Molecular evolution of plant haemoglobin: Two haemoglobin genes in nymphaeaceae Euryale ferox

Journal of Evolutionary Biology

Volumn 17, Issue 1, 2004, Pages 48-54

  Guldner, E ^a,b   Desmarais, E ^a   Galtier, N ^a   Godelle, B ^a  

^a UNIV MONTPELLIER   (France)

^b CNRS   (France)

Author keywords

Duplication; Nonsynonymous substitution rate; Nymphaeaceae; Plant haemoglobin; Symbiosis

Indexed keywords

HEMOGLOBIN; PRIMER DNA;

HEMOGLOBIN;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; NYMPHAEACEAE; PHYLOGENY; STATISTICAL MODEL;

BAYES THEOREM; CLUSTER ANALYSIS; DNA PRIMERS; EVOLUTION, MOLECULAR; HEMOGLOBINS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; NYMPHAEACEAE; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EMBRYOPHYTA; EURYALE FEROX; LILIOPSIDA; MAGNOLIOPHYTA; NYMPHAEACEAE;

EID: 0842309237     PISSN: 1010061X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1420-9101.2004.00658.x     Document Type: Article

References (38)

1. Andersson, C.R., Jensen, E.O., Llewellyn, D.J., Dennis, E.S. & Peacock, W.J. 1996. A new haemoglobin gene from soybean : a role for haemoglobin in all plants. Proc. Natl. Acad. Sci. U. S. A. 93: 5682-5687.
2. Andersson, C.R., Llewellyn, D.J., Peacock, W.J. & Dennis, E.S. 1997. Cell-specific expression of the promoters of two nonlegume haemoglobin genes in a transgenic legume, Lotus corniculatus. Plant Physiol. 113: 45-57.
3. Appleby, C. 1992. The origin and functions of haemoglobin in plants. Sci. Progress 76: 365-398.
4. Arredondo-Peter, R., Hargrove, M.S., Moran, J.F., Sarath, G. & Klucas, R.V. 1998. Plant haemoglobins. Plant Physiol. 118 1121-1125.
5. Arredondo-Peter, R., Ramirez, M., Sarath, G. & Klucas, R.V. 2000. Sequence analysis of an ancient haemoglobin cDNA isolated from the moss Physcomitrella patens. Plant Physiol. 122: 1457.
6. Bever, J.D. & Simms, E.L. 2000. Evolution of nitrogen fixation in spatially structured populations of Rhizobium. Heredity 85: 366-372.
7. Bogusz, D., Appleby, C., Landsmann, J., Dennis, E.S., Trinick, M.J. & Peacock, W.J. 1988. Functioning haemoglobin genes in non-nodulating plants. Nature 331: 178-180.
8. Bogusz, D., Llewellyn, D.J., Craig, S., Dennis, E.S., Appleby, C. & Peacock, W.J. 1990. Nonlegume haemoglobin genes retain organ-specific expression in heterologous transgenic plants. The Plant Cell 2: 633-641.
9. Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. 1978. A model of evolutionary change in proteins; Matrices for detecting distant relationships. In: Atlas of protein sequence and structure, pp. 345-358. National Biomedical Research Foundation, Washington, DC.
10. Denison, R.F. 2000. Legume sanctions and the evolution of symbiotic cooperation by Rhizobia. Am. Nat. 156: 567-576.
11. Duff, S.M.G., Guy, P.A., Nie, X., Durnin, D.C., Hill, R.D. & Nie, W.Z. 1998. Haemoglobin expression in germinating barley. Seed Sci. Res. 8: 431-436.
12. Felsenstein, J. 1978. The number of evolutionary trees. Syst. Zool. 27: 27-33.
13. Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (version 3.2). Cladistics 5: 164-166.
14. Franche, C., Diouf, D., Laplaze L., Auguy, F., Frutz, T., Rio, M., Duhoux, E. & Bogusz, D. 1998. Soybean (lbc3), Parasponia, and Trema haemoglobin gene promoters retain symbiotic specificity in transgenic Casuarinaceae : implications for haemoglobin gene evolution and root nodule symbioses. Mol. Plant-Microbe Interact 11: 887-894.
15. Galtier, N., Gouy, M. & Gautier, C. 1996. SEAVIEW and PHYLO_WIN: two graphic tools sequence alignment and molecular phylogeny. CABIOS 12: 543-548.
16. Goldman, N. & Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Biol. Mol. Evol. 11: 725-736.
17. Hendriks, T., Scheer, I., Quillet, M.-C., Randoux, B., Delbreil, B., Vasseur, J. & Hilbert, J.-L. 1998. A nonsymbiotic haemoglobin gene is expressed during somatic embryogenesis in Cichorium. Biochemica et Biophysica Acta 1143: 193-197.
18. Huelsenbeck, J. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
19. Hunt, R.A., Watts, R.A., Trevaskis, B., Llewellyn, D.J., Burnell, J., Dennis, E.S. & Peacock, W.J. 2001. Expression and evolution of functionally distinct haemoglobin genes in plants. Plant Mol. Biol. 47: 677-692.
20. Jacobsen-Lyon, K., Jensen, E.O., Jorgensen, J.-E., Marcker, K.A., Peacock, W.J. & Dennis, E.S. 1995. Symbiotic and nonsymbiotic haemoglobin genes of Casuarina glauca. The Plant Cell 7: 213-223.
21. Jensen, E.O., Paludan, K., Hyldig-Nielsen, J.J., Jorgensen, P. & Marcker, K.A. 1981. The structure of a chromosomal leghaemoglobin gene from soybean. Nature 291: 677-679.
22. Jones, D.T., Taylor, W.R. & Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8: 275-282.
23. Landsmann, J., Dennis, E.S., Higgins, T.J.V., Appleby, C., Kortt, A. & Peacock, W.J. 1986. Common evolutionary origin of legume and non-legume plant haemoglobins. Nature 324: 166-168.
24. Ota, S. & Li, W. 2001. NJML+ : an extension of the NJML method to handle protein sequence data and computer software implementation. Mol. Biol. Evol. 18: 1983-1992.
25. Robinson-Rechavi, M. & Huchon, D. 2000. RRTree : relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16: 296-297.
26. Robinson-Rechavi, M., Gouy, M., Gautier, C. & Mouchiroud, D. 1998. Sensitivity of the relative-rate test to taxonomic sampling. Mol. Biol. Evol. 15: 1091-1098.
27. Saitou, N. & Nei, M. 1987. The neighbor-joining method : a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
28. Soltis, P.S., Soltis, D.E. & Chase, M.W. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402: 402-403.
29. Soltis, D.E., Soltis, P.S., Chase, M.W., Mort, M.E., Albach, D.C., Zanis, M., Savolainen, V., Hahn, W.H., Hoot, S.B., Fay, M.F., Axtel, M., Swensen, S.M., Prince, L., Kress, W.J., Nixon, K.C. & Farris, J. 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133, 381-461.
30. Strozycki, P.M. & Legocki, A.B. 1995. Leghaemoglobins from an evolutionarily old legume, Lupinus luteus. Plant Science 110: 83-93.
31. Strozycki, P.M., Karlowski, W.M., Dessaux, Y., Petit, A. & Legocki, A.B. 2000. Lupine leghaemoglobin I: expression in transgenic Lotus and tobacco tissues. Mol. Gen. Genet. 263: 173-182.
32. Szabados, L., Ratet, P., Grunenberg, B. & Bruijn, F.G. 1990. Functional analysis of the Sesbania rostrata leghaemoglobin glb3 gene 5′-upstream region in transgenic Lotus corniculatus and Nicotiana tabacum plants. Plant Cell 2: 973-986.
33. Trevaskis, B., Watts, R.A., Andersson, C.R., Llewellyn, D.J., Hargrove, M.S., Olson, J.S., Dennis, E.S. & Peacock, W.J. 1997. Two haemoglobin genes in Arabidopsis thaliana: the evolutionary origins of leghaemoglobins. Proc. Natl. Acad. Sci. U. S. A. 94: 12230-12234.
34. West, S.A., Kiers, E.T., Simms, E.L. & Denison, R.F. 2002. Sanctions and mutualism stability: why do rhizobia fix nitrogen? Proc. Natl. Acad. Sci. U. S. A. 269: 685-694.
35. Wu, C. & Li, W.H. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. U. S. A. 82: 1741-1745.
36. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13: 555-556.
37. Yang, Z. (2000). Phylogenetic Analysis by Maximum Likelihood (PAML), Version 3.0. University College London, London, England (http://abacus.gene.ucl. ac.uk/software/paml.html)
38. Yang, Z. & Nielsen, R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17: 32-43.