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

作     者：Justin L.Conover Nisa Karimi Noah Stenz Cecile Ane Corrinne E.Grover Cynthia Skema Jennifer A.Tate Kirsten Wolff Samuel A.Logan Jonathan F.Wendel David A.Baum 

作者机构：Department of EcologyEvolutionand Organismal BiologyIowa State University Department of BotanyUniversity of Wisconsin Madison Department of StatisticsUniversity of Wisconsin Madison Morris Arboretum of the University of Pennsylvania Institute of Fundamental SciencesMassey University School of Natural and Environmental SciencesNewcastle University Wisconsin Institute for Discovery 

出 版 物：《Journal of Integrative Plant Biology》 (植物学报（英文版）)

年 卷 期：2019年第61卷第1期

页      面：12-31页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 0901[农学-作物学] 0703[理学-化学] 0902[农学-园艺学] 

基　　金：provided through the National Science Foundation (award 1354268 to DAB, CA, CEG, and JFW) Cotton Incorporated (to JFW) 

主　　题：research data 

摘      要：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.