Gene copy number evolution during tetraploid cotton radiation
Open accessAbstract
After polyploid formation, retention or loss of duplicated genes is not random. Genes with some functional domains are convergently restored to 'singleton' state after many independent genome duplications, and have been referred to as 'duplication-resistant' (DR) genes. To further explore the timeframe for their restoration to the singleton state, 27 cotton homologs of genes found to be 'DR' in Arabidopsis were selected based on diagnostic Pfam domains. Their copy numbers were studied using southern hybridization and sequence analysis in five tetraploid species and their ancestral A and D genome diploids. DR genes had significantly lower copy number than gene families hybridizing to randomly selected cotton ESTs. Three DR genes showed complete loss of D genome-derived homoeologs in some or all tetraploid species. Prior analysis has shown gene loss in polyploid cotton to be rare, and herein only one randomly selected gene showed loss of a homoeolog in only one of the five tetraploid species (Gossypium mustelinum). BAC sequencing confirmed two cases of gene loss in tetraploid cotton. Divergence among 5' sequences of DR genes amplified from G. arboreum, G. raimondii, and Gossypioides kirkii was correlated with gene copy number. These results show that genes containing Pfam domains associated with duplication resistance in Arabidopsis have also been preferentially restored to low copy number after a more recent polyploidization event in cotton. In tetraploid cotton, genes from the progenitor D genome seem to experience more gene copy number divergence than genes from the A genome. Together with D subgenome-biased alterations in gene expression, perhaps gene loss may contribute to the relatively larger portion of quantitative trait variation attributable to D than A subgenome chromosomes of tetraploid cotton.
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The higher number of CDK genes in G. hirsutum is likely due to whole genome duplication and polyploidization of the A and D genomes.
“this could be due to whole genome duplication (WGD), being tetraploid cotton emerged from the polyploidization of the A and D genomes [56].”
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Cites
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833 · see citing works
The Evolutionary Fate and Consequences of Duplicate Genes
Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988 · see citing works
The Sorghum bicolor genome and the diversification of grasses
Paterson, A. H., Bowers, J., Bruggmann, R., Dubchak, I. L., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., et al. (2009) · Nature · doi:10.1038/nature07723 · Cited by 3,100 · see citing works
Self-citationThe advantages and disadvantages of being polyploid
Comai, L. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1711 · Cited by 2,308 · see citing works
Synteny and Collinearity in Plant Genomes
Tang, H., Bowers, J., Wang, X., Ming, R., Alam, M. S., & Paterson, A. H. (2008) · Science · doi:10.1126/science.1153917 · Cited by 1,620 · see citing works
Self-citationUnravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
Bowers, J., Chapman, B., Rong, J., & Paterson, A. H. (2003) · Nature · doi:10.1038/nature01521 · Cited by 1,595 · see citing works
Self-citationThe Probability of Duplicate Gene Preservation by Subfunctionalization
Lynch, M. F., & Force, A. G. (2000) · Genetics · doi:10.1093/genetics/154.1.459 · Cited by 1,557 · see citing works
Paterson, A. H., Bowers, J., & Chapman, B. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307901101 · Cited by 1,090 · see citing works
Self-citationThe draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne‐Laporte, A., Saw, J. H. W., Senin, P., Wang, W., Ly, B. V., Lewis, K. L. T., et al. (2008) · Nature · doi:10.1038/nature06856 · Cited by 1,087 · see citing works
Self-citationFunctional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution[W]
Blanc, G., & Wolfe, K. H. (2004) · The Plant Cell · doi:10.1105/tpc.021410 · Cited by 1,068 · see citing works
Song, K., Lu, P., Tang, K., & Osborn, T. C. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.17.7719 · Cited by 1,019 · see citing works
Modeling gene and genome duplications in eukaryotes
Maere, S., Bodt, S. D., Raes, J., Casneuf, T., MONTAGU, M. V., Kuiper, M. T. R., & de Peer, Y. V. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501102102 · Cited by 917 · see citing works
Polyploidy and the evolutionary history of cotton
Wendel, J. F., & Cronn, R. (2003) · Advances in agronomy · doi:10.1016/s0065-2113(02)78004-8 · Cited by 851 · see citing works
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
Aury, J., Jaillon, O., Duret, L., Noël, B., Jubin, C., Porcel, B. M., Segurens, B., Daubin, V., Anthouard, V., Aiach, N. G., et al. (2006) · Nature · doi:10.1038/nature05230 · Cited by 835 · see citing works
Adams, K. L., Cronn, R., Percifield, R. J., & Wendel, J. F. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630618100 · Cited by 819 · see citing works
Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat
Kashkush, K., Feldman, M., & Levy, A. A. (2002) · Nature Genetics · doi:10.1038/ng1063 · Cited by 743 · see citing works
Shaked, H., Kashkush, K., Özkan, H., et al. (2001) · The Plant Cell · doi:10.1105/tpc.010083 · Cited by 698 · see citing works
He, X., & Zhang, J. (2005) · Genetics · doi:10.1534/genetics.104.037051 · Cited by 694 · see citing works
X-chromosome inactivation: counting, choice and initiation
Avner, P. R., & Heard, É. (2001) · Nature Reviews Genetics · doi:10.1038/35047580 · Cited by 693 · see citing works
Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops-Triticum) Group
Özkan, H., Levy, A. A., & Feldman, M. (2001) · The Plant Cell · doi:10.1105/tpc.010082 · Cited by 656 · see citing works
Gene Loss, Silencing and Activation in a Newly Synthesized Wheat Allotetraploid
Kashkush, K., Feldman, M., & Levy, A. A. (2002) · Genetics · doi:10.1093/genetics/160.4.1651 · Cited by 652 · see citing works
Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype
Gaeta, R. T., Pires, J. C., Iñiguez-Luy, F., et al. (2007) · The Plant Cell · doi:10.1105/tpc.107.054346 · Cited by 649 · see citing works
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene mapsPreprint
Tang, H., Wang, X., Bowers, J., Ming, R., Alam, M. S., & Paterson, A. H. (2008) · Genome Research · doi:10.1101/gr.080978.108 · Cited by 648 · see citing works
Self-citationNew World tetraploid cottons contain Old World cytoplasm
Wendel, J. F. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.11.4132 · Cited by 570 · see citing works
Paucity of Genes on the Drosophila X Chromosome Showing Male-Biased Expression
Parisi, M. J., Nuttall, R., Naiman, D. Q., Bouffard, G. G., Malley, J. D., Andrews, J., Eastman, S., & Oliver, B. (2003) · Science · doi:10.1126/science.1079190 · Cited by 541 · see citing works
Phenotypic Instability and Rapid Gene Silencing in Newly Formed Arabidopsis Allotetraploids
Comai, L., Tyagi, A. P., Winter, K., et al. (2000) · The Plant Cell · doi:10.1105/tpc.12.9.1551 · Cited by 533 · see citing works
Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops-Triticum) Group
Özkan, H. (2001) · The Plant Cell · doi:10.1105/tpc.13.8.1735 · Cited by 482 · see citing works
Feldman, M., Liu, B., Segal, G., et al. (1997) · Genetics · doi:10.1093/genetics/147.3.1381 · Cited by 473 · see citing works
O'Neill, R. J. W., O’Neill, M. J., & Graves, J. A. M. (1998) · Nature · doi:10.1038/29985 · Cited by 457 · see citing works
Freeling, M., & Thomas, B. C. (2006) · Genome Research · doi:10.1101/gr.3681406 · Cited by 451 · see citing works
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
Scannell, D. R., Byrne, K. P., Gordon, J., Wong, S., & Wolfe, K. H. (2006) · Nature · doi:10.1038/nature04562 · Cited by 429 · see citing works
Reinisch, A. J., Dong, J. M., Brubaker, C. L., et al. (1994) · Genetics · doi:10.1093/genetics/138.3.829 · Cited by 414 · see citing works
Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes
Brunet, F., Crollius, H. R., Paris, M., Aury, J., Gibert, P., Jaillon, O., Laudet, V., & Robinson‐Rechavi, M. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl049 · Cited by 413 · see citing works
Hawkins, J., Kim, H. R., Nason, J. D., Wing, R. A., & Wendel, J. F. (2006) · Genome Research · doi:10.1101/gr.5282906 · Cited by 410 · see citing works
Shaked, H. (2001) · The Plant Cell · doi:10.1105/tpc.13.8.1749 · Cited by 380 · see citing works
Chen, Z. J., & Pikaard, C. S. (1997) · Genes & Development · doi:10.1101/gad.11.16.2124 · Cited by 375 · see citing works
Rong, J., Abbey, C. A., Bowers, J., et al. (2004) · Genetics · doi:10.1534/genetics.166.1.389 · Cited by 371 · see citing works
Self-citationRate Variation Among Nuclear Genes and the Age of Polyploidy in Gossypium
Senchina, D. S. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg065 · Cited by 365 · see citing works
Polyploid formation in cotton is not accompanied by rapid genomic changes
Liu, B., Brubaker, C. L., Mergeai, G., et al. (2001) · Genome · doi:10.1139/g01-011 · Cited by 356 · see citing works
Polyploid formation created unique avenues for response to selection in Gossypium (cotton)
Jiang, C.-X., Wright, R., El‐Zik, K. M., et al. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.8.4419 · Cited by 354 · see citing works
The Part Played by Recurrent Mutation in Evolution
Haldane, J. B. S. (1933) · The American Naturalist · doi:10.1086/280465 · Cited by 324 · see citing works
Protein-coding genes are epigenetically regulated in Arabidopsis polyploids
Lee, H.-S., & Chen, Z. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.121064698 · Cited by 313 · see citing works
Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid
Adams, K. L., Percifield, R. J., & Wendel, J. F. (2004) · Genetics · doi:10.1534/genetics.104.033522 · Cited by 279 · see citing works
Dispersed Repetitive DNA Has Spread to New Genomes Since Polyploid Formation in CottonPreprint
Zhao, X., Si, Y., Hanson, R. E., et al. (1998) · Genome Research · doi:10.1101/gr.8.5.479 · Cited by 278 · see citing works
Rong, J., Feltus, F. A., Waghmare, V. N., et al. (2007) · Genetics · doi:10.1534/genetics.107.074518 · Cited by 272 · see citing works
Self-citationFunctional genomics of cell elongation in developing cotton fibers
Arpat, A. B., Waugh, M. E., Sullivan, J. P., et al. (2004) · Plant Molecular Biology · doi:10.1007/s11103-004-0392-y · Cited by 266 · see citing works
Udall, J. A., Quijada, P., & Osborn, T. C. (2004) · Genetics · doi:10.1534/genetics.104.033209 · Cited by 258 · see citing works
Chen, Z. J., & Pikaard, C. S. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.7.3442 · Cited by 249 · see citing works
Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
Seoighe, C., & Gehring, C. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.07.008 · Cited by 246 · see citing works
Yang, S. S., Cheung, F., Lee, J. J., Ha, M., Wei, N. E., Sze, S., Stelly, D. M., Thaxton, P. M., Triplett, B. A., Town, C. D., et al. (2006) · The Plant Journal · doi:10.1111/j.1365-313x.2006.02829.x · Cited by 213 · see citing works
Chapman, B., Bowers, J., Feltus, F. A., & Paterson, A. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507782103 · Cited by 198 · see citing works
Self-citationPATERSON, A., Chapman, B., Kissinger, J. C., Bowers, J., Feltus, F. A., & Estill, J. C. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.09.003 · Cited by 186 · see citing works
Self-citationPossible Significance of Duplication in Evolution
Stephens, S. G. (1951) · Advances in genetics · doi:10.1016/s0065-2660(08)60237-0 · Cited by 172 · see citing works
A global assembly of cotton ESTsPreprint
Udall, J. A., Swanson, J. M., Haller, K., et al. (2006) · Genome Research · doi:10.1101/gr.4602906 · Cited by 156 · see citing works
Buggs, R. J. A., Doust, A. N., Tate, J. A., et al. (2009) · Heredity · doi:10.1038/hdy.2009.24 · Cited by 152 · see citing works
Very Low Gene Duplication Rate in the Yeast Genome
Gao, L., & Innan, H. (2004) · Science · doi:10.1126/science.1102033 · Cited by 145 · see citing works
Extensive Concerted Evolution of Rice Paralogs and the Road to Regaining Independence
Wang, X., Tang, H., Bowers, J., et al. (2007) · Genetics · doi:10.1534/genetics.107.073197 · Cited by 139 · see citing works
Nicolas, S., Leflon, M., Monod, H., et al. (2009) · The Plant Cell · doi:10.1105/tpc.108.062273 · Cited by 123 · see citing works
Disteche, C. M., Filippova, G. N., & Tsuchiya, K. D. (2002) · Cytogenetic and Genome Research · doi:10.1159/000071572 · Cited by 116 · see citing works
Korbel, J. O., Kim, P. M., Chen, X., Urban, A. E., Weissman, S. M., Snyder, M. P., & Gerstein, M. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.02.005 · Cited by 105 · see citing works
Feltus, F. A., Singh, H. P., Lohithaswa, H. C., et al. (2006) · PLANT PHYSIOLOGY · doi:10.1104/pp.105.074203 · Cited by 100 · see citing works
Self-citationMicrocolinearity and genome evolution in theAdhAregion of diploid and polyploid cotton (Gossypium)
Grover, C. E., Kim, H., Wing, R. A., Paterson, A. H., & Wendel, J. F. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03102.x · Cited by 86 · see citing works
Self-citationThe (epi)genetic control of mammalian X-chromosome inactivation
Lee, J. T., & Jaenisch, R. (1997) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(97)80138-4 · Cited by 80 · see citing works
Parallel Domestication, Convergent Evolution and Duplicated Gene Recruitment in Allopolyploid Cotton
Hovav, R., Chaudhary, B., Udall, J. A., et al. (2008) · Genetics · doi:10.1534/genetics.108.089656 · Cited by 69 · see citing works
Small, R. L., & Wendel, J. F. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004119 · Cited by 63 · see citing works
Rong, J., Bowers, J., Schulze, S. R., Waghmare, V. N., Rogers, C. J., Pierce, G. J., Zhang, H., Estill, J. C., & Paterson, A. H. (2005) · Genome Research · doi:10.1101/gr.3907305 · Cited by 62 · see citing works
Self-citationWu, Y., Zhu, Z., Ma, L., et al. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn052 · Cited by 58 · see citing works
Brief communication. The mitochondrial genome of allotetraploid cotton (Gossypium L.)
Small, R. L. (1999) · Journal of Heredity · doi:10.1093/jhered/90.1.251 · Cited by 42 · see citing works
Expression of a lipid transfer protein gene family during cotton fibre development
Orford, S. J., & Timmis, J. N. (2000) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/s1388-1981(99)00194-8 · Cited by 41 · see citing works
Rapid differentiation of homeologous chromosomes in newly-formed allopolyploid wheat
Özkan, H., Levy, A. A., & Feldman, M. (2002) · Israel Journal of Plant Sciences · doi:10.1560/e282-pv55-g4xt-drwj · Cited by 36 · see citing works
O'Neill, R. J. W., O’Neill, M. J., & Graves, J. A. M. (2002) · Nature · doi:10.1038/nature01162 · Cited by 28 · see citing works
Characterisation of a cotton gene expressed late in fibre cell elongation
Orford, S. J., Carney, T. J., Olesnicky, N. S., et al. (1999) · Theoretical and Applied Genetics · doi:10.1007/s001220051132 · Cited by 6 · see citing works
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- Authors
- Rong, J., Feltus, F. A., Liu, L., Lin, L., & Paterson, A. H.
- Affiliations
- University of Georgia (US)
- Corresponding author
- Paterson, A H
- Venue
- Heredity
- Published
- 2010-02-17
- Volume
- 105
- Issue
- 5
- Pages
- 463-472
- ISSN
- 0018-067X (ISSN-L)
- 1365-2540
- OpenAlex
- W2094844584
- Cited by
- 31
- References
- 72
- Citations by year
- 2025: 1 · 2024: 5 · 2023: 1 · 2021: 2 · 2020: 4 · 2019: 1 · 2018: 2 · 2017: 1 · 2016: 1 · 2015: 1 · 2014: 4 · 2013: 2 · 2012: 4
- FWCI
- 3.07
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Heredity (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Research in Cotton Cultivation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- gene copy number, polyploidy, tetraploid cotton, whole-genome duplication, Pfam domains, Gossypium, Gossypium arboreum, Gossypium raimondii, Gossypium mustelinum, quantitative trait variation
- MeSH terms
- Autoradiography, Gossypium, Polyploidy, Blotting, Southern, Polymerase Chain Reaction, Gene Dosage, Evolution, Molecular, Expressed Sequence Tags, Gene Duplication
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