1. Supporting Fig. S1 OsRHR-GFP GFP ChlorophyllMerge GC Hoechst Merge GH Supporting Figure S1. The OsPHR-GFP fusion protein localizes to nuclei, chloroplasts, and mitochondria. Subcellular localization of a chimera comprising GFP and full- length rice CPD photolyase (OsPHR-GFP) in transgenic rice plants. Images of GFP fluorescence (GFP), Hoechst 33342 fluorescence (Hoechst), which stains nuclear DNA, and chlorophyll autofluorescence in chloroplasts (Chlorophyll) are shown. A merge of GFP and Hoechst is shown in upper panel (Merge GH). A merge of GFP and Chlorophyll is shown in lower panel (Merge GC). Scale bar: 10 μm.

2. Supporting Fig. S2 GFPChlorophyllMergeGFPChlorophyllMerge (No.) 1 4 7 10 13 16 19 22 25 28 31 (No.) All 3D Supporting Figure S2. Consecutive images from confocal Z-stack microscopy. Subcellular localization of a chimera comprising GFP and full-length rice CPD photolyase (OsPHR-GFP) in transgenic rice plants. Z stack images collected at 0.5 μm intervals (31 stacks in total) and at 1.5 μm intervals are shown (No. 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, and 31). Images of GFP fluorescence (GFP) and chlorophyll autofluorescence in chloroplasts (Chlorophyll), and a merged image (Merge) are shown. Orange fluorescence indicates co-localization between the green fluorescence of GFP and the red fluorescence of chloroplasts. Scale bar: 10 μm.

3. Supporting Fig. S3 Supporting Figure S3. Amino acids 391-401 of OsPHR are functional targeting sequence for transport into mitochondria. (a) Schematic representation illustrating the various constructs used to express chimras of GFP and truncated rice CPD photolyase (No. 9, No. 13-15) and GFP alone (control vector; No. 10). The constructs expressing truncated versions of OsPHR fused to GFP including residues 391- 401 (No. 9, C 391-401 -OsPHR-GFP), 391-400 (No. 13, C 391-400 -OsPHR-GFP), 391-399 (No. 14, C 391- 399 -OsPHR-GFP), and 391-398 (No. 15, C 391-398 -OsPHR-GFP). (b) Expression constructs were introduced into onion epidermal cells by particle bombardment. To visualize mitochondria, the mtDsRed expression construct was co-introduced with each GFP expression construct. Image of GFP fluorescence (GFP) and mtDsRed fluorescence (mtDsRed) are shown. Scale bar: 100 μm. (c) An expanded view of Supporting Figure S3 (b). Scale bar: 20 μm. Fluorescence of protein No. 9 was detected in mitochondoria. GFPNo. 10 399 C 391-399 -OsPHR-GFP 391 No. 14 C 391-398 -OsPHR-GFP 398391 No. 15 400 C 391-400 -OsPHR-GFP 391 No. 13 401 C 391-401 -OsPHR-GFP 391 No. 9 (a) No.9 No.10 No.14 No.13 No.15 GFPmtDsRed GFP (b)(c)

4. 506 496 489 597 612 640 400 565 472 ****** ***** 44 93 1 1 1 1 1 1 1 F Supporting Fig. S4 Supporting Figure S4. Sequence alignment of full-length CPD photolyases. The alignment was performed using ClustalX version 2.0.12. Class II CPD photolyases: Oryza sativa (OsPHRII), Arabidopsis thaliana (AtPHRII), Cucumis sativus (CsPHRII), Marchantia polymorpha (MpPHRII), Chlamydomonas reinhardtii (CrPHRII), Drosophila melanogaster (DmPHRII), and Myxococcus xanthus (MxPHRII). Class I CPD photolyases: Saccharomyces cerevisiae (ScPHRI) and Escherichia coli (EcPHRI). Black shading indicates identical residues and gray shading indicates similar residues, with 30% similarity set as the minimum threshold for shading. The putative mitochondrial targeting signal sequence of OsPHR is indicated with a line and is marked with asterisks.