Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation

New Phytologist

Volumn 186, Issue 1, 2010, Pages 184-193

  Flagel, Lex E ^a   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Gene expression; Gossypium (cotton); Homoeolog; Microarray; Polyploidy

Indexed keywords

COTTON; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOME; HYBRIDIZATION; INTERSPECIFIC VARIATION; PHYLOGENETICS; POLYPLOIDY; RNA; SPECIATION (BIOLOGY);

ARTICLE; COTTON; CROSS BREEDING; DUPLICATE GENE; EPIDEMIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HYBRIDIZATION; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENOME; POLYPLOIDY; SEQUENCE HOMOLOGY; SPECIES DIFFERENTIATION;

BIAS (EPIDEMIOLOGY); CROSSES, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, DUPLICATE; GENETIC SPECIATION; GENOME, PLANT; GOSSYPIUM; HYBRIDIZATION, GENETIC; PHYLOGENY; POLYPLOIDY; SEQUENCE HOMOLOGY, NUCLEIC ACID;

GOSSYPIUM; GOSSYPIUM HIRSUTUM;

EID: 77950931393     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2009.03107.x     Document Type: Article

References (49)

1. Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution 2008, 25:2445-2455.
2. Bottley A, Koebner RM. Variation for homoeologous gene silencing in hexaploid wheat. Plant Journal 2008, 56:297-302.
3. Bottley A, Xia GM, Koebner RMD. Homoeologous gene silencing in hexaploid wheat. Plant Journal 2006, 47:897-906.
4. Buggs RJA, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA, Paterson AH, Soltis PS, Soltis DE. Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 2009, 103:73-81.
5. Chaudhary B, Hovav R, Rapp R, Verma N, Udall JA, Wendel JF. Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evolution and Development 2008, 10:567-582.
6. Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel JF. Reciprocal silencing, transcriptional bias and functional divergence of homoeologs in polyploid cotton (Gossypium). Genetics 2009a, 182:503-517.
7. Chaudhary B, Hovav R, Flagel L, Mittler R, Wendel JF. Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genomics 2009b, 10:378.
8. Chen ZJ. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annual Review of Plant Biology 2007, 58:377-406.
9. Comai L. The advantages and disadvantages of being polyploid. Nature Reviews Genetics 2005, 6:836-846.
10. Conant GC, Wolfe KH. Turning a hobby into a job: how duplicated genes find new functions. Nature Reviews Genetics 2008, 9:938-950.
11. 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.
12. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6 2005, Distributed by the author, Seattle, WA, USA, Department of Genome Sciences, University of Washington
13. Flagel L, Udall JA, Nettleton D, Wendel JF. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology 2008, 6:16.
14. Force A, Lynch M, Pickett FB, Amores A, Yan Y-l, Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999, 151:1531-1545.
15. 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.
16. Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF. Incongruent patterns of local and global genome size evolution in cotton. Genome Research 2004, 14:1474-1482.
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. 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.
19. Hovav R, Udall JA, Chaudhary B, Flagel L, Rapp R, Wendel JF. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proceedings of the National Academy of Sciences, USA 2008, 105:6191-6195.
20. Krapovickas A, Seijo G. Gossypium ekmanianum (Malvaceae), algodón silvestre de la República Dominicana. Bonplandia 2008, 17:53-63.
21. Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploid plants. Science 2008, 320:481-483.
22. Nettleton D, Hwang JTG, Caldo RA, Wise RP. Estimating the number of true null hypotheses from a histogram of p values. Journal of Agricultural, Biological, and Environmental Statistics 2006, 11:337-356.
23. Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 2009, 457:327-331.
24. Ohno S. Evolution by gene duplication 1970, New York, NY, USA, Springer-Verlag
25. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee H-S, Comai L, Madlung A, Doerge RW, Colot V. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 2003, 19:141-147.
26. Paun O, Fay MF, Soltis DE, Chase MW. Genetic and epigenetic alterations after hybridization and genome doubling. Taxon 2007, 56:649-656.
27. Pires JC, Zhao J, 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.
28. Pumphrey M, Bai J, Laudencia-Chingcuanco D, Anderson O, Gill BS. Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 2009, 181:1147-1157.
29. Rabinowicz PD, Citek R, Budiman MA, Nunberg A, Bedell JA, Lakey N, O'Shaughnessy AL, Nascimento LU, McCombie WR, Martienssen RA. Differential methylation of genes and repeats in land plants. Genome Research 2005, 15:1431-1440.
30. Rapp RA, Wendel JF. Epigenetics and plant evolution. New Phytologist 2005, 168:81-91.
31. Rapp RA, Udall JA, Wendel JF. Genomic expression dominance in allopolyploids. BMC Biology 2009, 7:18.
32. Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, 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.
33. 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.
34. 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.
35. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS. Polyploidy and angiosperm diversification. American Journal of Botany 2009, 96:336-348.
36. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences, USA 2003, 100:9440-9445.
37. Stupar RM, Springer NM. Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 2006, 173:2199-2210.
38. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH. Synteny and collinearity in plant genomes. Science 2008, 320:486-488.
39. Tate JA, Ni Z, 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.
40. 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, 9:80.
41. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB. A global assembly of cotton ESTs. Genome Research 2006a, 16:441-450.
42. 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.
43. Veitia RA. Paralogs in polyploids: one for all and all for one? Plant Cell 2005, 17:4-11.
44. Veitia RA, Bottani S, Birchler JA. Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends in Genetics 2008, 24:390-397.
45. Wan C, Wilkins T. A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypium hirsutum L.). Analytical Biochemistry 1994, 223:7-12.
46. Wang J, Tian L, Lee H-S, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 2006, 172:507-517.
47. Wendel JF. Genome evolution in polyploids. Plant Molecular Biology 2000, 42:225-249.
48. Wendel JF, Cronn R. Polyploidy and the evolutionary history of cotton. Advances in Agronomy 2003, 78:139-186.
49. Wendel JF, Rowley R, Stewart JM. Genetic diversity in and phylogenetic relationships of the Brazilian endemic cotton, Gossypium mustelinum (Malvaceae). Plant Systematics and Evolution 1994, 192:49-59.