title: A genome triplication associated with early diversification of the core eudicots.
abstract: 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.
authors.affiliation: Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Yuannian
authors.initials: Y
authors.lastname: Jiao
authors.forename: Jim
authors.initials: J
authors.lastname: Leebens-Mack
authors.forename: Saravanaraj
authors.initials: S
authors.lastname: Ayyampalayam
authors.forename: John E
authors.initials: JE
authors.lastname: Bowers
authors.forename: Michael R
authors.initials: MR
authors.lastname: McKain
authors.forename: Joel
authors.initials: J
authors.lastname: McNeal
authors.forename: Megan
authors.initials: M
authors.lastname: Rolf
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Ruzicka
authors.forename: Eric
authors.initials: E
authors.lastname: Wafula
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Wickett
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Wu
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Yeting
authors.initials: Y
authors.lastname: Zhang
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Carpenter
authors.forename: Michael K
authors.initials: MK
authors.lastname: Deyholos
authors.forename: Toni M
authors.initials: TM
authors.lastname: Kutchan
authors.forename: Andre S
authors.initials: AS
authors.lastname: Chanderbali
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
authors.forename: Richard
authors.initials: R
authors.lastname: McCombie
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.forename: Claude W
authors.initials: CW
authors.lastname: Depamphilis
mesh_terms: D019143:Evolution, Molecular; D020440:Gene Duplication; D020869:Gene Expression Profiling; D049810:Genetic Speciation; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011123:Polyploidy
chemical_list: D010940:Plant Proteins