstract
Recent advances in biological instrumentation and associated experimental technologies now permit an unprecedented efficiency and scale for the acquisition of genomic data, at ever-decreasing costs. Further advances, with accompanying decreases in cost, are expected in the very near term. It now becomes appropriate to discuss the best uses of these technologies in the context of the angiosperms. This white paper proposes a complete genomic census of the approximately 500,000 species of flowering plants, outlines the goals of this census and their value, and provides a road map towards achieving these goals in a timely manner.
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Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LGG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga SI, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WWGT, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 2011; 332:960-3. [PMID: 21551031 PMCID: PMC3166216 DOI: 10.1126/science.1203810] [Citation(s) in RCA: 582] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
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Affiliation(s)
- Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
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Novák P, Neumann P, Macas J. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 2010; 11:378. [PMID: 20633259 PMCID: PMC2912890 DOI: 10.1186/1471-2105-11-378] [Citation(s) in RCA: 287] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 07/15/2010] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization. RESULTS We adapted a graph-based approach for similarity-based partitioning of whole genome 454 sequence reads in order to build clusters made of the reads derived from individual repeat families. The information about cluster sizes was utilized for assessing the proportion and composition of repeats in the genomes of two model species, Pisum sativum and Glycine max, differing in genome size and 454 sequencing coverage. Moreover, statistical analysis and visual inspection of the topology of the cluster graphs using a newly developed program tool, SeqGrapheR, were shown to be helpful in distinguishing basic types of repeats and investigating sequence variability within repeat families. CONCLUSIONS Repetitive regions of plant genomes can be efficiently characterized by the presented graph-based analysis and the graph representation of repeats can be further used to assess the variability and evolutionary divergence of repeat families, discover and characterize novel elements, and aid in subsequent assembly of their consensus sequences.
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Affiliation(s)
- Petr Novák
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Pavel Neumann
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Jiří Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
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Estill JC, Bennetzen JL. The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes. PLANT METHODS 2009; 5:8. [PMID: 19545381 PMCID: PMC2705364 DOI: 10.1186/1746-4811-5-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 06/19/2009] [Indexed: 05/09/2023]
Abstract
BACKGROUND High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of ab initio prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation. RESULTS We have designed, implemented, and assessed a Perl-based workflow named DAWGPAWS for the generation of computational results for human curation of the genes and transposable elements in plant genomes. The use of DAWGPAWS was found to accelerate annotation of 80-200 kb wheat DNA inserts in bacterial artificial chromosome (BAC) vectors by approximately twenty-fold and to also significantly improve the quality of the annotation in terms of completeness and accuracy. CONCLUSION The DAWGPAWS genome annotation pipeline fills an important need in the annotation of plant genomes by generating computational evidences in a high throughput manner, translating these results to a common file format, and facilitating the human curation of these computational results. We have verified the value of DAWGPAWS by using this pipeline to annotate the genes and transposable elements in 220 BAC insertions from the hexaploid wheat genome (Triticum aestivum L.). DAWGPAWS can be applied to annotation efforts in other plant genomes with minor modifications of program-specific configuration files, and the modular design of the workflow facilitates integration into existing pipelines.
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Affiliation(s)
- James C Estill
- Department of Plant Biology, The University of Georgia, Athens, Georgia 30602-7271, USA
| | - Jeffrey L Bennetzen
- Department of Genetics, The University of Georgia, Athens, Georgia 30602-7223, USA
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