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.
Erscheinungsjahr
2010
Zeitschriftentitel
BMC Plant Biology
Band
10
Ausgabe
1
Art.-Nr.
8
ISSN
1471-2229
Page URI
https://pub.uni-bielefeld.de/record/1665020
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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. https://doi.org/10.1186/1471-2229-10-8
Zakrzewski, Falk, Wenke, Torsten, Holtgräwe, Daniela, Weisshaar, Bernd, and Schmidt, Thomas. 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.
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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2019-09-06T08:48:06Z
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Daten bereitgestellt von European Bioinformatics Institute (EBI)
12 Zitationen in Europe PMC
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BNR - a LINE family from Beta vulgaris - contains a RRM domain in open reading frame 1 and defines a L1 sub-clade present in diverse plant genomes.
Heitkam T, Schmidt T., Plant J. 59(6), 2009
PMID: 19473321
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Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
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PMID: 6096873
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Ostermeier M, Nixon AE, Shim JH, Benkovic SJ., Proc. Natl. Acad. Sci. U.S.A. 96(7), 1999
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AUTHOR UNKNOWN, 1987
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
AUTHOR UNKNOWN, 1999
AUTHOR UNKNOWN, 1999
Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982
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The Phylogenetic Data Editor
AUTHOR UNKNOWN, 0
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
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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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