Fig 1.
Comparison of Ks distributions among WGD, local and dispersed duplicates in the investigated core eudicot genomes.
For Glycine max, Solanum tuberosum and Malus x domestica whose genomes are large and recent duplicates are rampant, a second plot is provided to show the right tails of Ks distributions.
Fig 2.
Different retention rates of dispersed duplicates during the evolution of core eudicots.
(A) Phylogenetic relationships between Arabidopsis thaliana and its outgroups used for estimating the epochs (ages) of dispersed duplicates according to colinearity conservation. (B) Retention rates of Arabidopsis thaliana dispersed duplicates in different epochs. Abbreviations: At: Arabidopsis thaliana; Al: Arabidopsis lyrata; Br: Brassica rapa; Cp: Carica papaya; Tc: Theobroma cacao; Pt: Populus trichocarpa; Vv: Vitis vinifera; St: Solanum tuberosum; Os: Oryza sativa. Dispersed duplicates created after At-Br divergence were named transposed duplicates, while those created between At-Pt and At-St divergence were named relocated γ duplicates. (C) Phylogenetic relationships between Lotus japonicus and its outgroups used for estimating the epochs (ages) of dispersed duplicates according to colinearity conservation. (D) Retention rates of Lotus japonicus dispersed duplicates in different epochs. Abbreviations: Lj: Lotus japonicas; Mt: Medicago truncatula; Gm: Glycine max; Md: Malus x domestica; Pt: Populus trichocarpa; At: Arabidopsis thaliana; Vv: Vitis vinifera; St: Solanum tuberosum; Os: Oryza sativa.
Fig 3.
Functional comparison of different origins of duplicates.
(A) Clustering of functional profiles. (B) Comparison of fold enrichment for essential genes. (C) Comparison of fold enrichment for the genes involved in protein-protein interactions (PPIs).
Fig 4.
Evolutionary significance of relocated γ duplicates.
(A) Comparison of Ks among γ, relocated γ and transposed duplicates. (B) Comparison of Ka/Ks among γ, relocated γ and transposed duplicates. (C) Comparison of expression divergence among γ, relocated γ and transposed duplicates. (D) Comparison of gene regulation divergence among γ, relocated γ and transposed duplicates.