Investigation of the demographic and selective forces shaping the nucleotide diversity of genes involved in nod factor signaling in Medicago truncatula

Genetics

Volumn 177, Issue 4, 2007, Pages 2123-2133

  De Mita, Stéphane ^a,d   Ronfort, Joëlle ^a   McKhann, Heather I ^b   Poncet, Charles ^a   El Malki, Redouane ^b   Bataillon, Thomas ^a,c  

^a CEMAGREF   (France)

^b CENTRE NATIONAL DE GÉNOTYPAGE   (France)

^c AARHUS UNIVERSITY   (Denmark)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NOD; UNCLASSIFIED DRUG;

ARTICLE; BARREL MEDIC; CONTROLLED STUDY; DEMOGRAPHY; DMI1 GENE; EVOLUTIONARY ADAPTATION; FORCE; GENE; GENE FUNCTION; GENE LOCUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC MODEL; GENETIC PARAMETERS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; GENOTYPE; HYPOTHESIS; LEGUME; MOLECULAR EVOLUTION; NFP GENE; NONHUMAN; NORK GENE; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SPECIES DISTRIBUTION; STANDARDIZATION; UNINDEXED SEQUENCE;

FABACEAE; MEDICAGO TRUNCATULA;

EID: 37249092429     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.076943     Document Type: Article

References (56)

1. ANÉ, J.-M., G. B. KISS, B. K. RIELY, R. V. PENMETSA, G. E. D. OLDROYD et al., 2004 Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 303: 1364-1367.
2. ARDOUREL, M., N. DEMONT, F. DEBELLÉ, F. MAILLET, F. DE BILLY et al., 1994 Rhizobium meliloti lipooligosaccharide nodulation factors: different structural requirements for bacterial entry into target root hair cells and induction of plant symbiotic developmental responses. Plant Cell 6: 1357-1374.
3. ARRIGHI, J.-F., A. BARRE, B. BEN AMOR, A. BERSOULT, L. CAMPOS SORIANO et al., 2006 The Medicago truncatula LysM-receptor kinase gene family includes NFP and new nodule-expressed genes. Plant Physiol. 142: 265-279.
4. BAMSHAD, M., and S. P. WOODING, 2003 Signatures of natural selection in the human genome. Nat. Rev. Genet. 4: 99-111.
5. BAUDRY, E., and F. DEPAULIS, 2003 Effect of misoriented sites on neutrality tests with outgroup. Genetics 165: 1619-1622.
6. BEN AMOR, B., S. L. SHAW, G. E. D. OLDROYD, F. MAILLET, R. V. PENMETSA et al., 2003 The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation. Plant J. 34: 495-506.
7. BROWNLIE, J. C., M. ADAMSKI, B. SLATKO and E. A. MCGRAW, 2007 Diversifying selection and host adaptation in two endosymbiont genomes. BMC Evol. Biol. 7: 68.
8. CATOIRA, R., C. GALERA, F. DE BILLY, R. V. PENMETSA, E.-P. JOURNET et al., 2000 Four genes of Medicago truncatula controlling components of a Nod factor transduction pathway. Plant Cell 12: 1647-1665.
9. CHARLESWORTH, D., 2006 Balancing selection and its effects on sequences in nearby genome regions. PLoS Genet. 2: e64.
10. COOK, D. R., 1999 Medicago truncatula: a model in the making! Curr. Opin. Plant Biol. 2: 301-304.
11. CULLIMORE, J., R. RANJEVA and J.-J. BONO, 2001 Perception of lipochitooligosaccharidic Nod factors in legumes. Trends Plant Sci. 6: 24-30.
12. DE MEAUX, J., and T. MITCHELL-OLDS, 2003 Evolution of plant resistance at the molecular level: ecological context of species interactions. Heredity 91: 345-352.
13. DE MITA, S., S. SANTONI, I. HOCHU, J. RONFORT and T. BATAILLON, 2006 Molecular evolution and positive selection of the symbiotic gene NORK in Medicago truncatula. J. Mol. Evol. 62: 234-244.
14. DEPAULIS, F., S. MOUSSET and M. VEUILLE, 2003 Power of neutrality tests to detect bottlenecks and hitchhiking. J. Mol. Evol. 57: S190-S200.
15. ENDRE, G., A. KERESZT, Z. KEVEI, S. MIHACEA, P. KALÒ et al., 2002 A receptor kinase gene regulating symbiotic nodule development. Nature 417: 962-966.
16. FAY, J. C., and C.-I. WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
17. FENN, K., and M. BLAXTER, 2006 Wolbachia genomes: revealing the biology of parasitism and mutualism. Trends Parasitol. 22: 60-65.
18. FOURMANN, M., P. BARRET, N. FROGER, C. BARON, F. CHARLOT et al., 2002 From Arabidopsis thaliana to Brassica napus: development of amplified consensus genetic markers (ACGM) for construction of a gene map. Theor. Appl. Genet. 105: 1196-1206.
19. GEURTS, R., E. FEDOROVA and T. BISSELING, 2005 Nod factor signaling genes and their function in the early stages of Rhizobium infection. Curr. Opin. Plant Biol. 8: 346-352.
20. HADDRILL, P. R., K. R. THORNTON, B. CHARLESWORTH and P. ANDOLFATTO, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15: 790-799.
21. HAMBLIN, M. T., A. M. CASA, H. SUN, S. C. MURRAY, A. H. PATERSON et al., 2006 Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor. Genetics 173: 953-964.
22. HEIN, J., M. H. SCHIERUP and C. WIUF, 2005 Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford University Press, Oxford.
23. HOGG, B. V., J. V. CULLIMORE, R. RANJEVA and J. J. BONO, 2006 The DMI1 and DMI2 early symbiotic genes of Medicago truncatula are required for a high-affinity nodulation factor-binding site associated to a particulate fraction of roots. Plant Physiol. 140: 365-373.
24. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
25. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
26. IMAIZUMI-ANRAKU, H., N. TAKEDA, M. CHARPENTIER, J. PERRY, H. MIWA et al., 2005 Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots. Nature 433: 527-531.
27. JIGGINS, F. M., 2006 Adaptive evolution and recombination of Rickettsia antigens. J. Mol. Evol. 62: 99-110.
28. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
29. 2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303: 1361-1364.
30. LIMPENS, E., C. FRANKEN, P. SMIT, J. WILLEMSE, T. BISSELING et al., 2003 LysM domain receptor kinases regulating rhizobial Nod factor-induced infection. Science 302: 630-633.
31. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-55.
32. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
33. MCVEAN, G., P. AWADALLA and P. FEARNHEAD, 2002 A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
34. NIELSEN, R., 2005 Molecular signatures of natural selection. Annu. Rev. Genet. 39: 197-218.
35. NORDBORG, M., T. T. HU, Y. ISHINO, J. JHAVERI, C. TOOMAJIAN et al., 2005 The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3: e196.
36. OSTROWSKI, M. F., J. DAVID, S. SANTONI, H. MCKHANN, X. REBOUD et al., 2006 Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Mol. Ecol. 15: 1507-1517.
37. R DEVELOPMENT CORE TEAM, 2007 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
38. RIELY, B. K., G. LOUGNON, J.-M. ANÉ and D. R. COOK, 2006 The symbiotic ion channel homolog DMI1 functions in the nuclear membrane of Medicago truncatula roots. Plant J. 49: 208-216.
39. RONFORT, J., T. BATAILLON, S. SANTONI, M. DELALANDE, J. DAVID et al., 2006 Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collections for studying naturally occurring variation in Medicago truncatula. BMC Plant Biol. 6: 28.
40. SCHAUSER, L., A. ROUSSIS, J. STILLER and J. STOUGAARD, 1999 A plant regulator controlling development of symbiotic root nodules. Nature 402: 191-195.
41. SCHMID, K. J., S. RAMOS-ONSINS, H. RINGYS-BECKSTEIN, B. WEISSHAAR and T. MITCHELL-OLDS, 2005 A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169: 1601-1615.
42. STACEY, G., M. LIBAULT, L. BRECHENMACHER, J. WAN and G. D. MAY, 2006 Genetics and functional genomics of legume nodulation. Curr. Opin. Plant Biol. 9: 110-121.
43. STADEN, R., 1996 The Staden sequence analysis package. Mol. Biotechnol. 5: 233-241.
44. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
45. TAKAHASHI, M., F. MATSUDA, N. MARGETIC and M. LATHROP, 2002 Automated identification of single nucleotide polymorphisms from sequencing data. Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford, CA, pp. 87-93.
46. TENAILLON, M. I., J. U'REN, O. TENAILLON and B. S. GAUT, 2004 Selection versus demography: a multilocus investigation of the domestication process in maize. Mol. Biol. Evol. 21: 1214-1225.
47. THOMPSON, J. N., 2006 The Geographic Mosaic of Coevolution. University of Chicago Press, Chicago.
48. THORNTON, K., and P. ANDOLFATTO, 2006 Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
49. TIFFIN, P., and D. A. MOELLER, 2006 Molecular evolution of plant immune system genes. Trends Genet. 22: 662-670.
50. VAN DER BIEZEN, E. A., and J. D. G. JONES, 1998 Plant disease-resistance proteins and the gene-for-gene concept. Trends Biochem. Sci. 23: 454-456.
51. WEISS, G., and A. VON HAESELER, 1998 Inference of population history using a likelihood approach. Genetics 149: 1539-1546.
52. WILLIAMSON, S. H., R. HERNANDEZ, A. FLEDEL-ALON, L. ZHU, R. NIELSEN et al., 2005 Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl. Acad. Sci. USA 102: 7882-7887.
53. WRIGHT, S. I., and B. S. GAUT, 2004 Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 22: 506-519.
54. WRIGHT, S. I., I. V. BI, S. G. SCHROEDER, M. YAMASAKI, J. F. DOEBLEY et al., 2005 The effects of artificial selection on the maize genome. Science 308: 1310-1314.
55. YANG, Z., 2006 Computational Molecular Evolution. Oxford University Press, Oxford.
56. ZENG, K., Y. X. FU, S. SHI and C. I. WU, 2006 Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174: 1431-1439.