Skip to main content
SpringerLink
Log in

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes

  • Genetics of Microorganisms
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

To date, molecular systematics of Myxogastria has been based primarily on small subunit ribosomal RNA (SSU rRNA) and elongation factor 1-alpha (EF-1α) genes. To establish a natural classification system for the organisms, we examined phylogenetic relationships among myxogastrian species using cytochrome c oxidase subunit I (COI) and SSU rRNA genes. Twenty new sequences were obtained, including 10 COI and 10 SSU rRNA sequences, were compared with sequences of related species from GenBank in order to construct phylogenic trees. The analysis of the two data sets supported the modern phylogeny of myxogastria: orders Liceida and Trichiida formed a sister group at the most basal clade, while orders Stemonitida and Physarida formed a close group, and order Echinostelida was a sister group to Stemonitida and Physarida. However, the partial COI sequences were too conserved to resolve of the branches in Stemonitida and Physarida. In addition, we also deemed the specific edited mRNA events of COI sequences in myxogastrian species.

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. Stephenson, S.L., From morphological to molecular: studies of myxomycetes since the publication of the Martin and Alexopoulos (1969) monograph, Fungal Diversity, 2011, vol. 50, no. 1, pp. 21–34.

    Article  Google Scholar 

  2. Alexopoulos, C.J., Blackwell, M., and Mims, C.W., Introductory Mycology, New York: Wiley, 1996, 4th ed.

    Google Scholar 

  3. Pawlowski, J. and Burki, F., Untangling the phylogeny of amoeboid protists, J. Eukaryotic Microbiol., 2009, vol. 56, no. 1, pp. 16–25.

    Article  CAS  Google Scholar 

  4. Fiore-Donno, A.M., Nikolaev, S.I., Nelson, M., et al., Deep phylogeny and evolution of slime moulds (Mycetozoa), Protist, 2010, vol. 161, no. 1, pp. 55–70.

    Article  CAS  PubMed  Google Scholar 

  5. Martin, G.W. and Alexopoulos, C.J., The Myxomycetes, Iowa City: University of Iowa Press, 1969.

    Google Scholar 

  6. Ross, I.K., The Stemonitomycetidae, a new subclass of myxomycetes, Mycologia, 1973, vol. 65, no. 2, pp. 477–485.

    Article  Google Scholar 

  7. Collins, O.N.R., Myxomycete biosystematics: some recent developments and future research opportunities, Bot. Rev., 1979, vol. 45, no. 2, pp. 145–201.

    Article  Google Scholar 

  8. Fiore-Donno, A.M., Berney, C.D., Pawlowski, J., et al., Higher-order phylogeny of plasmodial slime molds (Myxogastria) based on elongation factor 1-A and small subunit rRNA gene sequences, J. Eukaryotic Microbiol., 2005, vol. 52, no. 3, pp. 201–210.

    Article  CAS  Google Scholar 

  9. Shadwick, L.L., Spiegel, F.W., Shadwick, J.D.L., et al., Eumycetozoa = Amoebozoa?: SSUrDNA phylogeny of protosteloid slime molds and its significance for the amoebozoan supergroup, PLoS One, 2009, vol. 4, no. 8.

    Google Scholar 

  10. Cavalier-Smith, T., Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa, Eur. J. Protistol., 2013, vol. 49, no. 2, pp. 115–178.

    Article  PubMed  Google Scholar 

  11. Fiore-Donno, A.M., Clissmann, F., Meyer, M., et al., Two-gene phylogeny of bright-spored myxomycetes (slime moulds, superorder Lucisporidia), PLoS One, 2013, vol. 8, no. 5, e62586

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Batishcheva, N., Kartavtsev, Y.P., and Bogutskaya, N., Phylogenetic analysis of Altai osmans of the genus Oreoleuciscus (Pisces, Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (Co-1) sequence, Russ. J. Genet., 2011, vol. 47, no. 10, pp. 1188–1197.

    Article  CAS  Google Scholar 

  13. Kartavtsev, Y.P. and Lee, J.-S., Analysis of nucleotide diversity at the cytochrome b and cytochrome oxidase 1 genes at the population, species, and genus levels, Russ. J. Genet., 2006, vol. 42, no. 4, pp. 341–362.

    Article  CAS  Google Scholar 

  14. Demin, A., Polukonova, N., and Mugue, N., Molecular phylogeny and the time of divergence of minges (Chironomidae, Nematocera, Diptera) inferred from a partial nucleotide sequence of the cytochrome oxidase I gene (COI), Russ. J. Genet., 2011, vol. 47, no. 10, pp. 1168–1180.

    Article  CAS  Google Scholar 

  15. Hebert, PP. D., Ratnasingham, S. and de Waard, J.R., Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species, Proc. R. Soc. London, Ser. B, 2003, vol. 270, no. S1, pp. S96–S99.

    Article  CAS  Google Scholar 

  16. Nassonova, E., Smirnov, A., Fahrni, J., et al., Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae, Protist, 2010, vol. 161, no. 1, pp. 102–115.

    Article  CAS  PubMed  Google Scholar 

  17. Kamono, A., Meyer, M., Cavalier-Smith, T., et al., Exploring slime mould diversity in high-altitude forests and grasslands by environmental RNA analysis, FEMS Microbiol. Ecol., 2012, vol. 84, no. 1, pp. 98–109.

    Article  PubMed  Google Scholar 

  18. Stamatakis, A., RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 2006, vol. 22, no. 21, pp. 2688–2690.

    Article  CAS  PubMed  Google Scholar 

  19. Ronquist, F. and Huelsenbeck, J. PP., MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 2003, vol. 19, no. 12, pp. 1572–1574.

    Article  CAS  PubMed  Google Scholar 

  20. Bogdanov, A., Stakheev, V., Zykov, A., et al., Genetic variation and differentiation of wood mice from the genus Sylvaemus inferred from sequencing of the cytochrome oxidase subunit 1 gene fragment, Russ. J. Genet., 2012, vol. 48, no. 2, pp. 186–198.

    Article  CAS  Google Scholar 

  21. Lopatkin, A., Khrisanfova, G., Voronin, M., et al., Polymorphism of the cox1 gene in bird schistosome cercaria isolates (Trematoda, Schistosomatidae) from ponds of Moscow and Moscow oblast, Russ. J. Genet., 2010, vol. 46, no. 7, pp. 873–880.

    Article  CAS  Google Scholar 

  22. Horton, T.L. and Landweber, L.F., Evolution of four types of RNA editing in myxomycetes, RNA, 2000, vol. 6, no. 10, pp. 1339–1346.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Gott, J., Visomirski, L., and Hunter, J., Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum, J. Biol. Chem., 1993, vol. 268, no. 34, pp. 25483–25486.

    CAS  PubMed  Google Scholar 

  24. Pankratova, E.V. and Stepchenko, A.G., RNA editing in eukaryotic genome expression, Russ. J. Genet., 2010, vol. 46, no. 1, pp. 1–8.

    Article  CAS  Google Scholar 

  25. Gott, J.M., Parimi, N., and Bundschuh, R., Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNA, Nucleic Acids Res., 2005, vol. 33, no. 16, pp. 5063–5072.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Krishnan, U., Barsamian, A., and Miller, D.L., Evolution of RNA editing sites in the mitochondrial small subunit rRNA of the Myxomycota, Methods Enzymol., 2007, vol. 424, no. 4, pp. 197–220.

    Article  CAS  PubMed  Google Scholar 

  27. El-Hage, N., Little, C., Clark, J.D., et al., Biosystematics of the Didymium squamulosum complex, Mycologia, 2000, vol. 92, no. 1, pp. 54–64.

    Article  Google Scholar 

  28. Clark, J. and Stephenson, S.L., Biosystematics of the myxomycetes Didymium squamulosum, Physarum compressum, and Physarum melleum: additional isolates, Mycotaxon, 2003, vol. 85, no. 1, pp. 85–89.

    Google Scholar 

  29. Winsett, K.E. and Stephenson, S.L., Using ITS sequences to assess intraspecific genetic relationships among geographically separated collections of the myxomycete Didymium squamulosum, Rev. Mex. Micol., 2008, vol. 27, no. 1, pp. 59–65.

    Google Scholar 

  30. Li, S., Wang, Q., and Li, Y., Molecular analysis of Didymium squamulosum based on ribosomal gene sequences, Mycosystema, 2013, vol. 32, no. 4, pp. 764–770.

    Google Scholar 

  31. Nannenga-Bremekamp, N., A Guide to Temperate Myxomycetes, Bristol: Biopress Bristol, 1991.

    Google Scholar 

  32. Farr, M.L., Some new myxomycetes records for the neotropics and some taxonomic problems in the Myxomycetes, Proc. Iowa Acad. Sci., 1974, vol. 81, no. 1, pp. 37–40.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Life Sciences, Nanjing Normal University, no. 1 Wenyuan Road, Qixia District, Nanjing, 210046, China

    Q. Sh. Liu, Sh. Zh. Yan & Sh. L. Chen

Authors
  1. Q. Sh. Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sh. Zh. Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sh. L. Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Q. Sh. Liu.

Additional information

The article is published in the original.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, Q.S., Yan, S.Z. & Chen, S.L. Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes. Russ J Genet 51, 39–45 (2015). https://doi.org/10.1134/S1022795414110076

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795414110076

Keywords

Search

Navigation