Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Characteristics of Microsatellites in the Transcript Sequences of the Laccaria bicolor Genome

  • Li, Shuxian (The Key Laboratory of Forest Genetics and Biotechnology and Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University) ;
  • Zhang, Xinye (Hubei Forestry Academy) ;
  • Yin, Tongming (The Key Laboratory of Forest Genetics and Biotechnology and Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University)
  • Received : 2009.09.10
  • Accepted : 2009.10.23
  • Published : 2010.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

In this paper, we analyzed the microsatellites in the transcript sequences of the whole Laccaria bicolor genome. Our results revealed that, apart from the triplet repeats, length diversification and richness of the detected microsatellites positively correlated with their repeat motif lengths, which were distinct from the variation trends observed for the transcriptional microsatellites in the genome of higher plants. We also compared the microsatellites detected in the genic regions and in the nongenic regions of the L. bicolor genome. Subsequently, SSR primers were designed for the transcriptional microsatellites in the L. bicolor genome. These SSR primers provide desirable genetic resources to the ectomycorrhizae community, and this study provides deep insight into the characteristics of the micro satellite sequences in the L. bicolor genome.

Keywords

References

  1. Hancock, J. 1995. The contribution of slippage-like processes to genome evolution. J. Mol. Evol. 41: 1038-1047.
  2. He, P. 1998. Abundance, polymorphism and applications of microsatellite in Eukaryote. Hered. China 20: 42-47.
  3. Jewell, E., A. Robinson, D. Savage, T. Erwin, C. G. Love, G. A. C. Lim, et al. 2006. SSR primer and SSR taxonomy tree: Biome SSR discovery. Nucl. Acids Res. 34: 656-659. https://doi.org/10.1093/nar/gkl083
  4. Kashi, Y., D. King, and M. Soller. 1997. Simple sequence repeats as a source of quantitative genetic variation. Trends Genet. 13: 74-78. https://doi.org/10.1016/S0168-9525(97)01008-1
  5. Labbe, J., X. Zhang, T. Yin, J. Schmutz, J. Grimwood, F. Martin, G. A. Tuskan, and F. Le Tacon. 2008. A genetic linkage map for the ectomycorrhizal fungus L. bicolor and its alignment to the whole-genome sequence assemblies. New Phytol. 180: 316-328. https://doi.org/10.1111/j.1469-8137.2008.02614.x
  6. Li, S. and T. Yin. 2007. Map and analysis of microsatellites in genome of Populus: The first sequenced perennial plant. Sci. China C Life Sci. 50: 690-699. https://doi.org/10.1007/s11427-007-0073-6
  7. Li, Y. C., A. B Korol, T. Fahima, A. Beiles, and E. Nevo. 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: A review. Mol. Ecol. 11: 2453-2465. https://doi.org/10.1046/j.1365-294X.2002.01643.x
  8. Liu, H. N. and J. Q. Zhu. 2001. Advances on VA-mycorrhizal research in horticultural plant. J. Hubei Agric. College 21: 274-278.
  9. Lothe, R. 1997. Microsatellite instability in human solid tumors. Mol. Med. Today 3: 61-68. https://doi.org/10.1016/S1357-4310(96)10055-1
  10. Martin, F., A. Aerts, D. Ahren, A. Brun, E. G. J. Danchin, F. Duchaussoy, et al. 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452: 88-93. https://doi.org/10.1038/nature06556
  11. Reddy, P. and D. Housman. 1997. The complex pathology of trinucleotide repeats. Curr. Opin. Cell Biol. 9: 364-372. https://doi.org/10.1016/S0955-0674(97)80009-9
  12. Schlotterer, C. and D. Tautz. 1992. Slippage synthesis of simple sequence DNA. Nucl. Acids Res. 20: 211-215. https://doi.org/10.1093/nar/20.2.211
  13. Tautz, D. and M. Renz. 1984. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucl. Acids Res. 12: 4127-4137. https://doi.org/10.1093/nar/12.10.4127
  14. Tautz, D., M. Trick, and G. A. Dover. 1986. Cryptic simplicity in DNA is a major source of genetic variation. Nature 322: 652-656. https://doi.org/10.1038/322652a0
  15. Toth, G., Z. Gaspari, and J. Jurka. 2000. Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res. 10: 967-981. https://doi.org/10.1101/gr.10.7.967
  16. Weber, J. L. and P. E. May. 1989. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44: 388-396.
  17. Yin, T., S. P. Difazio, L. E. Gunter, X. Zhang, M. M. Sewell, S. A. Woolbright, et al. 2008. Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res. 18: 422-430. https://doi.org/10.1101/gr.7076308
  18. Yin, T. M., X. Y. Zhang, L. E. Gunter, S. X. Li, S. D. Wullschleger, M. R. Huang, and G. A. Tuskan. 2009. Microsatellite primers resource developed from the mapped sequence scaffolds of Nisqually-1 genome. New Phytol. 181: 498-503. https://doi.org/10.1111/j.1469-8137.2008.02663.x

Cited by

  1. Deep Insight into the Ganoderma lucidum by Comprehensive Analysis of Its Transcriptome vol.7, pp.8, 2010, https://doi.org/10.1371/journal.pone.0044031
  2. Development of Novel Microsatellite Markers for Strain-Specific Identification of Chlorella vulgaris vol.24, pp.9, 2014, https://doi.org/10.4014/jmb.1405.05047
  3. Characterization and comparison of EST-SSRs in Salix, Populus, and Eucalyptus vol.11, pp.1, 2010, https://doi.org/10.1007/s11295-014-0820-3