Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

Gene

Volumn 499, Issue 1, 2012, Pages 194-201

  Huang, Chi Chun ^a   Hung, Kuo Hsiang ^b   Wang, Wei Kuang ^a   Ho, Chuan Wen ^a   Huang, Chao Li ^a   Hsu, Tsai Wen ^c   Osada, Naoki ^d   Hwang, Chi Chuan ^a   Chiang, Tzen Yuh ^a  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^b NATIONAL PINGTUNG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Taiwan)

^c ENDEMIC SPECIES RESEARCH INSTITUTE   (Taiwan)

^d NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Arabidopsis; Evolutionary rates; Generation time; Nonsynonymous substitutions; Populus; Synonoymous substitutions

Indexed keywords

ARABIDOPSIS; ARTICLE; ASPEN; CHLOROPLAST; CHROMOSOME; INTRON; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL;

ARABIDOPSIS; BRASSICACEAE; CELL NUCLEUS; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC MARKERS; GENETIC SPECIATION; GENETIC VARIATION; GENOME, PLANT; MUTATION RATE; ORGANELLES; PHYLOGENY; POPULUS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRASSICACEAE; POPULUS;

EID: 84862800191     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.02.037     Document Type: Article

References (67)

1. Andreasen K., Baldwin B.G. Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): Evidence from 18S-26S rDNA internal and external transcribed spacers. Mol. Biol. Evol. 2001, 18:936-944.
2. Azhagiri A.K., Maliga P. Exceptional paternal inheritance of plastids in Arabidopsis suggests that low-frequency leakage of plastids via pollen may be universal in plants. Plant J. 2007, 52:817-823.
3. Baumel A., Ainouche M.L., Bayer R.J., Ainouche A.K., Misset M.T. Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae). Mol. Phylogenet. Evol. 2002, 22:303-314.
4. Beck J.B., Schmuths H., Schaal B.A. Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamics. Mol. Ecol. 2008, 17:902-915.
5. Beilstein M.A., Nagalingum N.S., Clements M.D., Manchester S.R., Mathews S. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:18724-18728.
6. Bohlenius H., et al. CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 2006, 312:1040-1043.
7. Broughton R.E., Milam J.E., Roe B.A. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res. 2001, 11:1958-1967.
8. Chiang T.Y., Hung K.H., Hsu T.W., Wu W.L. Lineage sorting and phylogeography in Lithocarpus formosanus and L. dodonaeifolius (Fagaceae) from Taiwan. Ann. Mo. Bot. Gard. 2004, 91:207-222.
9. Chiang Y.C., et al. Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms. BMC Evol. Biol. 2009, 9:161-179.
10. Chiang Y.C., Hung K.H., Schaal B.A., Gest X.J., Hsu T.W., Chiang T.Y. Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex. Mol. Ecol. 2006, 15:765-779.
11. Clauss M.J., Koch M.A. Poorly known relatives of Arabidopsis thaliana. Trends Plant Sci. 2006, 11:449-459.
12. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities. of fresh leaf tissue. Phytochem. Bull. 1987, 19:11-15.
13. Drouin G., Daoud H., Xia J. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Mol. Phylogenet. Evol. 2008, 49:827-831.
14. Eckenwalder J.E. Systematics and evolution of Populus. Biology of Populus and its Implications for Management and Conservation 1996, 7-32. NRC Research Press, National Research Council of Canada, Ottawa, Canada. R.F. Stettler, H.D.J. Bradshaw, P.E. Heilman, T.M. Hinckley (Eds.).
15. El-Assal S.E.D., Alonso-Blanco C., Peeters A.J.M., Raz V., Koornneef M. A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2. Nat. Genet. 2001, 29:435-440.
16. Fay J.C., Wu C.I. Sequence divergence, functional constraint, and selection in protein evolution. Annu. Rev. Genomics Hum. Genet. 2003, 4:213-235.
17. Flowers J.M., Hanzawa Y., Hall M.C., Moore R.C., Purugganan M.D. Population genomics of the Arabidopsis thaliana flowering time gene network. Mol. Biol. Evol. 2009, 26:2475-2486.
18. Gaut B.S. Molecular clocks and nucleotide substitution rates in higher plants. Evol. Biol. 1998, 30:93-120.
19. Gaut B.S., Morton B.R., McCaig B.C., Clegg M.T. Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:10274-10279.
20. Graur D., Li W.H. Fundamentals of molecular evolution 1999, Sinauer, Sunderland.
21. Graur D., Li W.H. Fundamentals of molecular evolution 2000, Sinauer Associates, Inc, Sunderland, Massachusetts. 2nd ed.
22. Heuertz M., et al. Chloroplast DNA phylogeography of European ashes, Fraxinus sp (Oleaceae): Roles of hybridization and life history traits. Mol. Ecol. 2006, 15:2131-2140.
23. Hung K.H., Schaal B.A., Hsu T.W., Chiang Y.C., Peng C.I., Chiang T.Y. Phylogenetic relationships of diploid and polyploid species in Ludwigia sect. Isnardia (Onagraceae) based on chloroplast and nuclear DNAs. Taxon 2009, 58:1216-1225.
24. Hurst L.D. The Ka/Ks ratio: Diagnosing the form of sequence evolution. Trends Genet. 2002, 18:486-487.
25. Kay K.M., Whittall J.B., Hodges S.A. A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: An approximate molecular clock with life history effects. BMC Evol. Biol. 2006, 6:36-44.
26. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16:111-120.
27. Koch M.A., Haubold B., Mitchell-Olds T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 2000, 17:1483-1498.
28. Larkin M.A., et al. Clustal W and clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
29. Lexer C., Fay M.F., Joseph J.A., Nica M.S., Heinze B. Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): The role of ecology and life history in gene introgression. Mol. Ecol. 2005, 14:1045-1057.
30. Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 1993, 36:96-99.
31. Li W.H. Molecular evolution 1997, Sinauer Associates, Massachusetts.
32. Masuzaki S., Shigyo M., Yamauchi N. Complete assignment of structural genes involved in flavonoid biosynthesis influencing bulb color to individual chromosomes of the shallot (Allium cepa L.). Genes Genet. Syst. 2006, 81:255-263.
33. McCauley D.E., Sundby A.K., Bailey M.F., Welch M.E. Inheritance of chloroplast DNA is not strictly maternal in Silene vulgaris (Caryophyllaceae): Evidence from experimental crosses and natural populations. Am. J. Bot. 2007, 94:1333-1337.
34. Melotto-Passarin D.M., et al. Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region. Crop Breed Appl. Biotechnol. 2008, 8:85-95.
35. Mower J.P., Touzet P., Gummow J.S., Delph L.F., Palmer J.D. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol. Biol. 2007, 7:135-148.
36. Nekrutenko A., Makova K.D., Li W.H. The Ka/Ks ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study. Genome Res. 2002, 12:198-202.
37. Ohta T. An examination of the generation-time effect on molecular evolution. Proc. Natl. Acad. Sci. U. S. A. 1993, 90:10676-10680.
38. Olsen K.M., Halldorsdottir S.S., Stinchcombe J.R., Weinig C., Schmitt J., Purugganan M.D. Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 2004, 167:1361-1369.
39. Palmer J.D. Evolution of chloroplast and mitochondrial DNA in plants and algae. Molecular Evolutionary Genetics 1985, 131-240. Plenum Press. R.J. MacIntyre (Ed.).
40. Pearl S.A., Welch M.E., McCauley D.E. Mitochondrial heteroplasmy and paternal leakage in natural populations of Silene vulgaris, a gynodioecious plant. Mol. Biol. Evol. 2009, 26:537-545.
41. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
42. Posada D., Crandall K.A. MODELTEST: Testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
43. Ramos-Onsins S.E., Stranger B.E., Mitchell-Olds T., Aguade M. Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata. Genetics 2004, 166:373-388.
44. Rhee S.Y., et al. The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 2003, 31:224-228.
45. Saitou N., Nei M. The neighbor-loining method : A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
46. Savolainen V., et al. Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst. Biol. 2000, 49:306-362.
47. Slowinski J.B., Page R.D.M. How should species phylogenies be inferred from sequence data?. Syst. Biol. 1999, 48:814-825.
48. Smith S.A., Donoghue M.J. Rates of molecular evolution are linked to life history in flowering plants. Science 2008, 322:86-89.
49. Soria-Hernanz D.F., Fiz-Palacios O., Braverman J.M., Hamilton M.B. Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms. BMC Evol. Biol. 2008, 8:344.
50. Stadler T., Roselius K., Stephan W. Genealogical footprints of speciation processes in wild tomatoes: Demography and evidence for historical gene flow. Evolution 2005, 59:1268-1279.
51. Sterck L., Rombauts S., Jansson S., Sterky F., Rouze P., Van de Peer Y. EST data suggest that poplar is an ancient polyploid. New Phytol. 2005, 167:165-170.
52. Taberlet P., et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 2007, 35:e14.
53. Tajima F. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 1993, 135:599-607.
54. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
55. Tuskan G.A., et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313:1596-1604.
56. Unneberg P., Stromberg M., Lundeberg J., Jansson S., Sterky F. Analysis of 70,000 EST sequences to study divergence between two closely related Populus species. Tree Genet. Genom. 2005, 1:109-115.
57. Wang W.K., et al. Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: Evidence of genome-wide admixture. New Phytol. 2010, 188:488-500.
58. Weigel D., Nilsson O. A developmental switch sufficient for flower initiation in diverse plants. Nature 1995, 377:495-500.
59. Wikstrom N., Savolainen V., Chase M.W. Evolution of the angiosperms: Calibrating the family tree. Proc. R. Soc. Lond. B Biol. Sci. 2001, 268:2211-2220.
60. Wolfe K.H., Li W.H., Sharp P.M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:9054-9058.
61. Wolfe K.H., Sharp P.M., Li W.H. Rates of synonymous substitution in plant nuclear genes. J. Mol. Evol. 1989, 29:208-211.
62. Wright S.I., Gaut B.S. Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 2005, 22:1158-1158.
63. Wright S.I., Lauga B., Charlesworth D. Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol. Biol. Evol. 2002, 19:1407-1420.
64. Yang L., Gaut B.S. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol. Biol. Evol. 2011, 28:2359-2369.
65. Zhou R.C., et al. Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol. Biol. Evol. 2007, 24:2746-2754.
66. Zhu Q.H., Zheng X.M., Luo J.C., Gaut B.S., Ge S. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice. Mol. Biol. Evol. 2007, 24:875-888.
67. Zou X.H., et al. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol. 2008, 9:R49.