Skip to main content
SpringerLink
Log in

Diversity within the genus Elymus (Poaceae: Triticeae) II: analyses of variation within 5S nrDNA restrict membership in the genus to species with StH genomes

  • Original Article
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

The genus Elymus is a repository for a large number of species that have been difficult to classify by traditional techniques due to their remarkable levels of polymorphism. Following the genome analyses of Yen and Yang (Genus Elymus 5:58–362, 2013), we used sequences of the nr5SDNA to investigate diversity within those 24 species having St and H haplomes (Baum et al. Mol Genet Genomics 290:329–42, 2015) and for which the genome status was known. The present work extends this analysis to include eight species for which there was no information on genomic status. Our results show that these eight have nr5SDNA sequences that can be assigned to unit classes of orthologous sequences found in St and H haplomes, suggesting that the presence of St and H haplomes is characteristic of the genus. We then carried out a set of canonical discriminant analyses based on 247 DNA new sequences from these 8 species plus the 1054 sequences previously identified from 24 Elymus species. Sequences were analyzed to answer the following questions: Do the species integrate or are they different? Are the tetraploids different from the higher-ploid species? Are the species united within sections, or the same within regions? How do the species fare when divided according to sections? The main results of the canonical discriminant analyses are that the species are united within the tetraploids and within the hexaploids, within each region and within each section. In addition, a series of classificatory discriminant analyses showed that the identification tests are different, although not sufficiently useful for the discrimination of all the species. We also demonstrate the power of our approach by showing that the voucher for Elymus mobilis is not Elymus at all, but Leymus.

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

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Madden TL, Schoffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Álvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417–434

    Article  PubMed  Google Scholar 

  • Appels R, Baum BR (1992) Evolution of the NOR and 5S DNA loci in the Triticeae. In Soltis PS, Soltis DE, Doyle JJ. Molecular Systematics of Plants. Chapman & Hall, New York

  • Batcher MS (2002) Element stewardship abstract for Elytrigia repens (L.) Desv. ex BD Jackson. The Nature Conservancy, Arlington, VA

  • Baum BR, Bailey LG (2012) Genetic diversity in the red wild einkorn: T. urartu Gandilyan (Poaceae: Triticeae). Genet Resour Crop Ev 60:77–87. doi:10.1007/s10722-012-9817-7

    Article  Google Scholar 

  • Baum BR, Johnson DA (1994) The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare). Genome 37:992–998

    Article  PubMed  CAS  Google Scholar 

  • Baum BR, Johnson DA (1996) The 5 s rRNA gene units in ancestral two rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5 s rDNA units of cultivated barley (H. vulgare L.). Genome 39:140–149

    Article  PubMed  CAS  Google Scholar 

  • Baum BR, Johnson DA (1998) The 5S rRNA gene in sea barley (Hordeum marinum Hudson sensu lato): sequence variation among repeat units and relationship to the X haplome in barley (Hordeum). Genome 41:652–661

    Article  PubMed  CAS  Google Scholar 

  • Baum BR, Johnson DA (2002) A comparison of the 5S rDNA diversity in the Hordeum brachyantherum–californicum complex with those of the eastern Asiatic Hordeum roshevitzii and the South American Hordeum cordobense (Triticeae: Poaceae). Can J Bot 80:752–762

    Article  CAS  Google Scholar 

  • Baum BR, Johnson DA (2004) Differences between South American H haplome diploids and I haplome diploids from the perspective of the 5S rDNA gene in the genus Hordeum. Czech J Genet Plant Breed 40:45–50

    Google Scholar 

  • Baum BR, Johnson DA (2008) Molecular confirmation of the genomic constitution of Douglasdeweya (Triticeae: Poaceae): demonstration of the utility of the 5S rDNA sequence as a tool for haplome identification. Mol Genet Genomics 279:621–628. doi:10.1007/s00438-008-0338-1

    Article  PubMed  CAS  Google Scholar 

  • Baum BR, Johnson DA, Bailey LG. (2001) Defining orthologous groups among multicopy genes prior to inferring phylogeny, with special emphasis on the Triticeae (Poaceae). Hereditas 135: 123–138. Lund, Sweden. ISSN0018-0661

  • Baum BR, Edwards T, Mamuti M, Johnson DA (2012) Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from 5S rDNA units (Triticeae: Poaceae). Genome 55:1–17

    Article  Google Scholar 

  • Baum BR, Edwards T, Johnson DA (2015) Diversity within the genus Elymus (Poaceae: Triticeae) as investigated by the analysis of the nr5S rDNA variation in species with St and H haplomes. Mol Genet Genomics 290:329–342. doi:10.1007/s00438-014-0907-4

    Article  PubMed  CAS  Google Scholar 

  • Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224

    Article  PubMed  CAS  Google Scholar 

  • Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325–338

    Article  Google Scholar 

  • Liu Q, Ge S, Tang H, Zhang X, Zhu G, Lu BR (2006) Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences. New Phytol 170:411–420

    Article  PubMed  CAS  Google Scholar 

  • Mason-Gamer RJ (2004) Reticulate evolution, Introgression, and Intertribal gene capture in an allohexaploid grass. Syst Biol 53:25–37

    Article  PubMed  Google Scholar 

  • Mason-Gamer RJ, Orme NL, Anderson CM (2002) Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets. Genome 45:991–1002

    Article  PubMed  CAS  Google Scholar 

  • Mason-Gamer RJ, Burns MM, Naum M (2010) Reticulate evolutionary history of a complex group of Grasses: phylogeny of Elymus StStHH allotetraploids based on three nuclear genes. PLoS One 5(6):e10989. doi:10.1371/journal.pone.0010989

    Article  PubMed  PubMed Central  Google Scholar 

  • Nicholas KB, Nicholas HB Jr (1997) GeneDoc©: a tool for editing and annotating multiple sequence alignments. Distributed by the authors Available from http://www.psc.edu/biomed/genedoc/ or http://www.nrbsc.org/downloads/ Accessed 2008

  • Peakall R, Smouse PE (2006) GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28: 2537-2539. http://bioinformatics.oxfordjournals.org/content/28/19/2537. Accessed 2013

  • Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539–544. doi:10.1038/msb.2011.75

    Article  PubMed  PubMed Central  Google Scholar 

  • Sun G, Li W (2005) Molecular diversity of species of the Elymus trachycaulus complex and their relationships to non-North American taxa. Plant Syst Evol 256:179–191. doi:10.1007/s00606-005-0368-7

    Article  Google Scholar 

  • Sun G, Ma X (2009) Nucleotide diversity and minisatellite in chloroplast Asp (GUC)–Thr(GGU) region in Elymus trachycaulus complex, Elymus alaskanus and Elymus caninus. Biochem Syst Ecol 37:67–75. doi:10.1016/j.bse.2008.12.002

    Article  CAS  Google Scholar 

  • Sun G, Zhang X (2011) Origin of the H genome in StH-genomic Elymus species based on the single-copy nuclear gene DMC1. Genome 54:655–662. doi:10.1139/G11-036

    Article  PubMed  CAS  Google Scholar 

  • Sun G, Ni Y, Daley T (2008) Molecular phylogeny of RPB2 gene reveals multiple origin, geographic differentiation of H genome, and the relationship of the Y genome to other genomes in Elymus species. Mol Phylogenet Evol 46:897–907. doi:10.1016/j.ympev.2007.12.024

    Article  PubMed  CAS  Google Scholar 

  • Yen C, Yang JL (2013) Biosystematics of the Triticeae. Genus Elymus. China Agriculture Press, Beijing. 5:58–362 (in Chinese)

Download references

Acknowledgments

We thank Jacques Cayouette for the verification of the Leymus specimens in the herbarium.

Author information

Authors and Affiliations

  1. University of Ottawa, PO Box 450, Station A, Ottawa, ON, K1N 6N5, Canada

    Bernard R. Baum

  2. Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A OC6, Canada

    Tara Edwards

  3. Ottawa-Carleton Institute of Biology, University of Ottawa, PO Box 450, Station A, Ottawa, ON, K1N 6N5, Canada

    Douglas A. Johnson

Authors
  1. Bernard R. Baum
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tara Edwards
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Douglas A. Johnson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bernard R. Baum.

Ethics declarations

This research was funded in part by grants from the Natural Sciences and Engineering Research Council of Canada and the University of Ottawa to D.A.J.

BR Baum declares that he has no conflict of interest. DA Johnson declares that he has no conflict of interest. T Edwards declares that she has no conflict of interest.

No animals were used in these experiments.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 90 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Baum, B.R., Edwards, T. & Johnson, D.A. Diversity within the genus Elymus (Poaceae: Triticeae) II: analyses of variation within 5S nrDNA restrict membership in the genus to species with StH genomes. Mol Genet Genomics 291, 217–225 (2016). https://doi.org/10.1007/s00438-015-1096-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-015-1096-5

Keywords

Search

Navigation