Skip to main content
SpringerLink
Log in

Map and analysis of microsatellites in the genome of Populus: The first sequenced perennial plant

  • Published:
Science in China Series C: Life Sciences Aims and scope Submit manuscript

Abstract

We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated that SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri-and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di-and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Wullschleger S D, Jansson S, Taylor G. Genomics and forest biology: Populus emerges as the perennial favortie. Plant Cell, 2002, 14: 2651–2655

    Article  PubMed  CAS  Google Scholar 

  2. Bradshaw H D, Ceulemans R, Davis J, et al. R. Emerging model systems in plant biology: Poplar (Populus) as a model torest tree. J Plant Growth Regul, 2000, 19: 306–313

    Article  CAS  Google Scholar 

  3. Tuskan G A, DiFazio S P, Teichmann T. Poplar genomics is getting popular: The impact of the poplar genome project on tree research. Plant Biol, 2004, 6: 2–4

    Article  PubMed  CAS  Google Scholar 

  4. Brunner A M, Busov V B, Strauss S H. Poplar genome sequence: Functional genomics in an ecologically dominant plant species. Trends Plant Sci, 2004, 9: 49–56

    Article  PubMed  CAS  Google Scholar 

  5. Tuskan G A, DiFazio S P, Hellsten U, et al. The genome of black cottonwood, Populus Trichocarpa (Torr.& Gray Ex Brayshaw). Science, 2006, 313: 1596–1604

    Article  PubMed  CAS  Google Scholar 

  6. Schlotterer C. Genealogical inference of closely related species based on microsatellites. Genet Res Camb, 2001, 78: 209–212

    CAS  Google Scholar 

  7. Powell W, Machray G C, Provan J. Polymorphism revealed by simple sequence repeats. Trends Plant Sci, 1996, 1: 215–222

    Google Scholar 

  8. Jewell E, Robinson A, Savage D, et al. SSR primer and SSR taxonomy tree: Biome SSR discovery. Nucl Acids Res, 2006, 34: W656–W659

    Article  PubMed  CAS  Google Scholar 

  9. Tuskan G A, Gunter L E, Yang Z M, et al. Characterization of microsatellites revealed by genomci sequencing of Populus Trichocarpa. Can For Res, 2004, 34: 85–93

    Article  CAS  Google Scholar 

  10. Wyman J, Bruneau A, Tremblay M F. Microsatellite analysis of gentic diversity in four populations of Populus tremuloides in Quebec. Can J Bot, 2003, 81: 367

    Article  Google Scholar 

  11. Yin T M, Difazio S P, Gunter L E, et al. Large-scale heterospecific segregation distortion in Populus revealed by a Dense Genetic Map. Theor Appl Genet, 2004, 109: 451–463

    Article  PubMed  CAS  Google Scholar 

  12. Tautz D, Trick M, Dover G A. Cryptic simplicity in DNA is a major source of genetic variation. Nature, 1986, 322: 652–656

    Article  PubMed  CAS  Google Scholar 

  13. Kashi Y, King D, Soller M. Simple sequence repeats as a source of quantitative genetic variation. Trends Genet, 1997, 13: 74–78

    Article  PubMed  CAS  Google Scholar 

  14. Li Y C, Korol A B, Beiles A, et al. Microsatellites: Genomic distribution, putative functions and mutational mechanisms: A review. Mol Ecol, 2002, 11: 2453–2465

    Article  PubMed  CAS  Google Scholar 

  15. Dieringer D, Schlotterer C. Two distinct modes of microsatellite mutation processes: Evidence from the complete genomic sequences of nine species. Genome Res, 2003, 13: 2242–2251

    Article  PubMed  CAS  Google Scholar 

  16. Voorrips R E. MapChart: Software for the graphical presentation of linkage maps and QTLs. J Heredity, 2002, 93: 77–78

    Article  CAS  Google Scholar 

  17. Smith E C. A study of cytology and speciation in the Genus Populus L. J Arnold Arb, 1943, 24: 275 305

    Google Scholar 

  18. Toth G, Gaspari Z, Jurka, J. Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res, 2000, 10: 967–981

    Article  PubMed  CAS  Google Scholar 

  19. Hancock J M. Simple sequences in a ‘minimal’ genome. Nat Genet, 1996, 14: 14–15

    Article  PubMed  CAS  Google Scholar 

  20. Brinkmann B, Klintschar M, Neuhuber F, et al. Mutation rate in hu-man microsatellites: Influence of the structure and length of the tandem repeat. Am J Hum Genet, 1998, 62: 1408–1415

    Article  PubMed  CAS  Google Scholar 

  21. Brohede J, Primmer C R, Moller A, et al. Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci. Nucl Acids Res, 2002, 30: 1997–2003

    Article  PubMed  CAS  Google Scholar 

  22. Shinde D, Lai Y, Sun F, et al. Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites. Nucleic Acids Res, 2003, 31: 974–980

    Article  PubMed  CAS  Google Scholar 

  23. Bachtrog D, Agis M, Imhof M, et al. Microsatellite variability differs between dinucleotide repeat motifs—Evidence from Drosophila melanogaster. Mol Biol Evol, 2000, 17: 1277–1285

    PubMed  CAS  Google Scholar 

  24. Hancock J M. The contribution of slippage-like processes to genome evolution. J Mol Evol, 1995, 41: 1038–1047

    Article  PubMed  CAS  Google Scholar 

  25. Reddy P S, Housman D E. The complex pathology of trinucleotide repeats. Curr Opin Cell Biol, 1997, 9: 364–372

    Article  PubMed  CAS  Google Scholar 

  26. Lothe R A. Microsatellite instability in human solid tumors. Mol Med Today, 1997, 3: 61–68

    Article  PubMed  CAS  Google Scholar 

  27. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 2000, 408: 796–815

    Google Scholar 

  28. Goff S A, Ricke D, Lan T H, et al. A draft sequence of the rice genome (Oryza Sativa L. Ssp. Japonica). Science, 2002, 296: 92–100

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Environment and Forest Resources, Nanjing Forestry University, Nanjing, 210037, China

    Li ShuXian & Yin TongMing

  2. Environmental Sciences Division, Oak Ridge National Laboratory, TN, USA

    Yin TongMing

Authors
  1. Li ShuXian
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yin TongMing
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yin TongMing.

Additional information

Supported by Program for New Century Excellent Talents in University (Grant No. NCET-04-0516), Fok Ying Tung Education Foundation, and the National Natural Science Foundation of China (Grant No. 30200224)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Li, S., Yin, T. Map and analysis of microsatellites in the genome of Populus: The first sequenced perennial plant. SCI CHINA SER C 50, 690–699 (2007). https://doi.org/10.1007/s11427-007-0073-6

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-007-0073-6

Keywords

Search

Navigation