Volume 8, Issue 6, Pages 885-898 (June 2015) Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events  Xiyin Wang, Jinpeng Wang, Dianchuan Jin, Hui Guo, Tae-Ho Lee, Tao Liu, Andrew H. Paterson  Molecular Plant  Volume 8, Issue 6, Pages 885-898 (June 2015) DOI: 10.1016/j.molp.2015.04.004 Copyright © 2015 The Author Terms and Conditions

Figure 1 Alignment of Grass Chromosomes. Based on gene colinearity, chromosomes are aligned using rice as reference. The whole-genome duplication (WDG) in the common ancestor of these grasses causes all to have at least two circles of chromosomes, and an additional lineage-specific WDG causes maize to have four. Each species has another circle to contain additional duplicated regions. Genes are colored according to their corresponding rice chromosome. For example, genes from all grasses with orthologs on rice chromosome 1 are in blue. A, Aegilops tauschii (wheat D genome); B, Brachypodium distachyon; F, Setaria italica; H, Hordeum vulgare L. (barley genome); O, Oryza sativa; S, Sorghum bicolor; T, Triticum urartu (wheat A genome); Z, Zea mays. Molecular Plant 2015 8, 885-898DOI: (10.1016/j.molp.2015.04.004) Copyright © 2015 The Author Terms and Conditions

Figure 2 Alignment of Barley and Diploid Wheat Chromosomes. Using gene colinearity, chromosomes from grasses are aligned by using barley as reference. The WDG in the common ancestor of all these grasses causes all to have two circles of chromosomes. A, Aegilops tauschii (wheat D genome); H, Hordeum vulgare L. (barley genome); T, Triticum urartu (wheat A genome). Molecular Plant 2015 8, 885-898DOI: (10.1016/j.molp.2015.04.004) Copyright © 2015 The Author Terms and Conditions

Figure 3 Alignment of Local Regions Sharing Homology. Ae, Aegilops tauschii; Bd, Brachypodium; Os, rice; Sb, sorghum; Si, Setaria italia; Tu, Triticum urartu; Zm, maize. Genes are shown with pointed boxes showing transcriptional direction. Homologous genes between neighboring chromosomes (shown with straight lines) are linked with lines with circles at their ends. Molecular Plant 2015 8, 885-898DOI: (10.1016/j.molp.2015.04.004) Copyright © 2015 The Author Terms and Conditions

Figure 4 Dating Evolutionary Events. (A) Distribution of average synonymous substitutions between syntenic gene pairs in intergenomic blocks (solid curves) and intragenomic blocks (dashed curves). (B) Distribution of average synonymous substitutions after correction to account for the slower evolution of rice genes. Curves of Ks distributions were produced by using R, and peaks and troughs were identified. (C) Considering recent fossil evidence that rice had already split with maize and sorghum by 70 million years ago (mya), we re-estimated the occurrence of other key evolutionary events. Molecular Plant 2015 8, 885-898DOI: (10.1016/j.molp.2015.04.004) Copyright © 2015 The Author Terms and Conditions

Figure 5 Reconstructed Tree of Grasses with Updated Evolutionary Times and Inferred Ancestral Gene Numbers. Molecular Plant 2015 8, 885-898DOI: (10.1016/j.molp.2015.04.004) Copyright © 2015 The Author Terms and Conditions

Figure 6 Alignment of Modern Grass Chromosomes to Seven Ancestral Chromosomes Inferred in the Grass Common Ancestor before Whole-Genome Duplication (Wang et al., 2015). The WDG in the common ancestor of all these grasses causes all to have at least two circles of chromosomes, and an additional lineage-specific WDG causes maize to have four. Each species has another circle to contain additional duplicated regions. Genes are colored according to their corresponding rice chromosome. A, Aegilops tauschii (wheat D genome); B, Brachypodium distachyon; F, Setaria italica; H, Hordeum vulgare; O, Oryza sativa; S, Sorghum bicolor; T, Triticum urartu (wheat A genome); Z, Zea mays. Molecular Plant 2015 8, 885-898DOI: (10.1016/j.molp.2015.04.004) Copyright © 2015 The Author Terms and Conditions