Molecular evolution and positive Darwinian selection of the chloroplast maturase matK

Journal of Plant Research

Volumn 123, Issue 2, 2010, Pages 241-247

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

^a DALIAN JIAOTONG UNIVERSITY   (China)

^b INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

Author keywords

Chloroplast matK; Maximum likelihood; Positive selection

Indexed keywords

MESSENGER RIBONUCLEIC ACID MATURASE; NUCLEOTIDYLTRANSFERASE; RIBONUCLEASE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CHLOROPLAST; ENZYMOLOGY; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PLANT; STATISTICAL MODEL;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CHLOROPLASTS; ENDORIBONUCLEASES; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; NUCLEOTIDYLTRANSFERASES; PLANTS; SELECTION, GENETIC;

EMBRYOPHYTA;

EID: 77951499889     PISSN: 09189440     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10265-009-0261-5     Document Type: Article

References (24)

1. APG II (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc 141: 399-436.
2. Barthet MM, Hilu KW (2008) Evaluating evolutionary constraint on the rapidly evolving gene matK using protein composition. J Mol Evol 66: 85-97.
3. Chaw SM, Walters TW, Chang CC, Hu SH, Chen SH (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, Pupko TA (2007) Combined empirical and mechanistic codon model. Mol Biol Evol 24: 388-397.
5. Duffy AM, Kelchner SA, Wolf PG (2009) Conservation of selection on matK following an ancient loss of its flanking intron. Gene 438: 17-25.
6. Freudenstein JV, Senyo DM (2008) Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae). Am J Bot 95: 498-505.
7. Gadek PA, Wilson PG, Quinn CJ (1996) Phylogenetic reconstruction in Myrtaceae using matK, with particular reference to the position of Psiloxylon and Heteropyxis. Aust Syst Bot 9: 283-290.
8. Hao DC, Xiao PG, Huang B, Ge GB, Yang L (2008) 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.
9. Hausner G, Olson R, Simon D, Johnson I, Sanders ER, Karol KG, McCourt RM, Zimmerly S (2006) Origin and evolution of the chloroplast trnK (matK) intron: a model for evolution of group II intron RNA structures. Mol Biol Evol 23: 380-391.
10. Hidalgo O, Garnatje T, Susanna A, Mathez J (2004) Phylogeny of Valerianaceae based on matK and ITS markers, with reference to matK individual polymorphism. Ann Bot (Lond) 93: 283-293.
11. Hilu KW, Borsch T, Müller K, Soltis DE, Soltis PS, Savolainen V et al (2003) Angiosperm phylogeny based on matK sequence information. Am J Bot 90: 1758-1776.
12. Kapralov MV, Filatov DA (2007) Widespread positive selection in the photosynthetic Rubisco enzyme. BMC Evol Biol 7: 73.
13. Mohr G, Perlman PS, Lambowitz AM (1993) Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res 21: 4991-4997.
14. Müller KF, Borsch T, Hilu KW (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.
15. Lys (UUU) gene from mustard (Sinapsis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Curr Genet 11: 251-257.
16. Okuyama Y, Kato M (2009) Unveiling cryptic species diversity of flowering plants: successful biological species identification of Asian Mitella using nuclear ribosomal DNA sequences. BMC Evol Biol 9: 105.
17. Okuyama Y, Fujii N, Wakabayashi M, Kawakita A, Ito M, Watanabe M, Murakami N, Kato M (2005) Nonuniform concerted evolution and chloroplast capture: heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (Saxifragaceae). Mol Biol Evol 22: 285-296.
18. Rønsted N, Law S, Thornton H, Fay MF, Chase MW (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.
19. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
20. Vogel J, Borner T, 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.
21. Wernersson R, Pedersen AG (2003) RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res 31: 3537-3539.
22. Xiang QY, Soltis DE, Soltis PS (1998) Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences. Am J Bot 85: 285-297.
23. Yang Z (2007) PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
24. Young ND, de Pamphilis CW (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.