Recent degeneration of an old duplicated flowering time gene in Brassica nigra

Heredity

Volumn 98, Issue 6, 2007, Pages 375-384

  Sjodin P ^a   Hedman, H ^a,b   Shavorskaya, O ^b,c   Finet, C ^a,d   Lascoux, M ^a   Lagercrantz, U ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c UNIVERSITY COLLEGE CORK   (Ireland)

^d UNIVERSITÉ DE LYON   (France)

Author keywords

Brassica; DNA polymorphism; Duplication; Pseudogene

Indexed keywords

ARABIDOPSIS PROTEIN; CONSTANS PROTEIN, ARABIDOPSIS; DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ALLELE; ANNUAL PLANT; EVOLUTION; FLOWERING; GENETIC VARIATION; GENOME; MUTATION; POLYMORPHISM; POPULATION BOTTLENECK; RECOMBINATION;

ARABIDOPSIS; ARTICLE; BRASSICA; FLOWERING; GENE; GENE DUPLICATION; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; PSEUDOGENE; TIME; TRANSGENIC PLANT;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; FLOWERING TOPS; GENE DUPLICATION; GENES, PLANT; MUSTARD PLANT; MUTATION; PHYLOGENY; PLANTS, GENETICALLY MODIFIED; POLYMORPHISM, GENETIC; PSEUDOGENES; TIME FACTORS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRASSICA; BRASSICA NIGRA;

EID: 34249062678     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800951     Document Type: Article

References (62)

1. Arabidopsis Genome Initiative (AGI) (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
2. Aldrich C, Wambebe C, Odama L, Di Rienzo A, Ober C (2002). Linkage disequilibrium and age estimates of a deletion polymorphism (1597DeltaC) in HLA-G suggest non-neutral evolution. Hum Immunol 63: 405-412.
3. Anderson SL, Kay SA (1995). Functional dissection of circadian clock- and phytochrome-regulated transcription of the Arabidopsis CAB2 gene. Proc Natl Acad Sci USA 92: 1500-1504.
4. Balakirev ES, Ayala FJ (2003). Pseudogenes: are they 'junk' or functional DNA? Annu Rev Genet 37: 123-151.
5. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000). Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101.
6. Blanc G, Hokamp K, Wolfe KH (2003). A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137-144.
7. Dvorak J, Luo MC, Yang ZL (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.
8. Filatov DA, Charlesworth D (1999). DNA polymorphism, haplotype structure and balancing selection in the Leavenworthia PgiC locus. Genetics 153: 1423-1434.
9. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999). Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
10. Gidoni D, Brosio P, Bond-Nutter D, Bedbrook J, Dunsmuir P (1989). Novel cis-acting elements in Petunia Cab gene promoters. Mol Gen Genet 215: 337-344.
11. Goldman N, Yang Z (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736.
12. Griffiths RC (2003). The frequency spectrum of a mutation, and its age, in a general diffusion model. Theor Pop Biol 64: 241-251.
13. Griffiths S, Dunford RP, Coupland G, Laurie DA (2003). The evolution of CONSTANS-like gene families in barley, rice and Arabidopsis. Plant Physiol 131: 1855-1867.
14. Hajdukiewicz P, Svab Z, Maliga P (1994). The small, versatile pPZP family of Agrobacterium binary vectors for plant transformation. Plant Mol Biol 25: 989-994.
15. Hellmann I, Ebersberger I, Ptak SE, Paabo S, Przeworski M (2003). A neutral explanation for the correlation of diversity with recombination rates in humans. Am J Hum Genet 72: 1527-1535.
16. Henderson IR, Shindo C, Dean C (2003). The need for winter in the switch to flowering. Annu Rev Genet 37: 371-392.
17. Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S et al. (2003). An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423: 91-96.
18. Hudson RR (1987). Estimating the recombination parameter of a finite population model without selection. Genet Res 50: 245-250.
19. Hudson RR (2001). Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
20. Hudson RR, Boos DD, Kaplan NL (1992). A statistical test for detecting geographic subdivision. Mol Biol Evol 9: 138-151.
21. Hudson RR, Kaplan NL (1985). Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
22. Hughes AL (1994). The evolution of functionally novel proteins after gene duplication. Proc Roy Soc London B 256: 119-124.
23. Jensen JD, Kim Y, Bauer DuMont V, Aquadro CF, Bustamante CD (2005). Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410.
24. Kaplan NL, Hudson RR, Langley CH (1989). The 'hitchhiking effect' revisited. Genetics 123: 887-899.
25. Kim Y, Stephan W (2002). Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
26. Kim Y, Nielsen R (2004). Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
27. Kraft T, Sall T, Magnusson-Rading I, Nilsson NO, Hallden C (1998). Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima). Genetics 150: 1239-1244.
28. Kruskopf-Österberg M, Shavorskaya O, Lascoux M, Lagercrantz U (2002). Naturally occurring indel variation in the B. nigra COL1 gene is associated with variation in flowering time. Genetics 161: 299-306.
29. Lagercrantz U (1998). Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150: 1217-1228.
30. Lagercrantz U, Axelsson T (2000). Rapid evolution of the family of CONSTANS LIKE genes in plants. Mol Biol Evol 17: 1499-1507.
31. Lagercrantz U, Kruskopf-Österberg M, Lascoux M (2002). Sequence variation and haplotype structure at the putative flowering-time locus COL1 of Brassica nigra. Mol Biol Evol 19: 1474-1482.
32. Lagercrantz U, Lydiate DJ (1996). Comparative genome mapping in Brassica. Genetics 144: 1903-1910.
33. Lagercrantz U, Putterill J, Coupland G, Lydiate D (1996). Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time. Plant J 9: 13-20.
34. Liscum M, Oeller P (1997). AFLP: not only for fingerprinting, but for positional cloning. http://carnegiedpbstanford.edu/methods/aflp.html.
35. Liu F, Zhang L, Charlesworth D (1998). Genetic diversity in Leavenworthia populations with different inbreeding levels. Proc Roy Soc London B Biol Sci 265: 293-301.
36. Lynch M, Conery JS (2000). The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
37. Lynch M, Force A (2000). The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
38. Lynch M, Walsh B (1998). Genetics and Analysis of Quantitative Traits. Sinauer: Sunderland, MA.
39. McPeek MS, Strahs A (1999). Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am J Hum Genet 65: 858-875.
40. McVean G, Awadalla P, Fearnhead P (2001). A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
41. Michaels SD, Amasino RM (1999). FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11: 949-956.
42. Mouradov A, Cremer F, Coupland G (2002). Control of flowering time: interacting pathways as a basis for diversity. Plant Cell 14 (Suppl): S111-S130.
43. Myers SR, Griffiths RC (2003). Bounds on the minimum number of recombination events in a sample history. Genetics 163: 375-394.
44. Nachman MW (1997). Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics 147: 1303-1316.
45. Nei M, Gojobori T (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
46. Ohno S (1970). Evolution by Gene Duplication. Springer Verlag: Berlin.
47. Przeworski M, Hudson RR, Di Rienzo A (2000). Adjusting the focus on human variation. Trends Genet 16: 296-302.
48. Putterill J, Robson F, Lee K, Simon R, Coupland G (1995). The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc-finger transcription factors. Cell 80: 847-857.
49. Robert LS, Robson F, Sharpe A, Lydiate D, Coupland G (1998). Conserved structure and function of the Arabidopsis flowering time gene CONSTANS in Brassica napus. Plant Mol Biol 37: 763-772.
50. Robson F, Costa MM, Hepworth SR, Vizir I, Pineiro M, Reeves PH et al. (2001). Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. Plant J 28: 619-631.
51. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
52. Schranz ME, Quijada P, Sung SB, Lukens L, Amasino R, Osborn TC (2002). Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 162: 1457-1468.
53. Slatkin M, Rannala B (2000). Estimating allele age. Annu Rev Genomics Hum Genet 1: 225-249.
54. Stephan W, Langley CH (1998). DNA polymorphism in lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593.
55. Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Mas P et al. (2000). Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289: 768-771.
56. Toomajian C, Ajioka RS, Jorde LB, Kushner JP, Kreitman M (2003). A method for detecting recent selection in the human genome from allele age estimates. Genetics 165: 287-297.
57. UN (1935). Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn J Bot 7: 389-452.
58. Vision TJ, Brown DG, Tanksley SD (2000). The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
59. Watterson GA (1983). On the time for gene silencing at duplicated loci. Genetics 105: 745-766.
60. Wendel JF (2000). Genome evolution in polyploids. Plant Mol Biol 42: 225-249.
61. Wernegreen JJ, Moran NA (1999). Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes. Mol Bio Evol 16: 83-97.
62. Westman AL, Kresovich S (1999). Simple sequence repeat (SSR)-based marker variation in Brassica nigra genebank accessions and weed populations. Euphytica 109: 85-92.