Physicochemical evolution and positive selection of the gymnosperm matK proteins

Journal of Genetics

Volumn 89, Issue 1, 2010, Pages 81-89

  Hao, Da Cheng ^a   Mu, Jun ^a   Chen, Shi Lin ^b   Xiao, Pei Gen ^b  

^a DALIAN JIAOTONG UNIVERSITY   (China)

^b INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

Author keywords

Cephalotaxaceae; chloroplast matK protein; physicochemical evolution; Pinaceae; positive selection; Taxaceae

Indexed keywords

AMINO ACID; PLANT DNA; VEGETABLE PROTEIN; CODON;

ARTICLE; BAYES THEOREM; CODON; GENETIC SELECTION; GENETICS; GYMNOSPERM; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENE; STATISTICAL MODEL;

AMINO ACIDS; BAYES THEOREM; CODON; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GYMNOSPERMS; LIKELIHOOD FUNCTIONS; PHYLOGENY; PLANT PROTEINS; SELECTION, GENETIC;

CEPHALOTAXACEAE; GYMNOSPERMAE; PINACEAE; TAXACEAE;

EID: 77955699285     PISSN: 00221333     EISSN: 09737731     Source Type: Journal    
DOI: 10.1007/s12041-010-0014-1     Document Type: Article

References (31)

1. Abascal F., Zardoya R. and Posada D. 2005 ProtTest: selection of best-fit models of protein evolution. Bioinformatics21, 2104-2105.
2. Barthet M. M. and Hilu K. W. 2008 Evaluating evolutionary constraint on the rapidly evolving gene matK using protein composition. J. Mol. Evol. 66, 85-97.
3. Chaw S. M., Walters T. W., Chang C. C., Hu S. H. and Chen S. H. 2005 A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region. Mol. Phylogenet. Evol. 37, 214-234.
4. Doron-Faigenboim A. and Pupko T. A. 2007 Combined empirical and mechanistic codon model. Mol. Biol. Evol. 24, 388-397.
5. Duffy A. M., Kelchner S. A. and Wolf P. G. 2009 Conservation of selection on matK following an ancient loss of its flanking intron. Gene438, 17-25.
6. Freudenstein J. V. and Senyo D. M. 2008 Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae). Am. J. Bot. 95, 498-505.
7. Gromiha M. M. and Ponnuswamy P. K. 1993 Relationship between amino acid properties and protein compressibility. J. Theo. Biol. 165, 87-100.
8. Hao D. C., Huang B. and Yang L. 2008a Phylogenetic relationships of the genus Taxus inferred from chloroplast intergenic spacer and nuclear coding DNA. Biol. Pharm. Bull. 31, 260-265.
9. Hao D. C., Xiao P. G., Huang B., Ge G. B. and Yang L. 2008b Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences. Plant Syst. Evol. 276, 89-104.
10. Hao D. C., Huang B., Chen S. L. and Mu J. 2009a Evolution of the chloroplast trnL-trnF region in the gymnosperm lineages Taxaceae and Cephalotaxaceae. Biochem. Genet. 47, 351-369.
11. Hao D. C., Yang L. and Huang B. 2009b Molecular evolution of paclitaxel biosynthetic genes TS and DBAT of Taxus species. Genetica135, 123-135.
12. Hidalgo O., Garnatje T., Susanna A. and Mathez J. 2004 Phylogeny of Valerianaceae based on matK and ITS markers, with reference to matK individual polymorphism. Ann. Bot. (Lond). 93, 283-293.
13. Kosakovsky Pond S. L. and Frost S. D. 2005a Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22, 1208-1222.
14. Kosakovsky Pond S. L. and Frost S. D. 2005b Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics21, 2531-2533.
15. Kosakovsky Pond S. L. and Frost S. D. 2005c A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol. 22, 478-485.
16. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H. et al. 2007 ClustalW and ClustalX version 2. Bioinformatics23, 2947-2948.
17. McClellan D. A. and McCracken K. G. 2001 Estimating the in-fluence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol. Biol. Evol. 18, 917-925.
18. McClellan D. A., Palfreyman E. J., Smith M. J., Moss J. L., Christensen R. G. and Sailsbery J. K. 2005 Physiocochemical evolution and molecular adaptation of the cetacean and artiodactyls cytochrome b proteins. Mol. Biol. Evol. 22, 437-455.
19. Mohr G., Perlman P. S. and Lambowitz A. M. 1993 Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acid Res. 21, 4991-4997.
20. Müller K. F., Borsch T. and Hilu K. W. 2006 Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F and rbcL in basal angiosperms. Mol. Phylogenet. Evol. 41, 99-117.
21. Neuhaus H. and Link G. 1987 The chloroplast tRNALys (UUU) gene from mustard (Sinapsis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Curr. Genet. 11, 251-257.
22. Posada D. 2006 ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res. 34, 700-703.
23. Ronquist F. and Huelsenbeck J. P. 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics19, 1572-1574.
24. Rønsted N., Law S., Thornton H., Fay M. F. and Chase M. W. 2005 Molecular phylogenetic evidence for the monophyly of Fritillaria and Lilium (Liliaceae; Liliales) and the infrageneric classification of Fritillaria. Mol. Phylogenet. Evol. 35, 509-527.
25. Stamatakis A., Hoover P. and Rougemont J. 2008 A rapid bootstrap algorithm for the RA×MLWeb-Servers. Syst. Biol. 75, 758-771.
26. Vogel J., Borner T. and Hess W. 1999 Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants. Nucleic Acids Res. 27, 3866-3874.
27. Wernersson R. and Pedersen A. G. 2003 RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 31, 3537-3539.
28. Woolley S., Johnson J., Smith M. J., Crandall K. A. and McClellan D. A. 2003 TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics19, 671-672.
29. Yang Z. 2007 PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591.
30. Yang Z., Nielsen R. and Goldman N. 2000 Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics155, 431-449.
31. Young N. D. and de Pamphilis C. W. 2000 Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants. Mol. Biol. Evol. 17, 1933-1941.