Figure 3
Expression signatures detected for relics and orthologous counterparts in Poaceae species. The log2 (FPKM + 1) values of expressed relics and orthologous counterparts in four species of Poaceae are shown in these heat maps. The orthologous counterpart in the adjacent species is selected for this expression analysis. For different species, each panel represents each dataset. The SRA accession number of RNA-seq dataset is SRP008505 for brachypodium, SRP008821 for rice, SRP008469 for sorghum and SRP006463 for maize. The vertical axis represents the number of the orthologous group where unitary gene loss occurred (OC means orthologous counterpart of the relic), and the horizontal axis represents the different samples in each dataset. The label “*” is shown if the relic or its orthologous counterpart shows significant differential expression between at least one pair of samples (FDR-adjusted pvalue < 0.05, Cuffdiff). The expression correlation of the relic and its orthologous counterpart is significantly high if they are enclosed in the red frame (Pearson’s R Correlation test, p-value < 0.05), while the conservation of the relic promoter is high if it is enclosed in the blue frame (two-tailed Wilcoxon Rank Sum test, FDR-adjusted p-value < 0.01). Only when both of the relic and its orthologous counterpart have expression signatures, their expression values are shown in this figure.