During a survey for new viruses affecting hop plants, a circular DNA molecule was identified via rolling circle amplification (RCA) and later characterized. A small region of the 5.7-kb long molecule aligned with a microsatellite region in the Humulus lupulus genome, and no coding sequence was identified. Sequence analysis and literature review suggest that the small DNA molecule is an extranuclear DNA element, specifically, an extrachromosomal circular DNA (eccDNA), and its presence was confirmed by electron microscopy. This work is the first report of eccDNAs in the family Cannabaceae. Additionally, this work highlights the advantages of using RCA to study extrachromosomal DNA in higher plants.

Keywords:
Hop, Rolling circle amplification, Extrachromosomal DNA, Circular DNA
1.
Cohen S, Segal D: Extrachromosomal circular DNA in eukaryotes: possible involvement in the plasticity of tandem repeats. Cytogenet Genome Res 124:327-338 (2009).
2.
Cohen S, Agmon N, Yacobi K, Mislovati M, Segal D: Evidence for rolling circle replication of tandem genes in Drosophila. Nucleic Acids Res 33:4519-4526 (2005).
3.
Cohen S, Houben A, Segal D: Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants. Plant J 53:1027-1034 (2008).
4.
Cohen S, Agmon N, Sobol O, Segal D: Extrachromosomal circles of satellite repeats and 5S ribosomal DNA in human cells. Mob DNA 1:11 (2010).
5.
Dean FB, Nelson JR, Giesler TL Lasken RS: Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11:1095-1099 (2001).
6.
Diaz-Lara A, Mosier NJ, Keller KE, Martin RR: A variant of Rubus yellow net virus with altered genomic organization. Virus Genes 50:104-110 (2014).
7.
Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, et al: Production of extrachromosomal microDNAs is linked to mismatch repair pathways and transcriptional activity. Cell Rep 11:1749-1759 (2015).
8.
Dykstra MJ, Reuss LE: Biological Electron Microscopy: Theory, Techniques, and Troubleshooting, ed 2 (Springer Science & Business Media, Berlin 2003).
9.
Haible D, Kober S, Jeske H: Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135:9-16 (2006).
10.
Kinoshita Y, Ohnishi N, Yamada Y, Kunisada T, Yamagishi H: Extrachromosomal circular DNA from nuclear fraction of higher plants. Plant Cell Physiol 26:1401-1409 (1985).
11.
Kolpakov R, Bana G, Kucherov G: mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31:3672-3678 (2003).
12.
Kunisada T, Yamagishi H: Rapid microscale procedure for visualizing intracellular plasmid DNA by electron microscopy. Plasmid 9:8-16 (1983).
13.
Kuttler F, Mai S: Formation of non-random extrachromosomal elements during development, differentiation and oncogenesis. Semin Cancer Biol 17:56-64 (2007).
14.
Laney AG, Hassan M, Tzanetakis IE: An integrated badnavirus is prevalent in fig germplasm. Phytopathology 102:1182-1189 (2012).
15.
Navrátilová A, Koblížková A, Macas J: Survey of extrachromosomal circular DNA derived from plant satellite repeats. BMC Plant Biol 8:90 (2008).
16.
Rush MG, Misra R: Extrachromosomal DNA in eucaryotes. Plasmid 14:177-191 (1985).
17.
Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, et al: Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 336:82-86 (2012).
© 2016 S. Karger AG, Basel
2016
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.
You do not currently have access to this content.