Polyploidy events in the history of angiosperm evolution. (A) Summary of polyploidy events in the history of angiosperm evolution, with a focus on the possible phylogenetic origins of the three subgenomes comprising the gamma paleohexaploidy event in core eudicots. Synteny analysis of the Nelumbo genome indicates that gamma is shared only within the core eudicots; however, phylogenomic analysis suggests a more complex history since around half of the gamma pairs were duplicated core-eudicot-wide and the other half eudicot-wide (See Table S10 in Additional file 1). AA, BB, and CC are three subgenomes of the ancestral hexaploidy. Three possible phylogenetic origins of the ancestral AA genome involved in gamma are denoted by 1, 2 and 3. Lamda is defined as the most recent polyploidy event in the evolutionary history of Nelumbo. All the other Greek symbols are well-known polyploidy events in the evolutionary history of angiosperms. Gamma: genome-triplication (hexaploid) event in core eudicot genomes [7, 23]; Sigma and rho: genome duplications detected in grass genomes ; Epsilon: angiosperm-wide duplication detected in large-scale gene family phylogenies. Based on gene tree phylogenomics, we hypothesize that the triplication event involved a tetraploid event (BBCC red star) first, then subgenome AA combined with BBCC to form hexaploidy AABBCC (blue dashed line). (B) Predicted gene tree topologies of hypothetical origins of the AA subgenome of the gamma paleohexaploidy. A, B, C indicate surviving genes inherited from AA, BB, CC subgenomes of the AABBCC ancestral hexaploidy. N indicates genes of Nelumbo.