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Fig. 5 | BMC Genomics

Fig. 5

From: Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Fig. 5

Molecular evolution of Nipponbare highly expressed jiDE genes. In panel a, the proportions of the five types of orthologous gene pairs between Nipponbare and 93-11 are shown for the four gene categories. The five types of orthologous gene pairs were as follows: 1) No ortholog: no orthologs in the 93-11 genome, 2) ORF not detected: ORF not detected in the 93-11 genome, 3) Different protein length: predicted 93-11 protein length was different, 4) Amino acid substitution: the predicted 93-11 protein was the same length with some amino acid substitutions, and 5) Same protein sequence: the predicted 93-11 protein was the same sequence. The four gene categories were as follows: 1) all genes: ORF were predicted in Nipponbare genome, 2) jiSE genes: Nipponbare highly expressed genes in any of endosperm, anther, panicle, root, and leaf, without expression differences in the NM combination, 3) changed-tissues jiDE genes: Nipponbare highly expressed jiDE genes detected in any of the five tissues in NM combination, and not Minghui63 silent genes, and 4) global jiDE genes: highly expressed genes in any of the Nipponbare five tissues, but not expressed in any of the 36 Minghui63 tissues. Numbers of genes in each category are indicated at the bottom of each column. In panel b, the proportions of conserved (K a/K s < 0.75), and neutrally (0.75 ≤ K a/K s < 1.25) or rapidly (K a/K s ≥ 1.25) evolved orthologous gene pairs with the same predicted protein length are shown for the four gene categories

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