Homolog gene conservation between wheat and cereal sequenced genomes. (a) Cereal genome paleohistory. Schematic representation of the phylogenetic relationships between grass species adapted from [2, 4]. Divergence times from a common ancestor are indicated below the branches of the phylogenetic tree (in million years). Whole genome duplication events are illustrated with red circles on the tree branches. The evolution of chromosome numbers of modern species from the ancestral genome structure is indicated with the number of chromosome fusion (CF) events. Genome features (number of chromosomes, physical size, and the number of annotated unigenes) of the six cereal genomes investigated are shown at the right-hand side. Modern genome architectures are illustrated using a color code that represents the n = 5 and 12 extinct ancestors (left). (b) Homologous gene groups between wheat and rice, Brachypodium, sorghum, and maize genomes. The Venn diagram illustrates the number of conserved protein domain-based homologs between wheat (RNA-seq gene clusters) and rice/Brachypodium/sorghum/maize (annotated proteins). (c) Simulated synteny-based gene order model in bread wheat. The chromosomal location of the RNA-seq gene clusters are shown on the seven bread wheat chromosome groups based on a consensus gene order derived from the observed synteny between wheat and rice ('R', in green), Brachypodium ('B', in grey), sorghum ('S', in blue), and maize ('M', in pink) chromosomes (numbers are shown at the bottom of the chromosomes). The bottom inset illustrates a micro-synteny example of 26 re-ordered genes in bread wheat chromosome 1 (red dots) based on orthologous genes identified in Brachypodium (chromosome 2, 92 annotated genes, 0.9 Mb), sorghum (chromosome 9, 108 annotated genes, 1.1 Mb), rice (chromosome 5, 112 annotated genes, 0.9 Mb), maize (chromosomes 6 to 8, 145 annotated genes, 12.6 Mb). Non-conserved genes are illustrated using dotted lines and conserved genes are linked with black lines.