Cytogenetic and Genome Research

Original Article

Distribution of the tandem repeat sequences and karyotyping in cucumber (Cucumis sativus L.) by fluorescence in situ hybridization

Han Y.H.a, b · Zhang Z.H.c · Liu J.H.a · Lu J.Y.a · Huang S.W.c · Jin W.W.a

Author affiliations

aNational Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome Ministry of Agriculture, China Agricultural University, Beijing bCollege of Life Sciences, Guangxi Normal University, Guilin cInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing (China)

Related Articles for ""
Cytogenet Genome Res 122:80–88 (2008)
https://doi.org/10.1159/000151320

Log in to MyKarger to check if you already have access to this content.




Forgot your password
Sign up to MyKarger

Buy

  • FullText & PDF
  • Unlimited re-access via MyKarger
  • Unrestricted printing, no saving restrictions for personal use
read more
CHF 38.00 *
EUR 35.00 *
USD 39.00 *

Select

KAB

Buy a Karger Article Bundle (KAB) and profit from a discount!


If you would like to redeem your KAB credit, please log in.

Save over 20% compared to the individual article price.

Learn more

Rent/Cloud

  • Rent for 48h to view
  • Buy Cloud Access for unlimited viewing via different devices
  • Synchronizing in the ReadCube Cloud
  • Printing and saving restrictions apply
Rental: USD 8.50
Cloud: USD 20.00

Select

Subscribe

  • Access to all articles of the subscribed year(s) guaranteed for 5 years
  • Unlimited re-access via Subscriber Login or MyKarger
  • Unrestricted printing, no saving restrictions for personal use
read more

Subcription rates

Select
* The final prices may differ from the prices shown due to specifics of VAT rules.

Article / Publication Details

First-Page Preview
Abstract of Original Article

Accepted: June 12, 2008
Published online: October 14, 2008
Issue release date: October 2008

Number of Print Pages: 9
Number of Figures: 4
Number of Tables: 3

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: https://www.karger.com/CGR

Abstract

We analyzed repeat sequences composition in the genome of cucumber inbred line 9930 using whole-genome shotgun reads. The analysis showed that satellite DNA sequences are the most dominant components in the cucumber genome. The distribution pattern of several tandem repeat sequences (Type I/II, Type III and Type IV) on cucumber chromosomes was visualized using fluorescence in situ hybridization (FISH). The FISH signals of the Type III and 45S rDNA provide useful cytogenetic markers, whose position and fluorescence intensity allow for easy identification of all somatic metaphase chromosomes. A karyotype showing the position and fluorescence intensity of several tandem repeat sequences is constructed. The establishment of this FISH-based karyotype has created the basis for the integration of molecular, genetic and cytogenetic maps in Cucumis sativus and for the ultimate genome sequencing project as well.

© 2008 S. Karger AG, Basel



Related Articles:

References

  1. Ananiev EV, Phillips RL, Rines HW: Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA 95:13073–13078 (1998).
    External Resources
  2. Ayyangar KR: Taxonomy of Cucurbitaceae. Bull Natl Inst Sci India 34:331–337 (1967).
  3. Bennett MD, Smith JB: Nuclear DNA amounts in Angiosperms. Phil Trans R Soc Lond 274:227–274 (1976).
    External Resources
  4. Bhaduri PN, Bose PC: Cytogenetical investigations in some common cucurbits, with special reference to fragmentation of chromosomes as physical basis of speciation. J Genet 48:237–256 (1947).
    External Resources
  5. Chen J, Staub JE, Jiang J: A reevaluation of karyotype in cucumber (Cucumis sativus L.). Genet Resour Crop Evol 45:301–305 (1998).
    External Resources
  6. Chen J, Staub JE, Adelberg JW, Jiang J: Physical mapping of 45S rRNA genes in Cucumis species by fluorescence in situhybridization. Can J Bot 77:389–393 (1999).
    External Resources
  7. Cheng Z, Dong F, Langdon T, Ou S, Buell CR, et al: Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691–1704 (2002).
    External Resources
  8. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, et al: Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286:2468–2474 (1999).
    External Resources
  9. Csink AK, Henikoff S: Something from nothing: The evolution and utility of satellite repeats. Trends Genet 14:200–204 (1998).
    External Resources
  10. Fajkus J, Kovarik A, Kralovics R, Bezdek M: Organization of telomeric and subtelomeric chromatin in the higher plant Nicotiana tabacum. Mol Gen Genet 247:633–638 (1995).
    External Resources
  11. Ganal M, Hemleben V: Insertion and amplification of a DNA sequence in satellite DNA of Cucumis sativus L. (cucumber). Theor Appl Genet 75:357–361 (1988).
    External Resources
  12. Ganal M, Riede I, Hemleben V: Organization and sequence analysis of two related satellite DNAs in cucumber (Cucumis sativus L.). J Mol Evol 23:23–30 (1986).
    External Resources
  13. Grewal SI, Elgin SC: Transcription and RNA interference in the formation of heterochromatin. Nature 447:399–406 (2007).
    External Resources
  14. Henikoff S, Ahmad K, Malik HS: The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098–1102 (2001).
    External Resources
  15. Hoshi Y, Plader W, Malepszy S: New C-banding pattern for chromosome identification in cucumber (Cucumis sativus L.). Plant Breed 117:77–82 (1998).
    External Resources
  16. Hoshi Y, Plader W, Malepszy S: Physical mapping of 45S rRNA gene loci in the cucumber (Cucumis sativus L.) using fluorescence in situhybridization. Caryologia 52:49–57 (1999).
    External Resources
  17. International Rice Genome Sequencing Project: The map-based sequence of the rice genome. Nature 436:793–800 (2005).
    External Resources
  18. Jackson SA, Wang ML, Goodman HM, Jiang J: Application of Fiber-FISH in genome analysis of Arabidopsis thaliana. Genome 41:566–572 (1998).
    External Resources
  19. Jiang J, Gill BS: Nonisotopic in situhybridization and plant genome mapping: the first 10 years. Genome 37:717–725 (1994).
    External Resources
  20. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC: Metaphase and interphase fluorescence in situhybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92:4487–4491 (1995).
    External Resources
  21. Jiang J, Birchler JA, Parrott WA, Dawe RK: A molecular view of plant centromeres. Trends Plant Sci 8:570–575 (2003).
    External Resources
  22. Jin W, Melo JR, Nagaki K, Talbert PB, Henikoff S, et al: Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell 16:571–581 (2004).
    External Resources
  23. Kato A, Lamb JC, Birchler JA: Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci USA 101:13554–13559 (2004).
    External Resources
  24. Koo DH, Hur Y, Jin DC, Bang JW: Karyotype analysis of a Korean cucumber cultivar (Cucumis sativus L. cv. Winter Long) using C-banding and bicolor fluorescence in situhybridization. Mol Cells 13:413–418 (2002).
    External Resources
  25. Koo DH, Choi HW, Cho J, Hur Y, Bang JW: A high-resolution karyotype of cucumber (Cucumis sativus L. ‘Winter Long’) revealed by C-banding, pachytene analysis, and RAPD-aided fluorescence in situhybridization. Genome 48:534–540 (2005).
    External Resources
  26. Kumar A, Bennetzen JL: Plant retrotransposons. Annu Rev Genet 33:479–532 (1999).
    External Resources
  27. Lamb JC, Meyer JM, Corcoran B, Kato A, Han F, Birchler JA: Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Res 15:33–49 (2007).
    External Resources
  28. Martienssen RA: Maintenance of heterochromatin by RNA interference of tandem repeats. Nat Genet 35:213–214 (2003).
    External Resources
  29. Meyers BC, Tingey SV, Morgante M: Abundance, distribution and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660–1676 (2001).
    External Resources
  30. Ohno S: So much ‘junk’ DNA in our genome. Brookhaven Symp Biol 23:366–370 (1972).
    External Resources
  31. Ohtsubo H, Umeda M, Ohtsubo E: Organization of DNA sequences highly repeated in tandem in rice genomes. Jpn J Genet 66:241–245 (1991).
    External Resources
  32. Peacock WJ, Dennis ES, Phoades MM, Pryor AJ: High repeated DNA sequence limited to knob heterochromatin in maize. Proc Natl Acad Sci USA 78:4490–4494 (1981).
    External Resources
  33. Plohl M, Luchetti A, Meštrovié N, Mantovani B: Satellite DNAs between selfishness and functionality: Structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409:72–82 (2008).
    External Resources
  34. Ramachandran C, Seshadri VS: Cytological analysis of the genome of cucumber (Cucumis sativus L.) and muskmelon (Cucumis melo L.). Z Pflanzenzüchtg 96:25–38 (1986).
  35. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, et al: Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–768 (1996).
    External Resources
  36. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF: Genomic and genetic definition of a functional human centromere. Science 294:109–115 (2001).
    External Resources
  37. Sharma S, Raina SN: Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes. Cytogenet Genome Res 109:15–26 (2005).
    External Resources
  38. Sullivan BA, Blower MD, Karpen GH: Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet 2:584–596 (2001).
    External Resources
  39. Trivedi RN, Roy RP: Cytological studies in Cucumis and Citrullus. Cytologia 35:561–569 (1970).
    External Resources
  40. Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K: Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol 35:791–799 (1997).
    External Resources
  41. Vershinin AV, Schwarzacher T, Heslop-Harrison JS: The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes. Plant Cell 7:1823–1833 (1995).
    External Resources
  42. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS: Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837 (2002).
    External Resources
  43. Wu HK: Note on preparing of pachytene chromosomes by double mordant. Sci Agric 15:40–44 (1967).
  44. Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, et al: Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14:2825–2836 (2002).
    External Resources
  45. Zhong XB, Fransz PF, Eden JW, Ramanna MS, Kammen A, et al: FISH studies reveal the molecular and chromosomal organization of individual telomere domains in tomato. Plant J 13:507–517 (1998).
    External Resources

Article / Publication Details

First-Page Preview
Abstract of Original Article

Accepted: June 12, 2008
Published online: October 14, 2008
Issue release date: October 2008

Number of Print Pages: 9
Number of Figures: 4
Number of Tables: 3

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: https://www.karger.com/CGR

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.

Article Tools
Article Details

2008, Vol.122, No. 1

October 2008

Article

Recommend This
Additional Information

This research was supported by the Program for New Century Excellent Talents in University (NCET-07-08 11) to W.W. Jin and by the Ministry of Agriculture (‘948’ program 2008-Z42) and the Ministry of Science and Technology (2006DFA32 140) to S.W. Huang.
TOP