J Integr Plant Biol. ›› 2019, Vol. 61 ›› Issue (1): 12-31.DOI: 10.1111/jipb.12746

• Research Articles • Previous Articles     Next Articles

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Justin L. Conover1†, Nisa Karimi2†, Noah Stenz2‡, Cecile Ane2,3, Corrinne E. Grover1, Cynthia Skema4, Jennifer A. Tate5, Kirsten Wolff6, Samuel A. Logan6, Jonathan F. Wendel1 and David A. Baum2,7*   

  1. 1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
    2Department of Botany, University of Wisconsin Madison, WI, 53706, USA
    3Department of Statistics, University of Wisconsin Madison, WI, 53706, USA
    4Morris Arboretum of the University of Pennsylvania, 100 E. Northwestern Avenue, Philadelphia, PA, 19118, USA
    5Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
    6School of Natural and Environmental Sciences, Newcastle University, NE1 7RU, UK
    7Wisconsin Institute for Discovery, 330 N Orchard St, Madison, WI 53715, USA

    These authors contributed equally to this work.
    Current address: 7421 Allemande Way, Chattanooga, TN, 37421, USA

    Email: David A. Baum (dbaum@wisc.edu)
  • Received:2018-08-23 Accepted:2018-11-18 Online:2018-11-26 Published:2019-01-01

Abstract: Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

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