Czech J. Genet. Plant Breed., 2005, 41(10):39-51 | DOI: 10.17221/6131-CJGPB
Inferring genetic relationship among haplomes in Triticeae: The utility of the 5S DNA units with examples
Keywords: cloning; sequence alignment; maximum likelihood; Bayesian analysis; evolutionary inference; unit classes; twat of orthology
Published: December 31, 2005 Show citation
References
- A S.F., G W., M W., M E.W., L D.J. (1990): Basic local alignment search tool. Journal of Molecular Biology, 215: 403-410.
Go to original source...
Go to PubMed...
- A R., B B.R. (1992): Evolution of the Nor and 5SDna loci in the Triticeae. In: S P.S., S D.E., D J.J. (eds.): Molecular Systematics of Plants. Chapman & Hall, New York, U.S.A.: 92-116.
Go to original source...
- A L., B A.-C., L J., S B. (2003): Bioinformatics, 10 (Suppl. 1): i7-i15.
- B B.R. (1992): Combining trees as a way of combining datasets for phylogenetic inference, and the desirability of combining gene trees. Taxon, 41: 3-10.
Go to original source...
- B B.R., A R. (1992): Evolutionary change at the 5S DNA loci of species in the Triticeae. Plant Systematics and Evolution, 183: 195-208.
Go to original source...
- B B.R., B L.G. (1997): The molecular diversity of the 5S rRNA gene in Kengyilia alatavica (Drobov) J.L. Yang, Yen & Baum (Poaceae: Triticeae): potential genomic assignment of different rDNA units. Genome, 40: 215-228.
Go to original source...
Go to PubMed...
- B B.R., B L.G. (2000): The 5S rDNA units in Kengyilia (Poaceae: Triticeae): diversity of the non-transcribed spacer and genomic relationships. Canadian Journal of Botany, 78: 1571-1579.
Go to original source...
- B B.R., B L.G. (2001): The 5S rRNA gene sequence variation in wheats and some polyploid wheat progenitors (Poaceae: Triticeae). Genetic Resources and Crop Evolution, 48: 35-51.
Go to original source...
- B B.R., J D.A. (1994): The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare). Genome, 37: 992-998.
Go to original source...
Go to PubMed...
- B B.R., J D.A. (1996): The 5S rRNA gene units in ancestral two-row barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units in cultivated barley (H. vulgare L.). Genome, 39: 140-149.
Go to original source...
Go to PubMed...
- B B.R., J D.A. (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.
Go to original source...
Go to PubMed...
- B B.R., J D.A. (1999): The 5S rRNA gene in wall barley (Hordeum murinum L. sensu lato): sequence variation among repeat units and relationship to the Y haplome in the genus Hordeum (Poaceae: Triticeae). Genome, 42: 854-866.
Go to original source...
Go to PubMed...
- B B.R., J D.A. (2000): The 5S rRNA gene units in the native New World annual Hordeum species (Triticeae: Poaceae). Canadian Journal of Botany, 78: 1590-1602.
Go to original source...
- B B.R., J D.A. (2002): A comparison of the 5S rDNA diversity in the Hordeum brachyantherumcalifornicum complex with those of the eastern Asiatic Hordeum roshevitzii and the South American Hordeum cordobense (Triticeae: Poaceae). Canadian Journal of Botany, 80: 752-762.
Go to original source...
- B B.R., J D.A. (2003): The South African Hordeum capense is more closely related to some American Hordeum species than to the European Hordeum secalinum: a perspective based on the 5S DNA units (Triticeae: Poaceae). Canadian Journal of Botany, 81: 1-11.
Go to original source...
- B B.R., R M.A. (2004): The MRP method. In: B -E O.R.P. (ed.): Phylogenetic Supertrees. Combining information to reveal the tree of life. Kluwer, Dordrecht, the Netherlands: 17-34.
Go to original source...
- B B.R., B L.G., J D.A., A A.V. (2003): Molecular diversity of the 5S rDNA units in the Elymus dahuricus complex (Poaceae: Triticeae) supports the genomic constitution of St, Y, and H haplomes. Canadian Journal of Botany, 81: 1091-1103.
Go to original source...
- B B.R., B L.G., B A., R O., N E. (2004): The utility of the nontranscribed spacer of 5S rDNA units grouped into unit classes assigned to haplomes - a test on cultivated wheat and wheat progenitors. Genome, 47: 590-599.
Go to original source...
Go to PubMed...
- B B.R., J D.A., B L.G. (2001): Defining groups among multicopy genes prior to inferring phylogeny, with special emphasis on the Triticeae (Poaceae). Hereditas, 135: 123-138.
Go to original source...
Go to PubMed...
- B B.R., J D.A., B L.G. (2005): Ancient differentiation of the H and I haplomes in diploid Hordeum species based on 5S rDNA. Genome, 48: 610´618.
Go to original source...
Go to PubMed...
- B R., F J., L T. (1986): Meiosis in Interspecific Hordeum hybrids. I. Diploid combinations. Canadian Journal of Genetics and Cytology, 28: 525-535.
Go to original source...
- B R., F J., L T. (1987): Meiosis in Interspecific Hordeum hybrids. II. Triploid hybrids. Evolutionary Trends in Plants, 1: 41-50.
- B R., J N. (1991): Interspecific hybrids within the genus Hordeum. In: G P.K., T T. (eds.): Chromosome Engineering in Plants: Genetics, Breeding, Evolution, Part A. Elsevier, Amsterdam, the Netherlands: 411-431.
Go to original source...
- E J.A. (1998): Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research, 8: 163-167.
Go to original source...
Go to PubMed...
- F J. (1985): Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783-791.
Go to original source...
Go to PubMed...
- F J. (2004): Inferring phylogenies. Sinauer Associates, Sunderland.
- G N. (1990): Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis. Systematic Zoology, 39: 345-361.
Go to original source...
- H M., K K., Y T. (1985): Dating the human-ape spli ing by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22: 160-174.
Go to original source...
Go to PubMed...
- H J.P., R F. (2001): MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754-755.
Go to original source...
Go to PubMed...
- K A.G. (1989): A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology, 38: 7-25.
Go to original source...
- K A.G. (2004): On total evidence: for the record. Cladistics, 20: 205-207.
Go to original source...
Go to PubMed...
- O G.J., M H., H R., O R. (1994): FastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Computer Applications in the Biosciences, 10: 41-48.
Go to original source...
Go to PubMed...
- P G., S O. (2004): On the origin of the tetraploid species Hordeum capense and H. secalinum (Poaceae). Systematic Botany, 29: 862-873.
Go to original source...
- P D. (2003): Selecting models of evolution. Theory. In: S M.; V A.-M. (eds.): The Phylogenetic Handbook. A practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge, U.K.
- P D., C K.A. (1998): Modeltest: Testing the model of DNA substitution. Bioinformatics, 14: 817-818.
Go to original source...
Go to PubMed...
- R M.A. (1992): Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution, 1: 53-58.
Go to original source...
Go to PubMed...
- S N., N M. (1987): The neighbour-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4: 406-425.
Go to PubMed...
- S R.L., C R.C., W J.F. (2004): Use of nuclear genes for phylogeny reconstruction in plants. Australian Journal of Botany, 17: 145-170.
Go to original source...
- S D.L. (1998): PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sinauer Associates, Sunderland. Massachuse s.
- T R.L., N D.A., G I.V., T T.A., S U.T., R B.S., K B., G M.Y., F N.D., K E.V. (2001): The COG database: new developments in phylogenetic classification of protein from complete genomes. Nucleic Acid Research, 29: 22-28.
Go to original source...
Go to PubMed...
- W S., L, G N. (2001): Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends in Genetics, 17: 262-272.
Go to original source...
Go to PubMed...
- W W. (1996): Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics, 12: 1-9.
Go to original source...
- W W.C. (1999): Fixed character States and the optimization of molecular sequence data. Cladistics, 15: 379-385.
Go to original source...
Go to PubMed...
- W W., G D., D L J. (2003): POY version 3.011 available at h p://research.amnh.org/ scicomp/projects/poy.php.
- Y Z. (1994): Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39: 306-314.
Go to original source...
Go to PubMed...
- Y -P C., V J., M J. (1985): Improved M13 phage cloning vectors and host strains: nucleotide sequence of M13mp18 and pUC19 vectors. Gene, 33: 103-119.
Go to original source...
Go to PubMed...
- Z C.M., E S.R. (2002): RIO: Analyzing proteomes by automated phylogenomics using resampled inference orthologs. BMC Bioinformatics, 3: 14-33.
Go to original source...
Go to PubMed...
This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.