Mating system and recombination affect molecular evolution in four Triticeae species

Genetics Research

Volumn 90, Issue 1, 2008, Pages 97-109

  Haudry, A ^a,b   Cenci, A ^a   Guilhaumon, C ^a   Paux, E ^c   Poirier, S ^a   Santoni, S ^a   David, J ^a   Glemin S ^b  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^b UNIV MONTPELLIER   (France)

^c UNIVERSITÉ CLERMONT AUVERGNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; GENETIC LOAD; GENETIC RECOMBINATION; MATING SYSTEM; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OUTCROSSING; PREDICTION; PROTEIN CONTENT; RYE; SELFING; TRITICUM MONOCOCCUM; TRITICUM URARTU; WHEAT;

ANIMALS; EVOLUTION, MOLECULAR; MODELS, GENETIC; POACEAE; RECOMBINATION, GENETIC; REPRODUCTION; SELECTION (GENETICS);

AEGILOPS SPELTOIDES; SECALE CEREALE; TRITICEAE; TRITICUM MONOCOCCUM; TRITICUM URARTU;

EID: 39749201582     PISSN: 00166723     EISSN: 14695073     Source Type: Journal    
DOI: 10.1017/S0016672307009032     Document Type: Article

References (62)

1. Akashi, H. (1995). Inferring weak selection from patterns of polymorphism and divergence at 'silent' sites in Drosophila DNA. Genetics 139, 1067-1076.
2. Akhunov, E. D., David, J. L., Chao, S., Lazo, G., Anderson, O. D., et al. (2003a). GC composition and codon usage in genes of inbreeding and outcrossing Triticeae species. In Tenth International Wheat Genetics Symposium, pp. 203-206. Italy: Paestum.
3. Akhunov, E. D., Goodyear, A. W., Geng, S., Qi, L. L., Echalier, B., Gill, B. S., Miftahudin, T., Gustafson, J. P., Lazo, G., Chao, S., et al. (2003b). The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Research 13, 753-763.
4. Baker, H. G. (1955). Self-compatibility and establishment after 'long-distance' dispersal. Evolution 9, 347-348.
5. Barakat, A., Carels, N. & Bernardi, G. (1997). The distribution of genes in the genome of gramineae. Proceedings of the National Academy of Sciences of the USA 94, 6857-6861.
6. Bengtsson, B. O. (1990). The effect of biased conversion on the mutation load. Genetical Research 55, 183-187.
7. Bielawski, J. P. & Yang, Z. (2004). A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution 59, 121-132.
8. Bulmer, M. (1991). The selection mutation drift theory of synonymous codon usage. Genetics 129, 897-907.
9. Carels, N. & Bernardi, G. (2000). Two classes of genes in plants. Genetics 154, 1819-1825.
10. Charlesworth, B. (1992). Evolutionary rates in partially self-fertilizing species. The American Naturalist 140, 126-148.
11. Charlesworth, B., Morgan, M. T. & Charlesworth, D. (1993). The effect of deleterious mutations on neutral molecular variation. Genetics 134, 1289-1303.
12. Charlesworth, D. & Wright, S. I. (2001). Breeding systems and genome evolution. Current Opinion in Genetics & Development 11, 685-690.
13. Dvorak, J., Diterlizzi, P., Zhang, H. B. & Resta, P. (1993). The evolution of polyploid wheats: Identification of the A-genome donor species. Genome 36, 21-31.
14. Dvorak, J., Luo, M. C. & Yang, Z. L. (1998). Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics 148, 423-434.
15. Endo, T. R. & Gill, B. S. (1996). The deletion stocks of common wheat. Journal of Heredity 87, 295-307.
16. Felsenstein, J. (1989). PHYLIP: Phylogeny inference package (version 3.2). Cladistics 5, 164-166.
17. Galtier, N. & Duret, L. (2007). Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends in Genetics 23, 273-277.
18. Glémin, S., Bazin, E. & Charlesworth, D. (2006). Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proceedings of the Royal Society of London, Series B 273, 3011-3019.
19. Guindon, S. E. P. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696-704.
20. Haddrill, P. R., Halligan, D. L., Tomaras, D. & Charlesworth, B. (2007). Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biology 8, R18.
21. Hamrick, J. L. & Godt, M. J. W. (1996). Effects of life history traits on genetic diversity in plants species. Philosophical Transactions of the Royal Society of London, Series B 351, 1291-1298.
22. Huang, S., Sirikhachornkit, A., Su, X., Faris, J., Gill, B., Haselkorn, R. & Gornicki, P. (2002). Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/ Aegilops complex and the evolutionary history of polyploid wheat. Proceedings of the National Academy of Sciences of the USA 99, 8133-8138.
23. Ikemura, T. (1985). Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution 2, 13-35.
24. Ingvarsson, P. K. (2002). A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants. Evolution 56, 2368-2373.
25. Kawabe, A. & Miyashita, N. T. (2003). Patterns of codon usage bias in three dicot and four monocot plant species. Genes and Genetic Systems 78, 343-352.
26. Kunzel, G., Korzun, L. & Meister, A. (2000). Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154, 397-412.
27. Liu, Q. & Xue, Q. (2005). Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. Journal of Genetics 84, 55-62.
28. Lukaszewski, A. J. (1992). A comparision of physical distribution of recombination in chromosome 1 R in diploid rye and in hexaploid triticale. Theoretical and Applied Genetics 83, 1048-1053.
29. Lukaszewski, A. J. & Curtis, C. A. (1993). Physical distribution of recombination in B-genome chromosomes of tetraploid wheat. Theoretical and Applied Genetics 86, 121-127.
30. Lundqvist, A. (1954). Studies on self-sterility in rye, Secale cereale L. Hereditas 40, 278-294.
31. Marais, G. (2003). Biased gene conversion: Implications for genome and sex evolution. Trends in Genetics 19, 330-338.
32. Marais, G., Charlesworth, B. & Wright, S. I. (2004). Recombination and base composition: The case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biology 5, R45.
33. Maynard-Smith, J. & Haigh, D. (1974). The hitch-hiking effect of a favourable gene. Genetical Research 23, 23-35.
34. Meunier, J. & Duret, L. (2004). Recombination drives the evolution of GC-content in the human genome. Molecular Biology and Evolution 21, 984-990.
35. Munkvold, J. D., Greene, R. A., Bertmudez-Kandianis, C. E., La Rota, C. M., Edwards, H., Sorrells, S. F., Dake, T., Benscher, D., Kantety, R., Linkiewicz, A. M., et al. (2004). Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics 168 639-650.
36. Nordborg, M. (2000). Linkage disequilibrium, gene trees and selling: An ancestral recombination graph with partial self-fertilization. Genetics 154, 923-929.
37. Nybom, H. (2004). Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology 13, 1143-1155.
38. Pal, C., Papp, B. & Hurst, L. D. (2001). Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Molecular Biology and Evolution 18, 2323-2326.
39. Paux, E., Roger, D., Badaeva, E., Gay, G., Bernard, M., Sourdille, P. & Feuillet, C. (2006). Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. The Plant Journal 48, 463-474.
40. Pollak, E. (1987). On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics 117, 353-360.
41. Pollard, K. S., Salama, S. R., King, B., Kern, A.D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., et al. (2006). Forces shaping the fastest evolving regions in the human genome. PLoS Genetics 2, e168.
42. Qi, L. L., Echalier, B., Chao, S., Lazo, G. R., Butler, G. E., Anderson, O. D., Akhunov, E. D., Dvorak, J., Linkiewicz, A. M., Ratnasiri, A., et al. (2004). A chromosome bin map of 16 000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168, 701-712.
43. Rota, M. & Sorrells, M. E. (2004). Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Functional and Integrative Genomics 4, 34-46.
44. Safar, J., Bartos, J., Janda, J., Bellec, A., Kubalakova, M., Valarik, M., Pateyron, S., Weiserova, J., Tuskova, R., Cihalikova, J., et al. (2004). Dissecting large and complex genomes: Flow sorting and BAC cloning of individual chromosomes from bread wheat. The Plant Journal 39, 960-968.
45. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., et al. (2002). The genome sequence and structure of rice chromosome 1. Nature 420, 312-316.
46. Schoen, D. J. & Brown, A. H. D. (1991). Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants. Proceedings of the National Academy of Sciences of the USA 88, 4494-4497.
47. Sears, E. R. (1954). The aneuploid of common wheat. Missouri Agricultural Experiment Station Research Bulletin 572, 1-58.
48. Sears, E. R. & Sears, L. (1978). The telocentric chromosomes of common wheat. In Proceedings of the Fifth International Wheat Genetics Symposium (ed. S. Ramanujams), pp. 389-407. New Delhi, India: Indian Agricultural Research Institute.
49. Sorrells, M. E., La Rota, M., Bermudez-Kandianis, C. E., Greene, R. A., Kantety, R., Munkvold, J. D., Miftahudin, T., Mahmoud, A., Ma, X. F., Gustafson, P. J., et al. (2003). Comparative DNA sequence analysis of wheat and rice genomes. Genome Research 13, 1818-1827.
50. Staden, R., Judge, D. P. & Bonfield, J. K. (2001). Sequence assembly and finishing methods. Methods of Biochemical Analysis 43, 303-322.
51. Sueoka, N. (1962). On the genetic basis of variation and heterogeneity of DNA base composition. Proceedings of the National Academy of Sciences of the USA 48, 582-592.
52. Takebayashi, N. & Morrell, P. L. (2001). Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach. American Journal of Botany 88, 1143-1150.
53. Wang, L. J. & Roossinck, M. J. (2006). Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants. Plant Molecular Biology 61, 699-710.
54. Wong, G. K., Wang, J., Tao, L., Tan, J., Zhang, J., Passey, D. A. & Yu, J. (2002). Compositional gradients in Gramineae genes. Genome Research 12, 851-856.
55. Wright, S. I., Lauga, B. & Charlesworth, D. (2002). Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Molecular Biology and Evolution 19, 1407-1420.
56. Wright, S. I., Iorgovan, G., Misra, S. & Mokhtari, M. (2007). Neutral evolution of synonymous base composition in the Brassicaceae. Journal of Molecular Evolution 64, 136-141.
57. Yamane, K. & Kawahara, T. (2005). Intra- and inter-specific phylogenetic relationships among diploid Triticum-Aegilops species (Poaceae based on base-pair substitutions, indels, and microsatellites in chloroplast noncoding sequences. American Journal of Botany 92 1887-1898.
58. Yang, Z. (1998). Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution 15, 568-573.
59. Yang, Z. & Nielsen, R. (1998). Synonymous and non-synonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution 46, 409-418.
60. Yang, Z. H. (1997). PAML: A program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 13 555-556.
61. Yang, Z. & Swanson, W. J. (2002). Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Molecular Biology and Evolution 19, 49-57.
62. Yang, Z., Wong, W. S. & Nielsen, R. (2005). Bayes empirical bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution 22, 1107-1118.