Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae)

Gene

Volumn 441, Issue 1-2, 2009, Pages 36-44

  Zhou, Dangwei ^a,b   Zhou, Jie ^c   Meng, Lihua ^b   Wang, Qingbiao ^c   Xie, He ^a   Guan, Yucheng ^a   Ma, Zeyang ^a   Zhong, Yang ^c   Chen, Fan ^a   Liu, Jianquan ^b  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b NORTHWEST INSTITUTE OF PLATEAU BIOLOGY   (China)

^c FUDAN UNIVERSITY   (China)

Author keywords

Adaptive evolution; COR15, Draba; Functional divergence; Gene duplication

Indexed keywords

AMINO ACID; COLD RESPONSE 15 PROTEIN; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ARTICLE; BRASSICACEAE; CLADISTICS; COLD TOLERANCE; CONTROLLED STUDY; GENE CLUSTER; GENE CONVERSION; GENE DUPLICATION; GENE SEQUENCE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PREDICTION; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; BRASSICACEAE; COLD TEMPERATURE; EVOLUTION; EVOLUTION, MOLECULAR; GENE CONVERSION; GENE DUPLICATION; MOLECULAR SEQUENCE DATA; PLANT PROTEINS;

ARABIDOPSIS THALIANA; BRASSICA; BRASSICACEAE; DRABA;

EID: 67349254731     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.06.024     Document Type: Article

References (62)

1. Al-shehbaz I.A. Novelties and notes on miscellaneous Asian Brassicaceae. Novon 14 (2004) 153-157
2. Al-Shehbaz I.A., Beilstein M.A., and Kellogg E.A. Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview. Pl. Syst. Evol. 259 (2006) 89-120
3. Artus N.N., Uemura M., Steponkus P.L., Gilmour S.J., Lin C., and Thomashow M.F. Constitutive expression of the cold-regulated Arabidopsis thaliana COR15a gene affects both chloroplast and protoplast freezing tolerance. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 13404-13409
4. Azocar A., Rada F., and Goldstein G. Freezing tolerance in Draba chionophila, a miniature caulescent rosette species. Oecologia 75 (1988) 156-160
5. Beilstein M.A., Al-Shehbaz I.A., and Kellogg E.A. Brassicaceae phylogeny and trichome evolution. Amer. J. Bot. 93 (2006) 607-619
6. Clark A.G. Invasion and maintenance of a gene duplication. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 2950-2954
7. Erixon P., and Oxelman B. Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene. Plos one 3 (2008) e1386
8. Force A., Lynch M., Pickett F.B., Amores A., Yan Y.L., and Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151 (1999) 1531-1545
9. Frankel N., Hasson E., Iusem N.D., and Rossi M.S. Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats. Mol. Biol. Evol. 20 (2003) 1955-1962
10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
11. Goldman N., and Yang Z.H. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11 (1994) 725-736
12. Grundt H.H., Kjølner S., Borgen L., Rieseberg L.H., and Brochmann C. High biological species diversity in the arctic flora. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 972-975
13. Gu X. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16 (1999) 1664-1674
14. Gu X., and Velden K.V. DIVERGE: phylogeny-based analysis for functional structural divergence of a protein family. Bioinformatics 18 (2002) 500-501
15. Hasegawa M., Kishino H., and Yano T. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
16. Hittinger C.T., and Carroll S.B. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449 (2007) 677-681
17. Huang R.F., Shen S.D., and Lu X.F. Chromosome numbers and ploidy of plants in the northeast Qinghai-Tibet Plateau. Acta Bot. Boreali-Occid. Sin. 16 (1996) 310-318
18. Hughes A.L. Adaptive evolution after gene duplication. Trends Genet. 18 (2002) 433-434
19. Kimura N. The Neutral Theory of Molecular Evolution (1983), Cambridge University Press, Cambridge, U.K
20. Kis-Papo T., Kirzhner V., Wasser S.P., and Nevo E. Evolution of genomic diversity and sex at extreme environments: fungal life under hypersaline Dead Sea stress. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 14970-14975
21. Koch M. Molecular systematics of the Brassicaceae: evidence from plastidic matK and Chs sequences. Amer. J. Bot. 88 (2001) 534-544
22. Koch M.A., and Al-Shehbaz I.A. Molecular data indicate complex intra- and intercontinental differentiation of American Draba (Brassicaceae). Ann. Missouri Bot. Gard. 89 (2002) 88-109
23. Koch M., Haubold B., and Mitchell-Olds T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis and related genera (Brassicaceae). Mol. Biol. Evol. 17 (2000) 1483-1498
24. Kong H.Z., Leebens-Mack J., Ni W.M., Pamphilis C.W., and Ma H. Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications. Mol. Biol. Evol. 21 (2004) 117-128
25. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17 (2001) 1244-1245
26. Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36 (1993) 96-99
27. Li W.H. Molecular Evolution (1997), Sinauer Associates Inc, Sunderland, Mass, U.S.A
28. Li P., and Bousquet J. Relative-rate test for nucleotide substitutions between two lineages. Mol. Biol. Evol. 9 (1992) 1185-1189
29. Lin C., and Thomashow M.F. DNA sequence analysis of a complementary DNA for cold-regulated Arabidopsis gene COR15 and characterization of the COR15 polypeptide. Plant Physiol. 99 (1992) 519-525
30. Morton B.R., Gaut B.S., and Clegg M.T. Evolution of alcohol dehydrogenase genes in the palm and grass families. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 11735-11739
31. Nei M. Selectionism and neutralism in molecular evolution. Mol. Biol. Evol. 22 (2005) 2318-2342
32. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
33. Nevo E. Evolution of genome-phenome diversity under environmental stress. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 6233-6240
34. Nielsen R. Molecular signatures of natural selection. Ann. Rev. Genet. 39 (2005) 197-218
35. Ohno S. Evolution by Gene Duplication (1970), Springer-Verlag Press, Heidelberg, Germany
36. Ohta T. Pattern of nucleotide substitution in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication. Genetics 134 (1993) 1271-1276
37. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
38. Sawyer S.A. Statistical tests for detecting gene conversion. Mol.Biol.Evol. 6 (1989) 526-538
39. Sawyer S.A. GENECONV: Statistical Tests for Detecting Gene Conversion-Version 1.81 (2000), Department of Mathematics, Washington University, St. Louis, Mo
40. Schein M., Yang Z.H., Mitchell-Olds T., and Schmid K.J. Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol. Biol. Evol. 21 (2004) 659-669
41. Schmidt T.R., Goodman M., and Grossman Y. Molecular evolution of the COX7A gene family in primates. Mol. Biol. Evol. 16 (1999) 619-626
42. Seki M., Kamei A., Yamaguchi-Shinozaki K., and Shinozaki K. Molecular responses to drought, salinity and frost: common and different paths for plant protection. Curr. Opin. Biotechnol. 14 (2003) 194-199
43. Steponkus P.L., Uemura M., Joseph R.A., Gilmour S.J., and Thomashow M.F. Mode of action of the COR15a gene on the freezing tolerance of Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 14570-14575
44. *: Phylogenetic Analysis Using Parsimony (PAUP and other methods).Version4.0 beta (2001), Sinauer Associates, Sunderland, Mass
45. Talyzina N.M., and Ingvarsson P.K. Molecular evolution of a small gene family of wound inducible Kunitz trypsin inhibitor in Populus. J. Mol. Evol. 63 (2006) 108-119
46. Terauchi R., and Konuma A. Microsatellite polymorphism in Dioscorea tokoro, a wild yam species. Genome 37 (1994) 794-801
47. Thomashow M.F. Role of cold responsive genes in plant freezing tolerance. Plant Physiol. 118 (1998) 1-7
48. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.J. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aides by quality analysis tools. Nucleic Acids Res. 25 (1997) 4875-4882
49. Walsh J.B. How often do duplicated genes evolve new functions?. Genetics 139 (1995) 421-428
50. Weretilnyk E., Orr W., White T.C., Iu B., and Singh J. Characterization of three related low-temperature-regulated cDNAs from Brassica napus. Plant Physiol. 101 (1993) 171-177
51. Wilhelm K.S., and Thomashow M.F. Arabidopsis thaliana cor15b, an apparent homologue of cor15a, is strongly responsive to cold and ABA, but not drought. Plant Mol. Biol. 23 (1993) 1073-1077
52. Wright B.E. Does selective gene activation direct evolution?. FEBS Lett. 402 (1997) 4-8
53. Yang Z.H. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15 (1998) 568-573
54. Yang Z.H., and Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19 (2002) 908-917
55. Yang Z.H., Kumar S., and Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141 (1995) 1641-1650
56. Yang J., Huang J.X., Gu H.Y., Yang Z., and Yang Z. Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol. Biol. Evol. 19 (2002) 1752-1759
57. Yang Z.H., Wong S.W., and Nielsen R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22 (2005) 1107-1118
58. Yang J., Wang Z.L., Zhao X.Q., Wang D.P., Qi D.L., Xu B.H., Ren Y.H., and Tian H.F. Natural selection and adaptive evolution of Leptin in the Ochotona family driven by the cold environmental stress. PLoS one 3 (2008) e1472
59. Yuri T., Kimball R.T., Braun E.L., and Braun M.J. Duplication of accelerated evolution and growth hormone gene in passerine birds. Mol. Biol. Evol. 25 (2008) 352-361
60. Zhang J.Z., Zhang Y.P., and Rosenberg H.F. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30 (2002) 411-415
61. Zhong Y., Zhao Q., Shi S.H., Huang Y.L., and Hasegawa M. Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives. Ecol. Lett. 5 (2002) 427-432
62. Zhou T.Y. Crucifereae. Flora Reipublicae Popularis Sinicae 33 (1987), Science Press, Beijing, China