Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome

Wollrab C, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T (2012)
The Plant Journal 72(4): 636-651.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Wollrab, Cora; Heitkam, Tony; Holtgräwe, DanielaUniBi ; Weisshaar, BerndUniBi ; Minoche, André E; Dohm, Juliane C; Himmelbauer, Heinz; Schmidt, Thomas
Abstract / Bemerkung
LTR retrotransposons and retroviruses are closely related. Although a viral envelope gene is found in some LTR retrotransposons and all retroviruses, only the latter show infectivity. The identification of Ty3-gypsy-like retrotransposons possessing putative envelope-like open reading frames blurred the taxonomical borders and led to the establishment of the Errantivirus, Metavirus and Chromovirus genera within the Metaviridae. Only a few plant Errantiviruses have been described, and their evolutionary history is not well understood. In this study, we investigated 27 retroelements of four abundant Elbe retrotransposon families belonging to the Errantiviruses in Beta vulgaris (sugar beet). Retroelements of the Elbe lineage integrated between 0.02 and 5.59 million years ago, and show family-specific variations in autonomy and degree of rearrangements: while Elbe3 members are highly fragmented, often truncated and present in a high number of solo LTRs, Elbe2 members are mainly autonomous. We observed extensive reshuffling of structural motifs across families, leading to the formation of new retrotransposon families. Elbe retrotransposons harbor a typical envelope-like gene, often encoding transmembrane domains. During the course of Elbe evolution, the additional open reading frames have been strongly modified or independently acquired. Taken together, the Elbe lineage serves as retrotransposon model reflecting the various stages in Errantivirus evolution, and allows a detailed analysis of retrotransposon family formation.
Erscheinungsjahr
2012
Zeitschriftentitel
The Plant Journal
Band
72
Ausgabe
4
Seite(n)
636-651
ISSN
0960-7412
Page URI
https://pub.uni-bielefeld.de/record/2532965

Zitieren

Wollrab C, Heitkam T, Holtgräwe D, et al. Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. The Plant Journal. 2012;72(4):636-651.
Wollrab, C., Heitkam, T., Holtgräwe, D., Weisshaar, B., Minoche, A. E., Dohm, J. C., Himmelbauer, H., et al. (2012). Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. The Plant Journal, 72(4), 636-651. doi:10.1111/j.1365-313X.2012.05107.x
Wollrab, C., Heitkam, T., Holtgräwe, D., Weisshaar, B., Minoche, A. E., Dohm, J. C., Himmelbauer, H., and Schmidt, T. (2012). Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. The Plant Journal 72, 636-651.
Wollrab, C., et al., 2012. Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. The Plant Journal, 72(4), p 636-651.
C. Wollrab, et al., “Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome”, The Plant Journal, vol. 72, 2012, pp. 636-651.
Wollrab, C., Heitkam, T., Holtgräwe, D., Weisshaar, B., Minoche, A.E., Dohm, J.C., Himmelbauer, H., Schmidt, T.: Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. The Plant Journal. 72, 636-651 (2012).
Wollrab, Cora, Heitkam, Tony, Holtgräwe, Daniela, Weisshaar, Bernd, Minoche, André E, Dohm, Juliane C, Himmelbauer, Heinz, and Schmidt, Thomas. “Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome”. The Plant Journal 72.4 (2012): 636-651.

9 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.).
Zakrzewski F, Schmidt M, Van Lijsebettens M, Schmidt T., Plant J 90(6), 2017
PMID: 28257158
Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.
Paz RC, Kozaczek ME, Rosli HG, Andino NP, Sanchez-Puerta MV., Genetica 145(4-5), 2017
PMID: 28776161
Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris).
Kowar T, Zakrzewski F, Macas J, Kobližková A, Viehoever P, Weisshaar B, Schmidt T., BMC Plant Biol 16(1), 2016
PMID: 27230558
Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe's oldest Camellia japonica.
Heitkam T, Petrasch S, Zakrzewski F, Kögler A, Wenke T, Wanke S, Schmidt T., Chromosome Res 23(4), 2015
PMID: 26582634
The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation.
Zakrzewski F, Schubert V, Viehoever P, Minoche AE, Dohm JC, Himmelbauer H, Weisshaar B, Schmidt T., Plant J 78(6), 2014
PMID: 24661787
Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades.
Heitkam T, Holtgräwe D, Dohm JC, Minoche AE, Himmelbauer H, Weisshaar B, Schmidt T., Plant J 79(3), 2014
PMID: 24862340
Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration.
Weber B, Heitkam T, Holtgräwe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T., Mob DNA 4(1), 2013
PMID: 23448600

80 References

Daten bereitgestellt von Europe PubMed Central.

Limitations of next-generation genome sequence assembly.
Alkan C, Sajjadian S, Eichler EE., Nat. Methods 8(1), 2010
PMID: 21102452
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Nuclear DNA content of some important plant species
Arumuganathan, Plant Mol. Biol. Rep. 9(), 1991
Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.
Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, Sanmiguel PJ, Bennetzen JL., PLoS Genet. 5(11), 2009
PMID: 19936065
Nuclear DNA amounts in angiosperms
Bennett, Ann. Bot. 76(), 1995
Transposable element contributions to plant gene and genome evolution.
Bennetzen JL., Plant Mol. Biol. 42(1), 2000
PMID: 10688140
Mechanisms of recent genome size variation in flowering plants.
Bennetzen JL, Ma J, Devos KM., Ann. Bot. 95(1), 2005
PMID: 15596462
GeneWise and Genomewise.
Birney E, Clamp M, Durbin R., Genome Res. 14(5), 2004
PMID: 15123596
Transcription and reverse transcription of retrotransposons.
Boeke JD, Corces VG., Annu. Rev. Microbiol. 43(), 1989
PMID: 2552899

Coffin, 1990
Molecular organization of terminal repetitive DNA in Beta species.
Dechyeva D, Schmidt T., Chromosome Res. 14(8), 2006
PMID: 17195925
Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).
Dohm JC, Lange C, Holtgrawe D, Sorensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H., Plant J. 70(3), 2012
PMID: 22211633
Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean
Du, Plant Cell 21(), 2009
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, BMC Bioinformatics 19(), 2004

Eickbush, 1994

Eickbush, 2002

Fauquet, 2005
The 7th ICTV Report
Fauquet, Virol. Div. News 146(), 2001
Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences?
Fayet O, Ramond P, Polard P, Prere MF, Chandler M., Mol. Microbiol. 4(10), 1990
PMID: 1963920
The genomic RNA in Ty1 virus-like particles is dimeric.
Feng YX, Moore SP, Garfinkel DJ, Rein A., J. Virol. 74(22), 2000
PMID: 11044130
Origin of the ‘Weisse Schlesische Ruebe’ (white beet) resynthesis of sugar beet
Fischer, Euphytica 41(), 1989
Genome size and the proportion of repeated nucleotide sequence DNA in plants.
Flavell RB, Bennett MD, Smith JB, Smith DB., Biochem. Genet. 12(4), 1974
PMID: 4441361
The HIV Env-mediated fusion reaction.
Gallo SA, Finnegan CM, Viard M, Raviv Y, Dimitrov A, Rawat SS, Puri A, Durell S, Blumenthal R., Biochim. Biophys. Acta 1614(1), 2003
PMID: 12873764
Natural variation within the genus Beta and its possible use for breeding sugar beet: a review
Geyt, Euphytica 49(), 1990
In situ hybridization with automated chromosome denaturation
Heslop-Harrison, Technique 3(), 1991
TMbase - a database of membrane spanning proteins segments
Hofmann, Biol. Chem. Hoppe Seyler 347(), 1993
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
Krogh A, Larsson B, von Heijne G, Sonnhammer EL., J. Mol. Biol. 305(3), 2001
PMID: 11152613
The evolution of plant retroviruses: moving to green pastures
Kumar, Trends Plant Sci. 3(), 1998
Plant retrotransposons.
Kumar A, Bennetzen JL., Annu. Rev. Genet. 33(), 1999
PMID: 10690416
The size and sequence organization of the centromeric region of arabidopsis thaliana chromosome 5.
Kumekawa N, Hosouchi T, Tsuruoka H, Kotani H., DNA Res. 7(6), 2000
PMID: 11214966
High-throughput identification of genetic markers using representational oligonucleotide microarray analysis.
Lange C, Mittermayr L, Dohm JC, Holtgrawe D, Weisshaar B, Himmelbauer H., Theor. Appl. Genet. 121(3), 2010
PMID: 20379697
SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein.
Laten HM, Majumdar A, Gaucher EA., Proc. Natl. Acad. Sci. U.S.A. 95(12), 1998
PMID: 9618510
Retrotransposons and retroviruses: analysis of the envelope gene.
Lerat E, Capy P., Mol. Biol. Evol. 16(9), 1999
PMID: 10486975
Rapid recent growth and divergence of rice nuclear genomes.
Ma J, Bennetzen JL., Proc. Natl. Acad. Sci. U.S.A. 101(34), 2004
PMID: 15240870
Retrovirus-like elements in plants
Marco, Recent Res. Dev. Plant Sci. 3(), 2005
How Athila retrotransposons survive in the Arabidopsis genome
Marco, BMC Genomics 14(), 2008
Construction of a sugar beet BAC library from a hybrid with diverse traits
McGrath, Plant Mol. Biol. Rep. 22(), 2004
Mobilization and evolutionary history of miniature inverted-repeat transposable elements (MITEs) in Beta vulgaris L.
Menzel G, Dechyeva D, Keller H, Lange C, Himmelbauer H, Schmidt T., Chromosome Res. 14(8), 2006
PMID: 17171577
Diversity of a complex centromeric satellite and molecular characterization of dispersed sequence families in sugar beet (Beta vulgaris).
Menzel G, Dechyeva D, Wenke T, Holtgrawe D, Weisshaar B, Schmidt T., Ann. Bot. 102(4), 2008
PMID: 18682437
Envelope-like retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster).
Miguel C, Simoes M, Oliveira MM, Rocheta M., J. Mol. Evol. 67(5), 2008
PMID: 18925379
Athila, a new retroelement from Arabidopsis thaliana.
Pelissier T, Tutois S, Deragon JM, Tourmente S, Genestier S, Picard G., Plant Mol. Biol. 29(3), 1995
PMID: 8534844
Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW., Proc. Natl. Acad. Sci. U.S.A. 81(24), 1984
PMID: 6096873

Sambrook, 1989
Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons
SanMiguel, Ann. Bot. 82(), 1998
Nested retrotransposons in the intergenic regions of the maize genome.
SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL., Science 274(5288), 1996
PMID: 8864112
Cloning and characterization of a Beta vulgaris satellite DNA family.
Schmidt T, Metzlaff M., Gene 101(2), 1991
PMID: 2055488
Distribution and evolution of two satellite DNAs in the genus Beta.
Schmidt T, Jung C, Metzlaff M., Theor. Appl. Genet. 82(6), 1991
PMID: IND92005175
A complete physical map of a wild beet (Beta procumbens) translocation in sugar beet
Schulte, Mol. Gen. Genomics 275(), 2006
A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion.
Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P., Genome Res. 10(7), 2000
PMID: 10899140
Transposable elements and the epigenetic regulation of the genome.
Slotkin RK, Martienssen R., Nat. Rev. Genet. 8(4), 2007
PMID: 17363976
An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus.
Song SU, Gerasimova T, Kurkulos M, Boeke JD, Corces VG., Genes Dev. 8(17), 1994
PMID: 7958877
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M, Kumar S., Mol. Biol. Evol. 24(8), 2007
PMID: 17488738
An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris.
Wenke T, Holtgrawe D, Horn AV, Weisshaar B, Schmidt T., Plant Mol. Biol. 71(6), 2009
PMID: 19697140
Guidelines: a unified classification system for eukaryotic transposable elements
Wicker, Nature Rev. Genet. 8(), 2007
Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris.
Zakrzewski F, Wenke T, Holtgrawe D, Weisshaar B, Schmidt T., BMC Plant Biol. 10(), 2010
PMID: 20064260
Material in PUB:
Teil dieser Dissertation

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 22804913
PubMed | Europe PMC

Suchen in

Google Scholar