Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 16, 2008, Pages 6191-6195

  Hovav, Ran ^a   Udall, Joshua A ^a,b   Chaudhary, Bhupendra ^a   Rapp, Ryan ^a   Flagel, Lex ^a   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

Cotton; Polyploidy; Subfunctionalization

Indexed keywords

ARTICLE; CELL MATURATION; COTTON; EVOLUTION; GENE DUPLICATION; GENE EXPRESSION; PLANT DEVELOPMENT; POLYPLOIDY; PRIORITY JOURNAL; TRICHOME; DUPLICATE GENE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; MOLECULAR EVOLUTION;

ANIMALIA; EUKARYOTA; FUNGI; GOSSYPIUM; GOSSYPIUM HIRSUTUM; GOSSYPIUM THURBERI;

COTTON FIBER; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, DUPLICATE; GENOME, PLANT; GOSSYPIUM; POLYPLOIDY; TRANSCRIPTION, GENETIC;

EID: 43149114448     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0711569105     Document Type: Article

References (35)

1. Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34:401-437.
2. Leitch IJ, Bennett MD (1997) Polyploidy in angiosperms. Trends Plant Sci 2:470-476.
3. Rieseberg LH (2001) Polyploid evolution: Keeping the peace at genomic reunions. Curr Biol 11:R925-R928.
4. Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol 29:365-379.
5. Adams KL, Wendel JF (2005) Novel patterns of gene expression in polyploid plants. Trends Genet 21:539-543.
6. Lynch M (2007) The Origins of Genome Architecture (Sinauer, Sunderland, MA).
7. Ohno S (1970) Evolution by Gene Duplication (Springer, New York).
8. Lynch M (2002) Genomics - Gene duplication and evolution. Science 297:945-947.
9. Force A, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
10. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
11. Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100:4649-4654.
12. Mochida K, Yamazaki Y, Ogihara Y (2004) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Genet Genomics 270:371-377.
13. Adams KL, Percifield R, Wendel JF (2004) Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168:2217-2226.
14. Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459-473.
15. Rachel WA, Durrett R (2004) Subfunctionalization: How often does it occur? How long does it take? Theor Popul Biol 66:93-100.
16. Liu Z, Adams KL (2007) Expression partitioning between genes duplicated by polyploidy under abiotic stress and during organ development. Curr Biol 17.1699-1674.
17. Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Adv Agron 78:139-186.
18. Arpat AB, et al. (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Mol Biol 54:911-929.
19. Shi YH, et al. (2006) Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18:651-664.
20. Taliercio EW, Boykin D (2007) Analysis of gene expression in cotton fiber initials. BMC Plant Biol 10.1186/1471-2229-7-22.
21. Hovav R, et al. (2008) A majority of genes are expressed in the single-celled seed trichome of cotton. Planta 227:319-329.
22. Wu Y, Liewellyn DJ, Ruggiero K, Al-Ghazi Y, Dennis ES (2007) Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of rapidly expanding fibre initials cells on surface of cotton ovules. Planta 226:1475-1490.
23. Udall JA, Swanson JM, Nettleton D, Percifield RJ, Wendel JF (2006) A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 173:1823-1827.
24. Wang JL, et al. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507-517.
25. Hegarty MJ, et al. (2006) Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr Biol 16:1652-1659.
26. Stupar RM, et al. (2007) Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176:2055-2067.
27. Springer NM, Stupar RM (2007) Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 19:2391-2402.
28. Baudo MM, et al. (2006) Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J 4:369-380.
29. Poole R, Barker G, Wilson ID, Coghill JA, Edwards KJ (2007) Measuring global gene expression in polyploidy; a cautionary note from allohexaploid wheat. Funct Integr Genomics 7:207-219.
30. Yang SS, et al. (2006) Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant J 47:761-775.
31. Rong J, et al. (2007) Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development Genetics 176:2577-2588.
32. Brubaker CL, Wendel JF (1994) Reevaluating the origin of domesticated cotton (Gossypium hirsutum Malvaceae) using nuclear Restriction-Fragment- Length-Polymorphisms (RFLPs). Am J Bot 81:1309-1326.
33. Applequist WL, Cronn R, Wendel JF (2001) Comparative development of fiber in wild and cultivated cotton. Evol Dev 3:3-17.
34. Storey JD, Tibshirani R (2003) SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays. The Analysis of Gene Expression Data: Methods and Software, eds Parmigiani G, Garrett ES, Irizarry RA, Zeger SL (Springer, New York), pp 272-290.
35. Bluthgen N, et al. (2005) Biological profiling of gene groups utilizing Gene Ontology. Genome Inform Ser Workshop Genome Inform 16:106-115.