Mycorrhiza

, Volume 19, Issue 4, pp 247–254 | Cite as

Phylogenetic analysis of the Glomeromycota by partial β-tubulin gene sequences

Original Paper

Abstract

The 3’ end of the β-tubulin gene was amplified from 50 isolates of 45 species in Glomeromycota. The analyses included a representative selection of all families except Pacisporaceae and Geosiphonaceae. Phylogenetic analyses excluded three intron regions at the same relative positions in all species due to sequence and length polymorphisms. The β-tubulin gene phylogeny was similar to the 18S rRNA gene phylogeny at the family and species level, but it was not concordant at the order level. Species in Gigasporaceae and Glomeraceae grouped together but without statistical support. Paralogous sequences in Glomus species likely contributed to phylogenetic ambiguity. Trees generated using different fungal phyla as out-groups yielded a concordant topology. Family relationships within the Glomeromycota did not change regardless if the third codon position was included or excluded from the analysis. Multiple clones from three isolates of Scutellospora heterogama yielded divergent sequences. However, phylogenetic patterns suggested that only a single copy of the β-tubulin gene was present, with variation attributed to intraspecific sequence divergence.

Keywords

Glomeromycota Beta-tubulin Phylogeny Arbuscular mycorrhizal fungi 

Notes

Acknowledgements

The authors wish to thank Bill Wheeler, Robert Bills, and Sonia Purin for help with spore extraction and RFLP analysis. Funding was provided by a Fulbright scholarship to Zola Msiska and National Science Foundation grants DBI0650735 and DEB0649341 to Joseph Morton.

References

  1. Baurain D, Brinkmann H, Phillipe H (2007) Lack of resolution in the animal phylogeny: closely spaced cladogenesis or undetected systematic error. Mol Biol Evol 24:6–9, doi:10.1093/molbev/msl137 PubMedCrossRefGoogle Scholar
  2. Clapp JP, Fitter AH, Young JPW (1999) Ribosomal small subunit sequence variation within spores of an arbuscular mycorrhizal fungus, Scutellospora sp. Mol Ecol 8:915–921, doi:10.1046/j.1365-294x.1999.00642.x PubMedCrossRefGoogle Scholar
  3. Clapp JP, Rodriguez A, Dodd JC (2001) Inter-and intra-isolate rRNA large subunit variation in Glomus coronatum spores. New Phytol 149:539–554, doi:10.1046/j.1469-8137.2001.00060.x CrossRefGoogle Scholar
  4. Corradi N, Kuhn G, Sanders IR (2004a) Monophyly of b-tubulin and H+-ATPase gene variants in Glomus intraradices: consequences for molecular evolutionary studies of AM fungal genes. Fungal Genet Biol 41:262–273, doi:10.1016/j.fgb.2003.11.001 PubMedCrossRefGoogle Scholar
  5. Corradi N, Hijri M, Fumagalli L, Sanders IR (2004b) Arbuscular mycorrhizal fungi (Glomeromycota) harbour ancient fungal tubulin genes that resemble those of the chytrids (Chytridiomycota). Fungal Genet Biol 41:1037–1045, doi:10.1016/j.fgb.2004.08.005 PubMedCrossRefGoogle Scholar
  6. da Silva GA, Lumini E, Maia LC, Bonfante P, Bianciotto V (2006) Phylogenetic analysis of Glomeromycota by partial LSU rDNA sequences. Mycorrhiza 16:183–189, doi:10.1007/s00572-005-0030-9 PubMedCrossRefGoogle Scholar
  7. Dar SA, Kuenen JG, Muyzer G (2005) Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities. Appl Environ Microbiol 71:2325–2330, doi:10.1128/AEM.71.5.2325-2330.2005 PubMedCrossRefGoogle Scholar
  8. Einax S, Voigt K (2003) Oligonucleotide primers for the universal amplification of beta-tubulin genes facilitate phylogenetic analyses in the regnum fungi. Org Divers Evol 3:185–194, doi:10.1078/1439-6092-00069 CrossRefGoogle Scholar
  9. Helgason T, Watson IJ, Young JPW, (2003) Phylogeny of the Glomerales and Diversisporales (Fungi: Glomeromycota) from actin and elongation factor 1-alpha sequences. FEMS Microbiol Lett 229:127–132PubMedCrossRefGoogle Scholar
  10. Kuhn G, Hijri M, Sanders IR (2001) Evidence for the evolution of multiple genomes in arbuscular mycorrhizal fungi. Nature 414:745–748, doi:10.1038/414745a PubMedCrossRefGoogle Scholar
  11. Lanfranco L, Bianciotto V, Lumini E, Souza M, Morton JB, Bonfante P (2001) A combined morphological and molecular approach to characterize isolates of arbuscular mycorrhizal fungi in Gigaspora (Glomales). New Phytol 152:169–179, doi:10.1046/j.0028-646x.2001.00233.x CrossRefGoogle Scholar
  12. Lloyd-Macgilp SA, Chambers SM, Dodd JC, Fitter AH, Walker C, Young JPW (1996) Diversity of the ribosomal internal transcribed spacers within and among isolates of Glomus mosseae and related mycorrhizal fungi. New Phytol 133:103–111, doi:10.1111/j.1469-8137.1996.tb04346.x CrossRefGoogle Scholar
  13. Maddison DR, Maddison WP (2005) MacClade. Sinauer Associates, SunderlandGoogle Scholar
  14. Morton JB (1990) Evolutionary relationships among arbuscular mycorrhizal fungi in the Endogonaceae. Mycologia 82:192–207, doi:10.2307/3759848 CrossRefGoogle Scholar
  15. Pawlowska TE, Taylor JW (2004) Organization of genetic variation in individuals of arbuscular mycorrhizal fungi. Nature 427:733–737, doi:10.1038/nature02290 PubMedCrossRefGoogle Scholar
  16. Redecker D, Raab P (2006) Phylogeny of the Glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 98:885–895, doi:10.3852/mycologia.98.6.885 PubMedCrossRefGoogle Scholar
  17. Sanders IR (2004) Intraspecific variation in arbuscular mycorrhizal fungi and its consequences for molecular biology, ecology and development of inoculum. Can J Bot 82:1057–1062, doi:10.1139/b04-094 CrossRefGoogle Scholar
  18. Sanders IR, Alt M, Groppe K, Boller T, Wiemken A (1995) Identification of ribosomal DNA polymorphisms among and within spores of the Glomales: application to studies on the genetic diversity of arbuscular mycorrhizal fungal communities. New Phytol 130:419–427, doi:10.1111/j.1469-8137.1995.tb01836.x CrossRefGoogle Scholar
  19. Sanders IR, Clapp JP, Wiemken A (1996) The genetic diversity of arbuscular mycorrhizal fungi in natural ecosystems-a key to understanding the ecology and functioning of the mycorrhizal symbiosis. New Phytol 133:123–134, doi:10.1111/j.1469-8137.1996.tb04348.x CrossRefGoogle Scholar
  20. Schuessler A, Schwarzott D, Walker C (2001) A new fungal phylum, the Glomeromycota: Phylogeny and evolution. Mycol Res 105:1413–1421, doi:10.1017/S0953756201005196 CrossRefGoogle Scholar
  21. Shinde D, Lai Y, Sun F, Arnheim N (2003) Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites. Nucleic Acids Res 31:947–980, doi:10.1093/nar/gkg178 CrossRefGoogle Scholar
  22. Simmons MP, Miya M (2004) Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches. Mol Phylogenet Evol 31:351–362, doi:10.1016/j.ympev.2003.08.004 PubMedCrossRefGoogle Scholar
  23. Swofford DL (1998) PAUP: phylogenetic analysis using parsimony (and other methods). Sinauer Associates, SunderlandGoogle Scholar
  24. Walker C, Blaszkowski J, Schwarzott D, Schuessler A (2004) Gerdemannia gen. nov., a genus separated from Glomus, and Gerdemanniaceae fam. nov., a new family in the Glomeromycota. Mycol Res 108:707–718, doi:10.1017/S0953756204000346 PubMedCrossRefGoogle Scholar
  25. Yang X, Tuskan GA, Tschaplinski TJ, Cheng Z-M (2007) Third-codon transversion rate-based Nymphae basal angiosperm phylogeny-concordance with developmental evidence. Nature Precedings doi:10.1038/npre.2007.320.1

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.West Virginia UniversityMorgantownUSA

Personalised recommendations