1. Volume 11, Issue 3, Pages 414-428 (March 2018)
Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms 
Ren Ren, Haifeng Wang, Chunce Guo, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma, Ji Qi 
Molecular Plant 
Volume 11, Issue 3, Pages (March 2018)
DOI: /j.molp
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2. Figure 1
Comparisons of Ks Distributions of Duplicated Genes on Different Evolutionary Stages Divided by Phylogenetic Information for Arabidopsis thaliana.
(A) Numbers of GDs at different nodes (nodes 1–5, filled circles) of the species tree are colored in red, blue, green, orange, and purple, respectively.
(B) The distribution of Ks for GDs at each of the nodes (nodes 1–5), in colors consistent with (A). The black dotted line denotes the summarized GD counts from all nodes.
(C) Distribution of Ks for gene pairs recognized by using all-against-all BLAST matches.
(D) Distribution of Ks for gene pairs recognized by using reciprocal best hits of all-against-all BLAST matches. Three bell curves represent significant components fitted to Ks frequency by using mixture model test of the EMMIX software (McLachlan et al., 1999).
Molecular Plant  , DOI: ( /j.molp )
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3. Figure 2
A Model for Exponential Decrease over Time of Number of Duplication Events, with Actually Detected GDs.
Each dot denotes GDs corresponding to a WGD at a node on the species tree in Supplemental Figure 1. The analyses here of public genome and transcriptome datasets provided strong support for WGDs (blue and purple dots, respectively), consistent with previous reports. Red dots are newly detected WGDs in this study, and gray dots represent GDs for nodes not strong enough to be considered as WGD here. The blue solid curve represents proposed theoretical decay rate of GDs after duplication, estimated based on comparison of retained GD numbers with corresponding median Ks values from previously reported WGDs associated with available genomes, while the purple curve is based on reported WGDs with transcriptomic data in this study. The one-fold SDs for the two decay curves are colored by blue and yellow backgrounds, respectively. Linear regression analysis of Ks values and evolutionary time (calibrated by using fossil records [Magallón et al., 2015]) of previously reported WGDs is illustrated in the top right panel.
Molecular Plant  , DOI: ( /j.molp )
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4. Figure 3
Illustration of Phylogenetic Relationships of 105 Angiosperms and Proposed WGDs.
Previously reported WGDs by using genome and transcriptome information are denoted by blue dots and purple dots, respectively. Newly detected WGDs are represented by red dots. Numbers of detected GDs associated with previously reported and newly detected WGDs are available in Supplemental Figure 1. Branch lengths on the tree are not to scale.
Molecular Plant  , DOI: ( /j.molp )
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5. Figure 4
Enrichment Analysis for Duplicated Genes on Different GO Categories for Each WGD Shown in Figure 3.
Molecular Plant  , DOI: ( /j.molp )
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6. Figure 5
Comparison of GD Retention between Lineages with Multiple Rounds of WGDs with Their Sister Clades without Recent WGDs.
(A) Possible patterns of loss of gene duplicates from an ancient WGD, shared by Gossypium raimondii (labeled by “G”) and Theobroma cacao (labeled by “T”). G. raimondii underwent a further WGD after the divergence from T. cacao, which lacks a recent WGD. The number under each tree denotes the counts of corresponding type GD retention.
(B) Illustration of retention of recent gene duplicates when both ancient duplicates are preserved.
(C) Comparison of observed numbers gene pairs and expected counts for the three patterns in (B). Each dot represents for a node on the species tree with multiple rounds of studied or proposed WGDs, and is colored by level of its median Ks value.
Molecular Plant  , DOI: ( /j.molp )
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7. Figure 6
Comparison of Time Spans with Global Climate Changes with Predicted Ages of WGDs Calibrated by Using Fossil Data and Computational Estimation.
Molecular Plant  , DOI: ( /j.molp )
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8. Figure 7
Comparison of Speciation Rate for Different Families of Angiosperms Evolved in Figure 3.
(A) Illustration of speciation rates for different lineages, on which WGDs are labeled in colors as shown in Figure 3. Changes of speciation rate for each lineage were obtained by using BAMM and are represented by gradient colors.
(B) Comparison between species richness of groups with WGDs and those of corresponding sister groups.
(C) Display of speciation rate variations among three clades along with evolutionary time.
(D) Percentage of orders with or without WGDs and having fewer than 2000 species, 2000–5000 species, and more than 5000 species, respectively.
(E) Percentage of families with or without WGDs and consisting of fewer than 300 species, 300–2500 species, and more than 2500 species, respectively. p Values were calculated using Fisher's exact test.
(F–I) Comparison of GD numbers with Ks for orders and families are shown in (F) and (G), while their detailed species numbers are given in (H) and (I), respectively. Each dot represents an order/family and is colored red (size >5000), blue (2000–5000), or green (<2000), with size proportional to GD or species numbers (log-transformed).
Molecular Plant  , DOI: ( /j.molp )
Copyright © 2018 The Author Terms and Conditions