Figure 8.

Relationships of pCRE Site Turnover and Wound-Responsive Gene Expression between Orthologs.

(A) Types of pCRE sites. Shared: The sites of a pCRE are present in both orthologs and located at the same position. Specific: The site of a pCRE is present only in one ortholog but not the other. Compensatory: The sites are present in both species but in different locations. Others: Any situation that does not belong to the previous three types. Gray line: The defined regulatory regions from the orthologous gene pairs (see Methods).

(B) The conservation likelihood (Lc) of a pCRE in the UNNN (left panel), the UUNN (middle panel), and NDNN (right panel) clusters. For a pCRE, its Lc is defined as the log ratio between the proportions of sites that shared and those that are specific (see Methods). The Lc for each pCRE was evaluated using orthologous gene pairs with consistent (belong to the same wound response cluster, orange) and inconsistent (belong to different clusters, blue) wound responses, as well as orthologous genes that are not responsive to wounding (nonresponsive, gray). P values: Testing whether the likelihood scores generating based the blue or gray data sets differ from the orange one (one-sided Mann-Whitney U test).