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Compared those additional conserved motifs identified outside of the AP2/ERF domain regions in castor bean with other plants, eight motifs (including motifs 9, 10, 11, 13, 16, 17, 18 and 22) were shared by castor bean, Arabidopsis and rice, indicating most of additional motifs outside of AP2/ERF domain regions were conserved in plants.
Quartet decomposition analyses shown in supplementary figure 9 (Supplementary Material online) reveal that 419 (87%) gene families conflict with the plurality topology at 80% bootstrap cutoff, which suggests that most of additional homologs are not the result of recent within-lineage duplications (e.g., see supplementary fig. 10, Supplementary Material online).
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