Homoeologous nonreciprocal recombination in polyploid cotton

New Phytologist

Volumn 186, Issue 1, 2010, Pages 123-134

  Salmon, Armel ^a   Flagel, Lex ^a   Ying, Bao ^a,b   Udall, Joshua A ^c   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b QUFU NORMAL UNIVERSITY   (China)

^c BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

Allopolyploid speciation; Cotton; Expressed sequence tag (EST) assembly; Gene conversion; Gossypium; Homoeologous recombination

Indexed keywords

COTTON; DIVERGENCE; EVOLUTIONARY BIOLOGY; GENE; GENE EXPRESSION; GENOMICS; PHYLOGENETICS; POLYMORPHISM; POLYPLOIDY; RECOMBINATION; SPECIATION (BIOLOGY);

ARTICLE; CELL CLONE; COTTON; DIPLOIDY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENETIC RECOMBINATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENOME; POLYPLOIDY; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; TIME;

BASE SEQUENCE; CLONE CELLS; DIPLOIDY; EXPRESSED SEQUENCE TAGS; GENOME, PLANT; GOSSYPIUM; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY; RECOMBINATION, GENETIC; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

GOSSYPIUM; GOSSYPIUM ARBOREUM; GOSSYPIUM HIRSUTUM; GOSSYPIUM RAIMONDII; MYA;

EID: 77950929824     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2009.03093.x     Document Type: Article

References (70)

1. Adams KL, Cronn R, Percifield R, Wendel JF. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences, USA 2003, 100:4649-4654.
2. Adams KL, Percifield R, Wendel JF. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 2004, 168:2217-2226.
3. Albertin W, Balliau T, Brabant P, Chevre AM, Eber F, Malosse C, Thiellement H. Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 2006, 173:1101-1113.
4. Allers T, Lichten M. Differential timing and control of noncrossover and crossover recombination during meiosis. Cell 2001, 106:47-57.
5. Chapman BA, Bowers JE, Feltus FA, Paterson AH. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proceedings of the National Academy of Sciences, USA 2006, 103:2730-2735.
6. Chen ZJ. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annual Review of Plant Biology 2007, 58:377-406.
7. Chen JM, Cooper DN, Chuzhanova N, Ferec C, Patrinos GP. Gene conversion: mechanisms, evolution and human disease. Nature Reviews Genetics 2007, 8:762-775.
8. Conant GC, Wolfe KH. Turning a hobby into a job: how duplicated genes find new functions. Nature Reviews Genetics 2008, 9:938-950.
9. Cronn RC, Small RL, Wendel JF. Duplicated genes evolve independently after polyploid formation in cotton. Proceedings of the National Academy of Sciences, USA 1999, 96:14406-14411.
10. Cronn R, Cedroni M, Haselkorn T, Grover C, Wendel JF. PCR-mediated recombination in amplification products derived from polyploid cotton. Theoretical and Applied Genetics 2002, 104:482-489.
11. Doyle JJ. DNA protocols for plants. Molecular Techniques in Taxonomy 1991, 283-293. Hewitt GMJohnston A. In, eds, Berlin, Springer-Verlag
12. Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF. Evolutionary genetics of genome merger and doubling in plants. Annual Review of Genetics 2008, 42:443-461.
13. Endrizzi JE, Turcotte EL, Kohel RJ. Genetics, cytology and evolution of Gossypium. Advances in Genetics 1985, 23:271-375.
14. Flagel L, Wendel JF. Gene duplication and evolutionary novelty in plants. New Phytologist 2009, 183:557-563.
15. Flagel L, Udall J, Nettleton D, Wendel J. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology 2008, 6:16.
16. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 2007, 19:3403-3417.
17. Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF. Microcolinearity and genome evolution in the adha region of diploid and polyploid cotton (Gossypium). Plant Journal 2007, 50:995-1006.
18. Grover CE, Yu Y, Wing RA, Paterson AH, Wendel JF. A phylogenetic analysis of indel dynamics in the cotton genus. Molecular Biology and Evolution 2008, 25:1415-1428.
19. Ha M, Kim ED, Chen ZJ. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proceedings of the National Academy of Sciences, USA 2009, 106:2295-2300.
20. Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research 2006, 16:1252-1261.
21. Hegarty MJ, Barker GL, Wilson ID, Abbott RJ, Edwards KJ, Hiscock SJ. Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Current Biology 2006, 16:1652-1659.
22. Hendrix B, Stewart JM. Estimation of the nuclear DNA content of Gossypium species. Annals of Botany 2005, 95:789-797.
23. Hollingsworth NM, Brill SJ. The mus81 solution to resolution: generating meiotic crossovers without holliday junctions. Genes & Development 2004, 18:117-125.
24. Judo MSB, Wedel AB, Wilson C. Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Research 1998, 26:1819-1825.
25. Kovarik A, Matyasek R, Lim KY, Skalicka K, Koukalova B, Knapp S, Chase M, Leitch AR. Concerted evolution of 18-5.8-26s rDNA repeats in Nicotiana allotetraploids. Biological Journal of the Linnean Society 2004, 82:615-625.
26. Kovarik A, Pires JC, Leitch AR, Lim KY, Sherwood AM, Matyasek R, Rocca J, Soltis DE, Soltis PS. Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 2005, 169:931-944.
27. Kovarik A, Dadejova M, Lim YK, Chase MW, Clarkson JJ, Knapp S, Leitch AR. Evolution of rDNA in Nicotiana allopolyploids: a potential link between rDNA homogenization and epigenetics. Annals of Botany 2008, 101:815-823.
28. Krapovickas A, Seijo G. Gossypium ekmanianum (malvaceae), algodón silvestre de la República Dominicana. Bonplandia 2008, 17:55-63.
29. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R. Clustal w and clustal x version 2.0. Bioinformatics 2007, 23:2947-2948.
30. Liu B, Wendel JF. Epigenetic phenomena and the evolution of plant allopolyploids. Molecular Phylogenetics and Evolution 2003, 29:365-379.
31. Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, Osborn T. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiology 2006, 140:336-348.
32. Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155.
33. Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiology 2002, 129:733-746.
34. Martinez-Perez E, Colaiacovo MP. Distribution of meiotic recombination events: talking to your neighbors. Current Opinion in Genetics & Development 2009, 19:105-112.
35. de Massy B. Distribution of meiotic recombination sites. Trends in Genetics 2003, 19:514-522.
36. McGrath CL, Casola C, Hahn MW. Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics 2009, 182:615-622.
37. Mezard C, Vignard J, Drouaud J, Mercier R. The road to crossovers: plants have their say. Trends in Genetics 2007, 23:91-99.
38. Nicolas SD, Leflon M, Liu Z, Eber F, Chelysheva L, Coriton O, Chevre AM, Jenczewski E. Chromosome 'speed dating' during meiosis of polyploid Brassica hybrids and haploids. Cytogenetic and Genome Research 2008, 120:331-338.
39. Ohno S. Evolution by gene duplication 1970, New York, NY, USA, Springer-Verlag
40. Ozkan H, Levy AA, Feldman M. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 2001, 13:1735-1747.
41. Paques F, Haber JE. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews 1999, 63:349-404.
42. Parkin IAP, Sharpe AG, Keith DJ, Lydiate DJ. Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 1995, 38:1122-1131.
43. Pires JC, Zhao JW, Schranz ME, Leon EJ, Quijada PA, Lukens LN, Osborn TC. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biological Journal of the Linnean Society 2004, 82:675-688.
44. Pontes O, Neves N, Silva M, Lewis MS, Madlung A, Comai L, Viegas W, Pikaard CS. Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proceedings of the National Academy of Sciences, USA 2004, 101:18240-18245.
45. Ramsey J, Schemske DW. Neopolyploidy in flowering plants. Annual Review of Ecology and Systematics 2002, 33:589-639.
46. Rapp RA, Wendel JF. Epigenetics and plant evolution. New Phytologist 2005, 168:81-91.
47. Rapp RA, Udall JA, Wendel JF. Genomic expression dominance in allopolyploids. BMC Biology 2009, 7:18.
48. Rong JK, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding XL, Garza JJ, Marler BS. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 2004, 166:389-417.
49. Rozen S, Skaletsky H. Primer3 on the www for general users and for biologist programmers. Bioinformatics methods and protocols 2000, 365-386. Krawetz S, Misener S. In, eds, Totowa, NJ, USA, Humana Press
50. Salmon A, Ainouche ML, Wendel JF. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Molecular Ecology 2005, 14:1163-1175.
51. Seelanan T, Schnabel A, Wendel JF. Congruence and consensus in the cotton tribe (Malvaceae). Systematic Botany 1997, 22:259-290.
52. Senchina DS, Alvarez I, Cronn RC, Liu B, Rong JK, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Molecular Biology and Evolution 2003, 20:633-643.
53. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 2001, 13:1749-1759.
54. Small RL, Wendel JF. The mitochondrial genome of allotetraploid cotton (Gossypium L.). Journal of Heredity 1999, 90:251-253.
55. Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF. The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 1998, 85:1301-1315.
56. Stephens SG. Possible significance of duplication in evolution. Advances in Genetics Incorporating Molecular Genetic Medicine 1951, 4:247-265.
57. Szostak JW, Orrweaver TL, Rothstein RJ, Stahl FW. The double-strand-break repair model for recombination. Cell 1983, 33:25-35.
58. Tate JA, Ni ZF, Scheen AC, Koh J, Gilbert CA, Lefkowitz D, Chen ZJ, Soltis PS, Soltis DE. Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 2006, 173:1599-1611.
59. Tate JA, Joshi P, Soltis KA, Soltis PS, Soltis DE. On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae). BMC Plant Biology 2009, 9:10.
60. Teshima KM, Innan H. The effect of gene conversion on the divergence between duplicated genes. Genetics 2004, 166:1553-1560.
61. Udall JA, Quijada PA, Osborn TC. Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics 2005, 169:967-979.
62. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu YS, Wu YR, Dowd C, Arpat AB. A global assembly of cotton ESTs. Genome Research 2006a, 16:441-450.
63. Udall JA, Swanson JM, Nettleton D, Percifield RJ, Wendel JF. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 2006b, 173:1823-1827.
64. Wang JL, Tian L, Madlung A, Lee HS, Chen M, Lee JJ, Watson B, Kagochi T, Comai L, Chen ZJ. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 2004, 167:1961-1973.
65. Wang JL, Tian L, Lee HS, Wei NE, Jiang HM, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 2006, 172:507-517.
66. Wang XY, Tang HB, Bowers JE, Paterson AH. Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Research 2009, 19:1026-1032.
67. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25:1189-1191.
68. Wendel JF, Cronn RC. Polyploidy and the evolutionary history of cotton. Advances in Agronomy 2003, 78:139-186.
69. Wendel JF, Schnabel A, Seelanan T. An unusual ribosomal DNA-sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Molecular Phylogenetics and Evolution 1995, 4:298-313.
70. Xu SQ, Clark T, Zheng HK, Vang S, Li RQ, Wong GKS, Wang J, Zheng XG. Gene conversion in the rice genome. BMC Genomics 2008, 9:93.