Ry elements were identified in the BBX genes from two strawberry species (Table S9, Figure S5). We additional classified them into 20 groups according to their functions annotated by PlantCare and earlier research [220]. The light response element was the largest category, occupying 29.79 and 27.18 in wild strawberry and cultivated strawberry, respectively (Figure S6, Tables S10 and S11). This result indicates that the BBX genes may possibly play numerous roles in the light signal transduction pathway. Moreover, ABA response-related components are also Bisindolylmaleimide II site widely distributed on the promoters of BBX genes, since the percentages of ABA response-related elements are 11.94 and 13.16 in wild strawberry and cultivated strawberry, respectively, which indicates that the BBX genes may possibly take part in the strain response or fruit ripening processes in strawberry. Furthermore, MYB-related components are extensively distributed inside the promoters of BBXs in our study. To provide evolutionary details about the promoter region, we compared the arrangement from the light-responsive cis-regulatory element and phytohormone-responsive cis-Int. J. Mol. Sci. 2021, 22,9 ofregulatory element on the promoters of FvBBXs and FaBBXs on the F. vesca-like subgenome. As shown in Figure 6, a related distribution of cis-regulatory components was observed amongst most orthologs, which include FaBBX28c1-FvBBX28c, which indicates that they’re subjected to similar transcriptional regulatory mechanisms.Figure 6. A comparative illustration of cis-regulatory elements around the promoter of FvBBXs from wild strawberry and FaBBXs in the F. vesca-like subgenome of cultivated strawberry.The arrangement of cis-regulatory components on the promoter of FvBB16a and two orthologs (FaBBX16a1 and FaBBX16a2) shows clear conservatism, which supports our speculation that FaBBX16a1 and FaBBX16a2 are HS-1793 medchemexpress derived from segmental duplication events. In contrast, differences within the distribution of cis-regulatory components on FaBBX15a2 and FaBBX15a3 recommend that they’re perhaps derived from various progenitors. FaBBX15a2, which is far more diverse from FvBBX15a, may possibly undergo an exchange on the fragment of subgenomes, which final results in the gene translocation from other subgenomes to the F. vescalike subgenome. FvCO1 was previously identified as a important regulator of flowering time in wild strawberry [10]. In Arabidopsis, AtCO is regulated by many transcription aspects such as AtCDF1 [31]. A drastically discrepant cis-regulatory element distribution was identified among FvCO1 and FaBBX1a1, which implies a divergent regulatory mechanism among wild strawberry and cultivated strawberry. This divergence may perhaps be as a result of the domestication of cultivated strawberry for longer flowering time and higher fruit yield. two.six. The Expression of BBXs in Strawberry We further analyzed the expression pattern of FaBBXs inside the improvement stages of receptacle and achene, the distinct tissues, fruits beneath distinctive good quality treatment options, and leaves below different light good quality treatments (Figure 7C and Figure S7).Int. J. Mol. Sci. 2021, 22,10 ofFigure 7. Gene expression of FaBBXs. (A) Venn diagram of differentially expressed FaBBXs. (B) A heat map diagram of differentially expressed FaBBXs. (C) Heat map on the gene expression level of FaBBX genes in accordance with RNA-seq. TPM was utilized for normalization.We identified 47 differentially expressed FaBBXs (Figure 7A,B), which indicates that the BBXs in cultivated strawberry participated in different transcriptional regulat.
