Fig. 6

Schematic drawing of the proposed evolutionary trajectory. Changes in gene expression in response to a temperature increase are illustrated with transparent distributions, representing the well-known feedback regulatory mechanism in the heat shock response. The responsive states at heat shock are indicated with circles located at the peaks of the distributions indicated with the names of the ancestor and evolved cells. The equivalent heights of the distributions (i.e., the vertical distances from the X-axis to the peaks) indicate that the heat shock response (ΔHS) of both the ancestor and the evolved strains remained in common. The steady states of the evolved cells at the regular temperature are shown with circles located on the axis for genome evolution and are shadowed by the transparent distributions. The order of these strains (i.e., the distances from the starting point of the X-axis) represents the changes in gene expression (ΔG) mediated by the genotypes (i.e., genome mutations). The steady states of the ancestor and evolved cells at the corresponding growth temperatures are highlighted with bright yellow circles. These steady states (circles) are placed at the sides opposite to the regular states along the distributions, suggesting that the thermal adaptive states were distinct to the regular steady states. In addition, they are set on the tails of the distributions, which implies that the steady states under high temperatures were relaxed from the heat shock stress to the corresponding thermal adaptive states. The broken triangle represents an example (41B) of the negative epistasis at transcriptome, as described in the main text. The solid red line, linking up the four steady states at the corresponding evolutionary temperatures, indicates the trajectory of transcriptome evolution along with genome evolution