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Background  C 4  photosynthesis evolved from C 3  photosynthesis and has higher light, water, and nitrogen use efficiencies. Several C 4  photosynthesis genes show cell-specific expression patterns, which are required for these high resource-use efficiencies. However, the mechanisms underlying the evolution of  cis- regulatory elements that control these cell-specific expression patterns remain elusive.    Results  In the present study, we tested the hypothesis that the  cis- regulatory motifs related to C 4  photosynthesis genes were recruited from non-photosynthetic genes and further examined potential mechanisms facilitating this recruitment. We examined 65 predicted bundle sheath cell-specific motifs, 17 experimentally validated cell-specific  cis- regulatory elements, and 1,034 motifs derived from gene regulatory networks. Approximately 7, 5, and 1,000 of these three categories of motifs, respectively, were apparently recruited during the evolution of C 4  photosynthesis. In addition, we checked 1) the distance between the acceptors and the donors of potentially recruited motifs in a chromosome, and 2) whether the potentially recruited motifs reside within the overlapping region of transposable elements and the promoter of donor genes. The results showed that 7, 4, and 658 of the potentially recruited motifs might have moved via the transposable elements. Furthermore, the potentially recruited motifs showed higher binding affinity to transcription factors compared to randomly generated sequences of the same length as the motifs.    Conclusions  This study provides molecular evidence supporting the hypothesis that transposon-driven recruitment of pre-existing  cis- regulatory elements from non-photosynthetic genes into photosynthetic genes plays an important role during C 4  evolution. The findings of the present study coincide with the observed repetitive emergence of C 4  during evolution.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2519-3) contains supplementary material, which is available to authorized users.

Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis