Exploring the genomic mysteries of polyploidy in cotton

Biological Journal of the Linnean Society

Volumn 82, Issue 4, 2004, Pages 573-581

  Adams, Keith L ^a,b   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Duplicate gene evolution; Gene silencing; Genome duplication; rDNA; Transposons

Indexed keywords

COTTON; EVOLUTION; GENE EXPRESSION; POLYPLOIDY;

GOSSYPIUM HIRSUTUM; TRANSPOSONS;

EID: 0346091287     PISSN: 00244066     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1095-8312.2004.00342.x     Document Type: Conference Paper

References (61)

1. Adams KL, Cronn R, Percifield R, Wendel JF. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences, USA 100: 4649-4654.
2. Barrier M, Baldwin BG, Robichaux RH, Purugganan MD. 1999. Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications. Molecular Biology and Evolution 16: 1105-1113.
3. Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen A-C, Elven R. 2004. Polyploidy in arctic plants. Biological Journal of the Linnean Society 82: 521-536.
4. Brubaker CL, Bourland FM, Wendel JF. 1999. The origin and domestication of cotton. In: Smith CW, Cothren JT, eds. Cotton; origin, history, technology and production. New York: John Wiley and Sons, 3-31.
5. Brubaker CL, Wendel JF. 1994. Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). American Journal of Botany 81: 1309-1326.
6. Chen ZJ, Wang J, Tian L, Lee H-S, Wang JJ, Chen M, Lee JJ, Josefsson C, Madlung A, Watson B, Lippman Z, Vaughn M, Pires JC, Colot V, Doerge RW, Martienssen R, Comai L, Osborn TC. 2004. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society 82: 689-700.
7. Comai L. 2000. Genetic and epigenetic interactions in allopolyploid plants. Plant Molecular Biology 43: 387-399.
8. Comai L, Madlung A, Josefsson C, Tyagi AP. 2003. Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids? Philosophical Transactions of the Royal Society of London B 358: 1149-1155.
9. Cronn R, Adams KL. 2003. Quantitative analysis of transcript accumulation from genes duplicated by polyploidy using cDNA-SSCP. Biotechniques 34: 726-734.
10. Cronn RC, Small RL, Haselkorn T, Wendel JF. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. American Journal of Botany 84: 707-725.
11. Cronn R, Small RL, Wendel JF. 1999. Duplicated genes evolve independently following polyploid formation in cotton. Proceedings of the National Academy of Sciences, USA 96: 14406-14411.
12. Cronn RC, Zhao X, Paterson AH, Wendel JF. 1996. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. Journal of Molecular Evolution 42: 685-705.
13. Doyle JJ, Doyle JL, Rauscher JT, Brown AHD. 2004. Evolution of the perennial soybean complex (Glycine subgenus Glycine): a study of contrasts. Biological Journal of the Linnean Society 82: 583-597.
14. Elder JF, Turner BJ. 1995. Concerted evolution of repetitive DNA sequences in eukaryotes. Quarterly Review of Biology 70: 297-320.
15. Endrizzi JE, Turcotte EL, Kohel RJ. 1985. Genetics, cytogenetics, and evolution of Gossypium. Advances in Genetics 23: 271-375.
16. Ferris SD, Whitt GS. 1979. Evolution of the differential regulation of duplicate genes after polyploidization. Journal of Molecular Evolution 12: 267-317.
17. Force A, Lynch M, Pickett FB, Amores A, Yan Y-L, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
18. Grant V. 1981. Plant speciation. New York: Columbia University Press.
19. Hanson RE, Islam-Faridi MN, Crane CF, Zwick MS, Czeschin DG, Wendel JF, Mcknight TD, Price HJ, Stelly DM. 2000. Ty1-copia-retrotransposon behavior in a polyploid cotton. Chromosome Research 8: 73-76.
20. Hanson RE, Zhao X-P, Islam-Faridi MN, Paterson AH, Zwick MS, Crane CF, McKnight TD, Stelly DM, Price HJ. 1998. Evolution of interspersed repetitive elements in Gossypium (Malvaceae). American Journal of Botany 85: 1364-1368.
21. Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proceedings of the Royal Society of London B 256: 119-124.
22. Hughes AL, Green JA, Garbayo JM, Roberts RM. 2000. Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proceedings of the National Academy of Sciences, USA 97: 3319-3323.
23. Ji Y, De Donato M, Crane CF, Raska WA, Nurul Islam-Faridi MN, McKnight TD, Price HJ, Stelly DM. 1999. New ribosomal RNA gene locations in Gossypium hirsutum mapped by meiotic FISH. Chromosoma 108: 200-207.
24. Jiang C-X, Chee PW, Draye X, Morrell PL, Smith CW, Paterson AH. 2000. Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton). Evolution 54: 798-814.
25. Kashkush K, Feldman M, Levy AA. 2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genetics 33: 102-106.
26. Kellogg EA. 2003. What happens to genes in duplicated genomes. Proceedings of the National Academy of Sciences, USA 27: 6890-6891.
27. Kovarik A, Matyasek R, Lim KY, Skalická K, Koukalová B, Knapp S, Chase MW, Leitch AR. 2004. Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids. Biological Journal of the Linnean Society 82: 615-625.
28. Lee H-S, Chen ZJ. 2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proceedings of the National Academy of Sciences, USA 98: 6753-6758.
29. Levin DA. 1983. Polyploidy and novelty in flowering plants. American Naturalist 122: 1-25.
30. Levy AA, Feldman M. 2004. Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biological Journal of the Linnean Society 82: 607-613.
31. Lewis WH, ed. 1980. Polyploidy: biological relevance. New York: Plenum Press.
32. Li W-H. 1985. Accelerated evolution following gene duplication and its implications for the neutralist-selectionist controversy. In: Ohta T, Aoki K, eds. Population genetics and molecular evolution. Berlin: Springer-Verlag, 333-353.
33. Liu B, Brubaker CLGM, Cronn RC, Wendel JF. 2001a. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 43: 874-880.
34. Liu Q, Brubaker CL, Green AG, Marshall DR, Sharp PJ, Singh SP. 2001b. Evolution of the FAD2-1 fatty acid desaturase 5′ UTR intron and the molecular systematics of Gossypium (Malvaceae). American Journal of Botany 88: 92-102.
35. Lukens LN, Quijada PA, Udall J, Pires JC, Schranz ME, Osborn TC. 2004. Genome redundancy and plasticity within ancient and recent Brassica crop species. Biological Journal of the Linnean Society 82: 665-674.
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. Madlung A, Masuelli R, Watson B, Reynolds S, Davison J, Comai L. 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiology 129: 733-746.
39. Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P, Bachellerie JP, Brosius J, Huttenhofer A. 2002. Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Current Biology 10: 2002-2013.
40. Ohno S. 1970. Evolution by gene duplication. New York: Springer-Verlag.
41. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee H-S, Comai L, Madlung A, Doerge RW, Colot V, Martienssen R. 2003. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19: 141-147.
42. Otto SP. 2003. In polyploids, one plus one does not equal two. Trends in Ecology and Evolution 18: 431-433.
43. Pires JC, Zhao J, Schranz ME, Leon EJ, Quijada PA, Lukens L, Osborn TC. 2004. Flowering time divergence and genomic rearrangements in resynthesized polyploids (Brassica). Biological Journal of the Linnean Society 82: 675-688.
44. Richards E, Elgin S. 2002. Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108: 489-500.
45. Schranz ME, Osborn TC. 2000. Novel flowering time variation in the resynthesized polyploid Brassica napus. Journal of Heredity 91: 242-246.
46. Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF. 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Molecular Biology and Evolution 20: 633-643.
47. Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF. 1998. 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 85: 1301-1315.
48. Small RL, Ryburn JA, Wendel JF. 1999. Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Molecular Biology and Evolution 16: 491-501.
49. Small RL, Wendel JF. 1999. The mitochondrial genome of allotetraploid cotton (Gossypium L.). Journal of Heredity 90: 251-253.
50. Small RL, Wendel JF. 2000. Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155: 1913-1926.
51. Small RL, Wendel JF. 2002. Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Molecular Biology and Evolution 19: 597-607.
52. Soltis DE, Soltis PS. 1995. The dynamic nature of polyploid genomes. Proceedings of the National Academy of Sciences, USA 92: 8089-8091.
53. Song K, Lu P, Tang K, Osborn TC. 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Sciences, USA 92: 7719-7723.
54. Stebbins GL. 1950. Variation and evolution in plants. New York: Columbia University Press.
55. Wendel JF. 1989. New World tetraploid cottons contain Old World cytoplasm. Proceedings of the National Academy of Sciences, USA 86: 4132-4136.
56. Wendel JF. 2000. Genome evolution in polyploids. Plant Molecular Biology 42: 225-249.
57. Wendel JF, Cronn RC. 2003. Polyploidy and the evolutionary history of cotton. Advances in Agronomy 78: 139-186.
58. Wendel JF, Rowley R, Stewart JM. 1994. Genetic diversity in and phylogenetic relationships of the Brazilian endemic cotton, Gossypium mustelinum (Malvaceae). Plant Systematic Evolution 192: 49-59.
59. Wendel JF, Schnabel A, Seelanan T. 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences, USA 92: 280-284.
60. Wolffe AP, Matzke MA. 1999. Epigenetics: regulation through repression. Science 286: 481-486.
61. Zhao X-P, Si Y, Hanson RE, Crane CF, Price HJ, Stelly DM, Wendel JF, Paterson AH. 1998. Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Research 8: 479-492.