Skip to main content
SpringerLink
Log in

Assessing the monophyly of polyploid Gossypium species

  • Short Communication
  • Published:
Plant Systematics and Evolution Aims and scope Submit manuscript

Abstract

The origin and monophyly of the polyploid cotton (Gossypium) species has been largely accepted, despite the lack of explicit phylogenetic evidence. Recent studies in other polyploid systems have demonstrated that multiple origins for polyploid species are much more common than once thought, raising the possibility that Gossypium polyploids also had multiple origins, as postulated by some authors. To test the monophyly of polyploid cotton, we sequenced a 2.8-kb intergenic region from all diploid species belonging to the genome groups from which the polyploid originates. The resulting phylogenetic analyses strongly support a single origin of polyploid cotton involving a D-genome ancestor related to Gossypium raimondii and an A-genome ancestor that was sister to both extant A-genome species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

References

  • Adams KL, Wendel JF (2005) Novel patterns of gene expression in polyploid plants. Trends Genet 21(10):539–543

    PubMed  CAS  Google Scholar 

  • Adams KL, Wendel J (2006) Allele-specific, bi-directional silencing of an alcohol dehydrogenase gene in different organs of interspecific cotton hybrids. Genetics 17:2139–2142

    Google Scholar 

  • 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(8):4649–4654

    PubMed  CAS  Google Scholar 

  • Adams KL, Percifield R, Wendel JF (2004) Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168(4):2217–2226

    PubMed  CAS  Google Scholar 

  • Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F (2004) Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20(3):407–415

    PubMed  CAS  Google Scholar 

  • Alvarez I, Cronn R, Wendel JF (2005) Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes. Plant Syst Evol 252(3–4):199–214

    CAS  Google Scholar 

  • Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel JF (2009a) Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics 182(2):503–517

    PubMed  CAS  Google Scholar 

  • Chaudhary B, Hovav R, Flagel L, Mittler R, Wendel JF (2009b) Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genomics 10:378

    PubMed  Google Scholar 

  • 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. J Mol Evol 42(6):685–705

    PubMed  CAS  Google Scholar 

  • Cronn R, Small RL, Haselkorn T, Wendel JF (2003) Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57(11):2475–2489

    PubMed  CAS  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797. doi:10.1093/nar/gkh340

    PubMed  CAS  Google Scholar 

  • Endrizzi JE, Turcotte EL, Kohel RJ (1985) Genetics, cytology, and evolution of Gossypium. In: Caspari EW, John GS (eds) Advances in genetics, vol 23. Academic, London, pp 271–375

    Google Scholar 

  • Flagel LE, Chen L, Chaudhary B, Wendel JF (2009) Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton. J Hered 100(4):487–490 (pii: esp003)

    PubMed  CAS  Google Scholar 

  • Fryxell PA (1979) The natural history of the cotton tribe (Malvaceae, tribe Gossypieae), 1st edn. Texas A&M University Press, College Station

    Google Scholar 

  • Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF (2004) Incongruent patterns of local and global genome size evolution in cotton. Genome Res 14(8):1474–1482. doi:10.1101/gr.2673204

    PubMed  CAS  Google Scholar 

  • Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF (2007) Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant J 50(6):995–1006

    PubMed  CAS  Google Scholar 

  • Grover CE, Yu Y, Wing RA, Paterson AH, Wendel JF (2008) A phylogenetic analysis of indel dynamics in the cotton genus. Mol Biol Evol 25(7):1415–1428

    PubMed  CAS  Google Scholar 

  • Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5):696–704

    PubMed  Google Scholar 

  • Hall T (2007) BioEdit: biological sequence alignment editor written for Windows 95/98/NT/2000/XP. http://www.mbio.ncsu.edu/bioedit/bioedit.html

  • Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF (2006) Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16(10):1252–1261

    PubMed  CAS  Google Scholar 

  • Hawkins JS, Hu G, Rapp RA, Grafenberg JL, Wendel JF (2008) Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium. Genome 51(1):11–18

    PubMed  CAS  Google Scholar 

  • Hovav R, Chaudhary B, Udall JA, Flagel L, Wendel JF (2008) Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton. Genetics 179(3):1725–1733

    PubMed  Google Scholar 

  • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754–755

    PubMed  CAS  Google Scholar 

  • Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473(7345):97–100

    PubMed  CAS  Google Scholar 

  • Johnson BL (1975) Gossypium palmeri and a Polyphyletic Origin of New World Cottons. Bull Torrey Bot Club 102(6):340–349

    Google Scholar 

  • McDade L (1990) Hybrids and phylogenetic systematics I. patterns of character expression in hybrids and their implications for cladistic analysis. Evolution 44(6):1685–1700

    Google Scholar 

  • McDade L (1995) Hybridization and phylogenetics. In: Hoch PC, Stephenson AG (eds) Experimental and molecular approaches to plant biosystematics. Missouri Botanical Garden, Missouri

    Google Scholar 

  • Parks CR, Ezell WL, Williams DE, Dreyer DL (1975) The application of flavonoid distribution to taxonomic problems in the genus Gossypium. Bull Torrey Bot Club 102(6):350–361

    Google Scholar 

  • Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25(7):1253–1256

    PubMed  CAS  Google Scholar 

  • Rapp R, Udall J, Wendel J (2009) Genomic expression dominance in allopolyploids. BMC Biol 7(1):18

    PubMed  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572–1574

    PubMed  CAS  Google Scholar 

  • Salmon A, Flagel L, Ying B, Udall JA, Wendel JF (2010) Homoeologous nonreciprocal recombination in polyploid cotton. New Phytol 186(1):123–134. doi:10.1111/j.1469-8137.2009.03093.x

    PubMed  CAS  Google Scholar 

  • Small RL, Wendel JF (1999) The mitochondrial genome of allotetraploid cotton (Gossypium L.). J Hered 90:251–253

    Google Scholar 

  • Small RL, Wendel JF (2002) Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Mol Biol Evol 19(5):597–607

    PubMed  CAS  Google Scholar 

  • Soltis D, Soltis P (1993) Molecular data facilitate a reevaluation of traditional tenets of polyploid evolution. Crit Rev Plant Sci 12:243

    CAS  Google Scholar 

  • Soltis D, Soltis P (1999) Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14:348

    PubMed  Google Scholar 

  • Soltis DE, Soltis PS, Tate JA (2004) Advances in the study of polyploidy since plant speciation. New Phytol 161(1):173–191. doi:10.1046/j.1469-8137.2003.00948.x

    CAS  Google Scholar 

  • Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS (2009) Polyploidy and angiosperm diversification. Am J Bot 96(1):336–348

    PubMed  Google Scholar 

  • Tate J, Ni Z, Scheen A, Koh J, Gilbert C (2006) Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173:1599

    PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Chapter 2:Unit 2.3. doi:10.1002/0471250953.bi0203s00

  • Wendel JF (1989) New World tetraploid cottons contain Old World cytoplasm. Proc Natl Acad Sci 86(11):4132–4136

    PubMed  CAS  Google Scholar 

  • Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. In: Advances in agronomy, vol 78. Academic Press, London, pp 139–186

  • Wendel JF, Schnabel A, Seelanan T (1995) Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad Sci 92(1):280–284

    PubMed  CAS  Google Scholar 

  • Wendel JF, Brubaker CL, Seelanan T (2010) The origin and evolution of Gossypium. In: Stewart JM, Oosterhuis DM, Heitholt JJ (eds) Physiology of cotton. Springer, Dordrecht, pp 1–18

    Google Scholar 

  • Wilgenbusch JC, Swofford D (2003) Inferring evolutionary trees with PAUP*. Curr Protoc Bioinformatics Chapter 6: Unit 6.4

Download references

Author information

Authors and Affiliations

  1. Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA

    C. E. Grover, K. K. Grupp, R. J. Wanzek & J. F. Wendel

Authors
  1. C. E. Grover
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. K. K. Grupp
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. J. Wanzek
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. F. Wendel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to C. E. Grover.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLS 54 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Grover, C.E., Grupp, K.K., Wanzek, R.J. et al. Assessing the monophyly of polyploid Gossypium species. Plant Syst Evol 298, 1177–1183 (2012). https://doi.org/10.1007/s00606-012-0615-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00606-012-0615-7

Keywords

Search

Navigation