2.1.4. Genes Upregulated by Both Warming and Minor-Warming Treatment

change or downregulation under the other conditions.

**(Treatment) Comparison No. of Genes** 

2.1.4. Genes Upregulated by Both Warming and Minor-Warming Treatment Among DEGs, we attempted to identify genes that were upregulated by warming, minor warming, and both treatments (Table 1; Tables S6–S14). The numbers of genes upregulated under each condition were the same as those listed in Figures 1–3, but 759 and 726 genes were upregulated by both conditions in Chiifu and Kenshin, respectively (Table S6). We reasoned that these genes might be involved in acquired thermotolerance and/or long-term adaptation to HT in both Chiifu and Kenshin. To specifically identify genes that might be involved in long-term adaptation to HT in the subtropical species Kenshin, we extracted specifically expressed genes (SEGs) from our data set (Tables S8–S13). We identified 85 genes that were specifically upregulated over 2-fold by both minor-warming and warming conditions in Chiifu but not in Kenshin (Table S10). In addition, 86 genes were specifically upregulated over 2-fold by both minor-warming and warming conditions in Kenshin but not in Chiifu (Table S13). Among these, 27 genes were nonannotated and unknown Among DEGs, we attempted to identify genes that were upregulated by warming, minor warming, and both treatments (Table 1; Tables S6–S14). The numbers of genes upregulated under each condition were the same as those listed in Figures 1–3, but 759 and 726 genes were upregulated by both conditions in Chiifu and Kenshin, respectively (Table S6). We reasoned that these genes might be involved in acquired thermotolerance and/or long-term adaptation to HT in both Chiifu and Kenshin. To specifically identify genes that might be involved in long-term adaptation to HT in the subtropical species Kenshin, we extracted specifically expressed genes (SEGs) from our data set (Tables S8–S13). We identified 85 genes that were specifically upregulated over 2-fold by both minor-warming and warming conditions in Chiifu but not in Kenshin (Table S10). In addition, 86 genes were specifically upregulated over 2-fold by both minor-warming and warming conditions in Kenshin but not in Chiifu (Table S13). Among these, 27 genes were nonannotated and unknown genes. Genes commonly upregulated in both Chiifu and Kenshin under both minor-warming and warming conditions included

represent genes showing an over 2-fold change in expression under the indicated condition but no

12 °C/22 °C: LT conditions; 28 °C/12 °C: warming conditions; 28 °C/22 °C: minor-warming

**SEGs (Tables** 

28 °C/22 °C 1651 121 12 °C/22 °C 1532 28 °C/12 °C 2010 49 28 °C/12 °C 2010 Both 759 85 Both 40

28 °C/22 °C 1841 193 12 °C/22 °C 1669 28 °C/12 °C 2093 146 28 °C/12 °C 2093 Both 726 86 Both 59

**S7–S12) Comparison No. of Genes** 

**(Table S6)** 

**(Table S5)** 

genes. Genes commonly upregulated in both Chiifu and Kenshin under both minor-warming and warming conditions included 15 *HSP*s and chaperone genes (Table S14). We subjected the genes 15 *HSP*s and chaperone genes (Table S14). We subjected the genes listed in Tables S12–S14 to further GO enrichment analysis (Tables 2–4).

**Table 1.** Summary of genes upregulated by various treatments. SEGs (specifically expressed genes) represent genes showing an over 2-fold change in expression under the indicated condition but no change or downregulation under the other conditions.


12 ◦C/22 ◦C: LT conditions; 28 ◦C/12 ◦C: warming conditions; 28 ◦C/22 ◦C: minor-warming conditions.

**Table 2.** Functional classification of genes specifically expressed in response to HT acclimation and/or adaption conditions. The table was constructed based on Tables S11–S13 using agriGO (http://bioinfo.cau.edu.cn/agriGO/) based on GO information for *Arabidopsis* homologs. W, warming, MW, minor warming.



**Table 3.** Genes associated with the adaptation of Kenshin to HT based on microarray analysis. The selection criteria were (1) intrinsic levels of expression in Kenshin at 22 ◦C over 2-fold higher than those in Chiifu; and (2) expression levels under both warming and minor-warming conditions at least 2-fold higher in Kenshin than in Chiifu. HSR, heat shock response; TF, transcription factor; SF, splicing factor.








\* Gene in Table S13 (genes upregulated in both Chiifu and Kenshin under both minor-warming and warming conditions).



\* Notable genes possibly related to the HT response in *B. rapa*.

**Table 4.** Summary of the expression levels of *B. rapa* genes shown to be HT responsive in *Arabidopsis*.
