Figure 5

Hox gene expression from RNA-seq within the salmon notochord during segmentation. 71 out of 118 salmon hox genes were expressed and the average expression (on log2 scale) of hox genes in all salmon notochord libraries (A). (B) Heatmap showing RNA-seq expression (in log2 scale) of hox genes in nine notochord libraries; x-axis primarily grouped by developmental stage (T1:510 ± 20 d°, T2: 610 ± 20 d°, T3: 710 ± 20 d°); y-axis grouped by four major clades in hox clusters. (C) K-mean clustered heatmap showing RNA-seq expression (in log2 scale) of hox genes in nine notochord libraries. Lowly expressed posterior genes were represented in G1; generally lowly expressed genes were grouped in G2; most highly-expressed genes were grouped in G3; G4 represented anteriorly-expressed genes and G5 shown the highly-expressed hox genes either in mid- and posterior segments or had no clear pattern. The horizontal clustering indicates a closer distance in overall expression pattern of hox genes between temporal libraries (T1, T2, T3) and, to a further distance between spatial libraries (A, M, P). Abbreviations: A (anterior), M (mid), P (posterior). Note that a total of 110 hox genes were plotted in all figures (A-C), since the rest 8 hox genes are pseudogenes.