Heterologous genome-wide wheat expression map. (a) The five Brachypodium chromosomes are illustrated in the inner circle (labeled Bd) and the seven paleoduplications (in black) shared within cereals are displayed in the center (Dp1 to Dp7). The second circle (labeled Ta) illustrates the orthologous relationships identified between Brachypodium and wheat using a seven color code. Dots around the two circles illustrate the Brachypodium transcription factors (red; labeled TFTa), the 454 RNA-seq reads from bread wheat (black; labeled 454Ta) and associated TFs (green; labeled TFBb). (b) CNVs and homoeologous gene localization in bread wheat is illustrated with a single COS marker (CT753726) that has been located on chromosome 2A (CNV of 2), 2B and 2D using the adapted cytogenetic material illustrated in the top. The arrows illustrate the observed amplification loss observed for the illustrated cytogenetic material (N2A, N2B, N2D respectively for the absence of the 2A, 2B, 2D chromosomes). The COS marker (CT753726) expression (SSCP amplification) profiles observed in the five RNA samples from wheat grain development, as well as in leaves (RNA and DNA amplifications) and roots (RNA) considered as negative control. Colored arrows highlight the loss of expression of the considered CNV or homoeologous copies. (c) Wheat (chromsomes 1 to 3) and Brachypodium (chromosome 2) heat maps for Brachydopium coding sequence (CDS; blue < 40, yellow approximately 41 to 50, red > 51 genes/500 kb), wheat RNA-seq ortholog (blue < 9, yellow approximately 10 to 19, red > 20 genes/500 kb), Brachypodium paralog (blue = 0, yellow approximately 1 to 5, red > 6 genes/500 kb), wheat RNA-seq paralog (blue = 0, yellow approximately 1 to 3, red > 4 genes/500 kb) distributions. The 44 RNA-seq TFs are illustrated with their corresponding orthologous positions on the Brachypodium chromosome as black vertical bars. (d) Paralogous chromosomal regions are shown in the center, involving Brachypodium chromosome 1 (2.1 Mb, 252 genes) and 3 (2.9 Mb, 181 genes), and annotated genes are shown with horizontal bars. Orthologous wheat chromosomes are shown at the right (consensus group 1 and homoeologous chromosomes in red) and left (consensus group 4 and homoeologous chromosomes in yellow). Orthologous genes identified between wheat and Brachypodium are linked with black lines. Paralogous genes identified between Brachypodium chromosomes are linked with green lines. Expression data from wheat RNA-seq cluster alignment against the considered Brachypodium chromosome sequences are shown with colored dots. Blue dots illustrate paralogous gene pairs for which only one copy is associated with wheat RNA-seq clusters while red dots illustrate paralogous pairs for which both duplicates are associated with wheat RNA-seq clusters.