A genome triplication associated with early diversification of the core eudicots

Yuannian Jiao, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E. Bowers, Michael R. McKain, Joel McNeal, Megan Rolf, Daniel R. Ruzicka, Eric Wafula, Norman J. Wickett, Xiaolei Wu, Yong Zhang, Jun Wang, Yeting Zhang, Eric J. Carpenter, Michael K. Deyholos, Toni M. Kutchan, Andre S. Chanderbali, Pamela S. Soltis, Dennis W. StevensonRichard McCombie, J. C. Pires, Gane Ka Shu Wong, Douglas E. Soltis, Claude W. dePamphilis*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

337 Scopus citations


Background: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear.Results: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago.Conclusions: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.

Original languageEnglish (US)
Article numberR3
JournalGenome biology
Issue number1
StatePublished - Jan 26 2012

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Cell Biology


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