Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris

Zakrzewski F, Wenke T, Holtgräwe D, Weisshaar B, Schmidt T (2010)
BMC Plant Biology 10(1): 8.

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BACKGROUND: Repetitive DNA is a major fraction of eukaryotic genomes and occurs particularly often in plants. Currently, the sequencing of the sugar beet (Beta vulgaris) genome is under way and knowledge of repetitive DNA sequences is critical for the genome annotation. We generated a c0t-1 library, representing highly to moderately repetitive sequences, for the characterization of the major B. vulgaris repeat families. While highly abundant satellites are well-described, minisatellites are only poorly investigated in plants. Therefore, we focused on the identification and characterization of these tandemly repeated sequences. RESULTS: Analysis of 1763 c0t-1 DNA fragments, providing 442 kb sequence data, shows that the satellites pBV and pEV are the most abundant repeat families in the B. vulgaris genome while other previously described repeats show lower copy numbers. We isolated 517 novel repetitive sequences and used this fraction for the identification of minisatellite and novel satellite families. Bioinformatic analysis and Southern hybridization revealed that minisatellites are moderately to highly amplified in B. vulgaris. FISH showed a dispersed localization along most chromosomes clustering in arrays of variable size and number with exclusion and depletion in distinct regions. CONCLUSION: The c0t-1 library represents major repeat families of the B. vulgaris genome, and analysis of the c0t-1 DNA was proven to be an efficient method for identification of minisatellites. We established, so far, the broadest analysis of minisatellites in plants and observed their chromosomal localization providing a background for the annotation of the sugar beet genome and for the understanding of the evolution of minisatellites in plant genomes.
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BMC Plant Biology
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10
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1
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8
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Zakrzewski F, Wenke T, Holtgräwe D, Weisshaar B, Schmidt T. Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biology. 2010;10(1): 8.
Zakrzewski, F., Wenke, T., Holtgräwe, D., Weisshaar, B., & Schmidt, T. (2010). Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biology, 10(1), 8. doi:10.1186/1471-2229-10-8
Zakrzewski, F., Wenke, T., Holtgräwe, D., Weisshaar, B., and Schmidt, T. (2010). Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biology 10:8.
Zakrzewski, F., et al., 2010. Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biology, 10(1): 8.
F. Zakrzewski, et al., “Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris”, BMC Plant Biology, vol. 10, 2010, : 8.
Zakrzewski, F., Wenke, T., Holtgräwe, D., Weisshaar, B., Schmidt, T.: Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biology. 10, : 8 (2010).
Zakrzewski, Falk, Wenke, Torsten, Holtgräwe, Daniela, Weisshaar, Bernd, and Schmidt, Thomas. “Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris”. BMC Plant Biology 10.1 (2010): 8.
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12 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
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
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
Cloning and characterization of chromosomal markers in alfalfa (Medicago sativa L.).
Yu F, Lei Y, Li Y, Dou Q, Wang H, Chen Z., Theor Appl Genet 126(7), 2013
PMID: 23636612
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., Plant J 72(4), 2012
PMID: 22804913
Epigenetic profiling of heterochromatic satellite DNA.
Zakrzewski F, Weisshaar B, Fuchs J, Bannack E, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T., Chromosoma 120(4), 2011
PMID: 21594600

73 References

Daten bereitgestellt von Europe PubMed Central.

Functional elements residing within satellite DNAs.
Ugarkovic D., EMBO Rep. 6(11), 2005
PMID: 16264428
Epigenetic regulation of transposable elements in plants.
Lisch D., Annu Rev Plant Biol 60(), 2009
PMID: 19007329
Transposable elements and the evolution of regulatory networks.
Feschotte C., Nat. Rev. Genet. 9(5), 2008
PMID: 18368054
Role of transposable elements in heterochromatin and epigenetic control.
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R., Nature 430(6998), 2004
PMID: 15269773
Epigenetic interactions between transposons and genes: lessons from plants.
Weil C, Martienssen R., Curr. Opin. Genet. Dev. 18(2), 2008
PMID: 18339541
Repetitive sequences in complex genomes: structure and evolution.
Jurka J, Kapitonov VV, Kohany O, Jurka MV., Annu Rev Genomics Hum Genet 8(), 2007
PMID: 17506661
Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery.
Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH., Genome Res. 12(5), 2002
PMID: 11997346
A rapid procedure for the isolation of C0t-1 DNA from plants.
Zwick MS, Hanson RE, Islam-Faridi MN, Stelly DM, Wing RA, Price HJ, McKnight TD., Genome 40(1), 1997
PMID: 18464813
High-Cot sequence analysis of the maize genome.
Yuan Y, SanMiguel PJ, Bennetzen JL., Plant J. 34(2), 2003
PMID: 12694599
Isolation and characterization of the highly repeated fraction of the banana genome.
Hribova E, Dolezelova M, Town CD, Macas J, Dolezel J., Cytogenet. Genome Res. 119(3-4), 2007
PMID: 18253041
Evolutionary diversification of satellite DNA sequences from Leymus (Poaceae: Triticeae).
Anamthawat-Jonsson K, Wenke T, Thorsson AT, Sveinsson S, Zakrzewski F, Schmidt T., Genome 52(4), 2009
PMID: 19370093
Minisatellites: mutability and genome architecture.
Vergnaud G, Denoeud F., Genome Res. 10(7), 2000
PMID: 10899139
Plant highly repeated satellite DNA: molecular evolution, distribution and use for identification of hybrids
AUTHOR UNKNOWN, 2007
Minisatellite origins in yeast and humans.
Haber JE, Louis EJ., Genomics 48(1), 1998
PMID: 9503027
The contribution of short repeats of low sequence complexity to large conifer genomes.
Schmidt A, Doudrick RL, Heslop-Harrison JS, Schmidt T., Theor. Appl. Genet. 101(1/2), 2000
PMID: IND22294236
Genetic mapping of hypervariable minisatellite sequences in rice (Oryza sativa L.).
Gustafson JP, Yano M., Theor. Appl. Genet. 100(3/4), 2000
PMID: IND22069577
Repetitive, genome-specific probes in wheat (Triticum aestivum L. em Thell) amplified with minisatellite core sequences
AUTHOR UNKNOWN, 1996
Identification of new minisatellites loci in Arabidopsis thaliana
AUTHOR UNKNOWN, 1998
Characterization of minisatellites in Arabidopsis thaliana with sequence similarity to the human minisatellite core sequence.
Tourmente S, Deragon JM, Lafleuriel J, Tutois S, Pelissier T, Cuvillier C, Espagnol MC, Picard G., Nucleic Acids Res. 22(16), 1994
PMID: 8078766
Nuclear DNA content of some important plant species
AUTHOR UNKNOWN, 1991
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
PROJECT: Generation of a physical, BAC-based map of the sugar beet (Beta vulgaris) genome (GABI-BPM)
AUTHOR UNKNOWN, 0
Cloning and characterization of a Beta vulgaris satellite DNA family.
Schmidt T, Metzlaff M., Gene 101(2), 1991
PMID: 2055488
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
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
Molecular organization of terminal repetitive DNA in Beta species.
Dechyeva D, Schmidt T., Chromosome Res. 14(8), 2006
PMID: 17195925
Variability and evolution of highly repeated DNA sequences in the genus Beta.
Schmidt T, Heslop-Harrison JS., Genome 36(6), 1993
PMID: 8112571
Genomes, genes and junk: the large-scale organization of plant chromosomes
AUTHOR UNKNOWN, 1998
The physical and genomic organization of microsatellites in sugar beet.
Schmidt T, Heslop-Harrison JS., Proc. Natl. Acad. Sci. U.S.A. 93(16), 1996
PMID: 8710945
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
Construction of a sugar beet BAC library from a hybrid with diverse traits
AUTHOR UNKNOWN, 2004
The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age
AUTHOR UNKNOWN, 0
Genome-wide analysis of DNA methylation patterns.
Zilberman D, Henikoff S., Development 134(22), 2007
PMID: 17928417
Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants?
Cullis CA, Vorster BJ, Van Der Vyver C, Kunert KJ., Ann. Bot. 103(4), 2008
PMID: 18801916
Pervasive migration of organellar DNA to the nucleus in plants.
Blanchard JL, Schmidt GW., J. Mol. Evol. 41(4), 1995
PMID: 7563126
Homologies to chloroplast DNA in the nuclear DNA of a number of Chenopod species.
Ayliffe MA, Timmis JN, Scott NS., Theor. Appl. Genet. 75(2), 1988
PMID: IND87107983
The distribution of 5-methylcytosine in the nuclear genome of plants.
Montero LM, Filipski J, Gil P, Capel J, Martinez-Zapater JM, Salinas J., Nucleic Acids Res. 20(12), 1992
PMID: 1620618
PlantSat: a specialized database for plant satellite repeats.
Macas J, Meszaros T, Nouzova M., Bioinformatics 18(1), 2002
PMID: 11836208
Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase.
Jackson JP, Lindroth AM, Cao X, Jacobsen SE., Nature 416(6880), 2002
PMID: 11898023
Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE., Science 292(5524), 2001
PMID: 11349138
Use of haploids of Beta vulgaris L. for the study of orcein and giemsa stained chromosomes
AUTHOR UNKNOWN, 1978
Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements.
Armour JA, Wong Z, Wilson V, Royle NJ, Jeffreys AJ., Nucleic Acids Res. 17(13), 1989
PMID: 2762114
Evolution of a complex minisatellite DNA sequence.
Barros P, Blanco MG, Boan F, Gomez-Marquez J., Mol. Phylogenet. Evol. 49(2), 2008
PMID: 18723095
Birth and evolutionary history of a human minisatellite.
Boan F, Blanco MG, Quinteiro J, Mourino S, Gomez-Marquez J., Mol. Biol. Evol. 21(2), 2003
PMID: 14595097
Analysis of the centromeric regions of the human genome assembly.
Rudd MK, Willard HF., Trends Genet. 20(11), 2004
PMID: 15475110
The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes.
Vershinin AV, Schwarzacher T, Heslop-Harrison JS., Plant Cell 7(11), 1995
PMID: 8535136
Size-dependent palindrome-induced intrachromosomal recombination in yeast.
Lisnic B, Svetec IK, Stafa A, Zgaga Z., DNA Repair (Amst.) 8(3), 2009
PMID: 19124276
Hypervariable 3' UTR region of plant LTR-retrotransposons as a source of novel satellite repeats.
Macas J, Koblizkova A, Navratilova A, Neumann P., Gene 448(2), 2009
PMID: 19563868
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
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
Combinatorial protein engineering by incremental truncation.
Ostermeier M, Nixon AE, Shim JH, Benkovic SJ., Proc. Natl. Acad. Sci. U.S.A. 96(7), 1999
PMID: 10097076

AUTHOR UNKNOWN, 1987
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
AUTHOR UNKNOWN, 1999
Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982
The Phylogenetic Data Editor
AUTHOR UNKNOWN, 0
Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG., Bioinformatics 23(21), 2007
PMID: 17846036

AUTHOR UNKNOWN, 1989

AUTHOR UNKNOWN, 2000

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