Skip to main content
PMC home page
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1995 Nov;61(11):3943–3949. doi: 10.1128/aem.61.11.3943-3949.1995

A microsatellite marker for studying the ecology and diversity of fungal endophytes (Epichloë spp.) in grasses.

K Groppe 1, I Sanders 1, A Wiemken 1, T Boller 1
PMCID: PMC167701  PMID: 8526508

Abstract

Randomly amplified polymorphic DNA fingerprinting, which is based on PCR with arbitrary 10-nucleotide primers, were used to analyze genetic diversity among isolates of the endophytic ascomycete Epichloë typhina, which were collected at a single field site from a population of one of its hosts, the grass Bromus erectus. One of the polymorphic randomly amplified polymorphic DNA PCR products occurred in all isolates as single bands with different but closely related sizes. Two of the size variants of this product were cloned and sequenced, and they were found to represent the same DNA sequence, except for a stretch of tandem repeats of the trinucleotide AAG.TTC, which differed in size, consisting of 8 and 18 repeats, respectively. Tandem repeats of this type are called microsatellites. Oligonucleotides were synthesized corresponding to portions of the sequence flanking the microsatellite and were used for PCR amplification of the loci from the genomic DNAs of different Epichloë isolates. A single PCR product was found for most isolates, indicating that the sequence represented a single genetic locus. Five alleles that could clearly be distinguished in size were found in a population of 91 field isolates. PCR with (AAC)8 and (AAG)8 as primers yielded a number of amplified bands from genomic DNA of Epichloë isolates, indicating that these types of microsatellites occur frequently in the genome of this fungus. A survey of all fungal DNA sequences currently deposited in the DNA sequence databases of EMBL and GenBank revealed that microsatellites of different repeating units are widespread in fungi.(ABSTRACT TRUNCATED AT 250 WORDS)

Full Text

The Full Text of this article is available as a PDF (949.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bruford M. W., Wayne R. K. Microsatellites and their application to population genetic studies. Curr Opin Genet Dev. 1993 Dec;3(6):939–943. doi: 10.1016/0959-437x(93)90017-j. [DOI] [PubMed] [Google Scholar]
  2. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Hamada H., Petrino M. G., Kakunaga T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6465–6469. doi: 10.1073/pnas.79.21.6465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Lieckfeldt E., Meyer W., Börner T. Rapid identification and differentiation of yeasts by DNA and PCR fingerprinting. J Basic Microbiol. 1993;33(6):413–425. doi: 10.1002/jobm.3620330609. [DOI] [PubMed] [Google Scholar]
  5. Morgante M., Olivieri A. M. PCR-amplified microsatellites as markers in plant genetics. Plant J. 1993 Jan;3(1):175–182. [PubMed] [Google Scholar]
  6. Schardl C. L., Leuchtmann A., Tsai H. F., Collett M. A., Watt D. M., Scott D. B. Origin of a fungal symbiont of perennial ryegrass by interspecific hybridization of a mutualist with the ryegrass choke pathogen, Epichloë typhina. Genetics. 1994 Apr;136(4):1307–1317. doi: 10.1093/genetics/136.4.1307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Schönian G., Meusel O., Tietz H. J., Meyer W., Gräser Y., Tausch I., Presber W., Mitchell T. G. Identification of clinical strains of Candida albicans by DNA fingerprinting with the polymerase chain reaction. Mycoses. 1993 May-Jun;36(5-6):171–179. doi: 10.1111/j.1439-0507.1993.tb00746.x. [DOI] [PubMed] [Google Scholar]
  8. Stallings R. L. Distribution of trinucleotide microsatellites in different categories of mammalian genomic sequence: implications for human genetic diseases. Genomics. 1994 May 1;21(1):116–121. doi: 10.1006/geno.1994.1232. [DOI] [PubMed] [Google Scholar]
  9. Tautz D. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 1989 Aug 25;17(16):6463–6471. doi: 10.1093/nar/17.16.6463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Tsai H. F., Liu J. S., Staben C., Christensen M. J., Latch G. C., Siegel M. R., Schardl C. L. Evolutionary diversification of fungal endophytes of tall fescue grass by hybridization with Epichloë species. Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2542–2546. doi: 10.1073/pnas.91.7.2542. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Valle G. TA-repeat microsatellites are closely associated with ARS consensus sequences in yeast chromosome III. Yeast. 1993 Jul;9(7):753–759. doi: 10.1002/yea.320090709. [DOI] [PubMed] [Google Scholar]
  12. Weber J. L. Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics. 1990 Aug;7(4):524–530. doi: 10.1016/0888-7543(90)90195-z. [DOI] [PubMed] [Google Scholar]
  13. Williams J. G., Kubelik A. R., Livak K. J., Rafalski J. A., Tingey S. V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990 Nov 25;18(22):6531–6535. doi: 10.1093/nar/18.22.6531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Wu K. S., Jones R., Danneberger L., Scolnik P. A. Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res. 1994 Aug 11;22(15):3257–3258. doi: 10.1093/nar/22.15.3257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Zolan M. E., Pukkila P. J. Inheritance of DNA methylation in Coprinus cinereus. Mol Cell Biol. 1986 Jan;6(1):195–200. doi: 10.1128/mcb.6.1.195. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES