Genome size is not correlated with effective population size in the oryza species

Evolution

Volumn 66, Issue 10, 2012, Pages 3302-3310

  Ai, Bin ^a,b   Wang, Zhao Shan ^a   Ge, Song ^a,b  

^a INSTITUTE OF BOTANY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Effective population size; Genome size; Oryza; Polymorphism

Indexed keywords

CORRELATION; DEMOGRAPHY; EFFECTIVE POPULATION SIZE; GENOME; HETEROGENEITY; MUTATION; NEON; PHYLOGENETICS; POLYMORPHISM; RICE; STOCHASTICITY;

ARTICLE; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; GENOME SIZE; PLANT GENOME; POPULATION DENSITY; RICE;

GENOME SIZE; GENOME, PLANT; ORYZA SATIVA; POPULATION DENSITY; SEQUENCE ANALYSIS, DNA;

ORYZA;

EID: 84867099919     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2012.01674.x     Document Type: Article

References (59)

1. Ammiraju, J. S. S., M. Luo, J. L. Goicoechea, W. Wang, D. Kudrna, C. Mueller, J. Talag, H. Kim, N. B. Sisneros, B. Blackmon, et al. 2006. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res. 16:140-147.
2. Ammiraju, J. S. S., F. Lu, A. Sanyal, Y. Yu, X. Song, N. Jiang, A. C. Pontaroli, T. Rambo, J. Currie, K. Collura, et al. 2008. Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical dataset. Plant Cell 20:3191-3209.
3. Barbier, P. 1989. Genetic variation and ecotypic differentiation in the wild rice species Oryza rufipogon. II. influence of the mating system and life-history traits on the genetic structure of populations. Jap. J. Genet. 64:273-285.
4. Bennett, M. D., and I. J. Leitch 2005a. Plant DNA C-values database (release 4.0, Dec. 2005). Royal Botanic Gardens, Kew. Available at: http://data.kew.org/cvalues/.
5. Bennett, M. D., and I. J. Leitch. 2005b. Genome size evolution in plants. Pp. 89-162 in T. R. Gregory, ed. The evolution of the genome. Elsevier, Amsterdam
6. Boussau, B., J. M. Brown, and M. K. Fujita 2011. Nonadaptive evolution of mitochondrial genome size. Evolution 65:2706-2711.
7. Charlesworth, B. 2008. The origin of genomes-not by natural selection? Curr. Biol. 18:R140-R141.
8. Charlesworth B. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 10:195-205.
9. Charlesworth, B., and N. Barton 2004. Genome size: does bigger mean worse? Curr. Biol. 14:R233-R235.
10. Daubin, V., and N. A. Moran 2004. Comment on "The Origins of Genome Complexity". Science 306:978a.
11. Doolittle, W. F., and C. Sapienza 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603.
12. Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
13. Flowers, J. M., and M. D. Purugganan 2008. The evolution of plant genomes-scaling up from a population perspective. Curr. Opin. Genet. Dev. 18:565-570.
14. Fu, Y. X., and W. H. Li 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
15. Gao, L. Z., S. Ge, and D. Y. Hong 2001. High levels of genetic differentiation of Oryza officinalis Wall. et Watt. from China. J. Heredity 92:511-516.
16. Garland, T., P. H. Harvey, and A. R. Ives 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst. Biol. 41:18-32.
17. Gaut, B. S., B. R. Morton, B. C. McCaig, and M. T. Clegg 1996. 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. USA 93:10274-10279.
18. Ge, S., T. Sang, B. R. Lu, and D. Y. Hong 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA 96:14400-14405.
19. Gregory, T. R., and P. D. N. Hebert 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res. 9:317-324.
20. Gregory, T. R., and J. D. S. Witt 2008. Population size and genome size in fishes: a closer look. Genome 51:309-313.
21. Hawkins, J. S., C. E. Grover, and J. F. Wendel 2008. Repeated big bangs and the expanding universe: directionality in plant genome size evolution. Plant Sci. 174:557-562.
22. Hudson, R. R., and N. L. Kaplan 1985. Statistical properties of the number of recombination events in the history of a sample of DNA-sequences. Genetics 111:147-164.
23. Hudson, R. R., M. Kreitman, and M. Aguade 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
24. Jayasuriya, A. H. M., and D. A. Vaughan 2003. Conservation and use of crop wild relatives. Proceedings of the joint Department of Agriculture, Sri Lanka and National Institute of Agrobiological Sciences, Japan workshop. Plant Genetic Resource Center, Department of Agriculture, Peradeniya, Sri Lanka
25. Kuo, C. H., N. A. Moran, and H. Ochman 2009. The consequences of genetic drift for bacterial genome complexity. Genome Res. 19:1450-1454.
26. Li, Z. M., X. M. Zheng, and S. Ge 2011. Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences. Theor. Appl. Genet. 123:21-31.
27. Librado, P., and J. Rozas 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
28. Lu, F., J. S. S. Ammiraju, A. Sanyal, S. L. Zhang, R. T. Song, J. F. Chen, G. S. Li, Y. Sui, X. Song, Z. K. Cheng, et al. 2009. Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc. Natl. Acad. Sci. USA 106:2071-2076.
29. Lynch, M. 2007. The origins of genome architecture. Sinauer Associates, Sunderland, MA
30. Lynch M.. 2011. Statistical inference on the mechanisms of genome evolution. PLoS Genet. 7: e1001389.
31. Lynch, M., and J. S. Conery 2003. The origins of genome complexity. Science 302:1401-1404.
32. Maddison, W. P., and D. R. Maddison 2010. Mesquite: a modular system for evolutionary analysis, v. 2.74. Available at: http://mesquiteproject.org.
33. Midford, P. E., T. Garland Jr, and W. Maddison 2002. PDAP:PDTREE package for Mesquite, v. 1.00. Available at: http://mesquiteproject.org/pdap_mesquite/.
34. Miyabayashi, T., K. I. Nonomura, H. Morishima, and N. Kurata 2007. Genome size of twenty wild species of Oryza determined by flow cytometric and chromosome analyses. Breed. Sci. 57:73-78.
35. Oliver, M. J., D. Petrov, D. Ackerly, P. Falkowski, and O. M. Schofield 2007. The mode and tempo of genome size evolution in eukaryotes. Genome Res. 17:594-601.
36. Pagel, M., and A. Meade 2009. BayesTraits. University of Reading, UK. Available at: http://www.evolution.rdg.ac.uk/BayesTraits.html.
37. Petrov, D. A. 2001. Evolution of genome size: new approaches to an old problem. Trends Genet. 17:23-28.
38. Petrov D.A.. 2002. Mutational equilibrium model of genome size evolution. Theor. Popul. Biol. 61:531-544.
39. Piegu, B., R. Guyot, N. Picault, A. Roulin, A. Saniyal, H. Kim, K. Collura, D. S. Brar, S. Jackson, R. A. Wing, et al. 2006. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16:1262-1269.
40. Qian, W., S. Ge, and D. Y. Hong 2001. Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor. Appl. Genet. 102:440-449.
41. Sanyal, A., J. S. S. Ammiraju, F. Lu, Y. Yu, T. Rambo, J. Currie, K. Kollura, H. Kim, J. F. Chen, J. X. Ma, et al. 2010. Orthologous comparisons of the Hd1 region across genera reveal Hd1 Gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Mol. Biol. Evol. 27:2487-2506.
42. Shimamoto, K., and J. Kyozuka 2002. Rice as a model for comparative genomics of plants. Annu. Rev. Plant Biol. 53:399-419.
43. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
44. Tang, L., X. H. Zou, G. Achoundong, C. Potgieter, G. Second, D. Y. Zhang, and S. Ge 2010. Phylogeny and biogeography of the rice tribe (Oryzeae): evidence from combined analysis of 20 chloroplast fragments. Mol. Phylogen. Evol. 54:266-277.
45. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
46. Vaughan, D. A. 2004. The wild relatives of rice: a genetic resources handbook. International Rice Research Institute, Manila, Philippines
47. Vinogradov, A. E. 2004. Evolution of genome size: multilevel selection, mutation bias or dynamical chaos? Curr. Opin. Genet. Dev. 14:620-626.
48. Whitney, K. D., and T. Garland Jr. 2010. Did genetic drift drive increases in genome complexity? PLoS Genet. 6:e1001080.
49. Whitney, K. D., E. J. Baack, J. L. Hamrick, M. J. Godt, B. C. Barringer, M. D. Bennett, C. G. Eckert, C. Goodwillie, S. Kalisz, I. J. Leitch, et al. 2010. A role for nonadaptive processes in plant genome size evolution? Evolution 64:2097-2109.
50. Whitney, K. D., B. Boussau, E. J. Baack, and T. Garland Jr. 2011. Drift and genome complexity revisited. PLoS Genet. 7: e1002092.
51. Wing, R. A., J. S. Ammiraju, M. Luo, H. Kim, Y. Yu, D. Kudrna, J. L. Goicoechea, W. Wang, W. Nelson, K. Rao, et al. 2005. The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol. Biol. 59:53-62.
52. Wright, S. I., B. Lauga, and D. Charlesworth 2002. Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol. Biol. Evol. 19:1407-1420.
53. Yi, S. V. 2006. Non-adaptive evolution of genome complexity. Bioessays 28:979-982.
54. Yi, S. V., and J. T. Streelman 2005. Genome size is negatively correlated with effective population size in ray-finned fish. Trends Genet. 21:643-646.
55. Zhang, L. B., and S. Ge 2007. Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives. Mol. Biol. Evol. 24:769-783.
56. Zhu, Q. H., and S. Ge 2005. Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol. 167:249-265.
57. Zhu, Q. H., X. M. Zheng, J. C. Luo, B. S. Gaut, and S. Ge 2007. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol. Biol. Evol. 24:875-888.
58. Zou, X. H., F. M. Zhang, J. G. Zhang, L. L. Zang, L. Tang, J. Wang, T. Sang, and S. Ge 2008. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol. 9:R49.
59. Zuccolo, A., A. Sebastian, J. Talag, Y. Yu, H. Kim, K. Collura, D. Kudrna, and R. A. Wing 2007. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol. Biol. 7:152.