Gene ID Accession No. DWD domain 1 DWD domain 2 DWD△△△△ R(16) domain 1 DWD△△△△ R(16) domain 2 Type

At1g11160 NP_172582 (63) FLASGSSDTNLRVWDTR (106) VVSGG-LDNVVKVWDLT (147) LLATGSADRTVKFWDLE C

At1g15440 NP_973836 (406) LLSAS-LDGTVRAWDFK C

At1g19750 NP_173405 (206) LYTGG-CDGAIRFWDIR (119) FITGS-FDHYVKVWDTN A

At1g20540 NP_173478 (183) AVAAT-GESSVQFWDLR (224) LVTAE-DESGIHVWDLR C

At1g27840 NP_174105 (206) LYTGG-CDGAIRFWDIR (119) FITGS-FDHYLKVWDTN (327) LLSAG-SDSRIRLWDIE D

At1g29260 NP_174220 (165) FASAS-GDCTLRIWDVR (207) ILATSSVDKTVKVWDVR (251) LIASCSYDMSVCLWDYM D

At1g29320 NP_174226 (316) VIASCGLDRYLRVYDVK B

At1g36070 NP_564469 (304) ILATGNQDTACRLWDIR A

At1g49040 NP_850959 (953) VLTAA-HDGTVKMWDVR (994) ILAAAGRDTVANIWDIR (870) FISGS-TDCLVKIWDPS I

At1g53090 NP_849802 (635) AFGSA—-DHKVYYYDLR (549) VASSN-FEGVVQVWDVA (676) LVSSS-TDNTLKLWDLS L

At1g55680 NP_564699 (331) TFSTGNQDKTCRVWDIR A

At1g61210 NP_176316 (114) FLASGSSDANLKIWDIR (157) VVSGG-LDNVVKVWDLT (198) LLATGSADRTVKFWDLE G

At1g65030 NP_176683 (278) LIGSASSDGIIRVWDVR D

At1g69400 NP_974113 (109) VISTG-FDEKIKFWDTR D

At1g73720 NP_177513 (362) IITAS-SDCTVKVWDSK (227) FLASSSVDGFIEVWDYI K

At1g76260 NP_177753 (224) LVSAD-DESGIHLWDLR B

At1g78070 NP_974167 (333) ILATGNQDTTCRLWDVR A

At1g80670 NP_178182 (128) LLATGSWDKTLKYWDTR (261) FATAG-SDGAFNFWDKD D

At1g80710 NP_178186 (363) VMATSSTDGTACLWDLR A

At2g01330 NP_178242 (66) FITVS-SDKKGMIYDGK (111) VLTVS-ADKSAKVWEVA D

At2g05720 NP_178635 (144) FKASSGFDSLARVWDLR (187) LASGG-EDNQCRIWDLR A

At2g16780 NP_179269 (232) LFGSAGEDGRLVIWDTR (319) VLASSGEDRRLMVWDLN A

At2g19430 NP_849989 (216) ILTGS-EDGTARIWDCK (174) VFTAA-GDSCAYCWDVE B

At2g19520 NP_565456 (308) FCSVG-DDSCLILWDAR B

At2g19540 NP_179544 (284) VFASCSVDGSVAVWDIR (376) LAVTS-GDNQLTIWDLS B

At2g20330 NP_179623 (388) LLSRS-FDGSLKVWDLR (294) VLTSS-EDGSLRIWDVN B

At2g32950 NP_180854 (522) AVGSA--DHHIHYYDLR (563) LASAS-TDSTLRLWDVK M

At2g33340 NP_850207 (409) FLATA-AEDGVRLWDLR J

At2g43770 NP_181905 (154) IISGS-DDGTAKLWDMR (195) IFTGG-VDNDVKVWDLR A

At2g46280 NP_182151 (67) LITGS-ADQTAKLWDVK (208) FLTGS-LDKTAKLWDMR (163) IVSGG-EDKVIRIWDAE D

At2g46290 NP_182152 (94) LITGS-ADQTAKLWDVK (235) FLTGS-HDKTAKLWDMR (190) IVSGG-EDAAIRIWDAE D

At2g46340 NP_182157 (865) LLAFGSADYKVYCYDLR (781) LASTD-YDGVVQIWDAG L

At2g46560 NP_182179 (2390) FLTGS-KDGEVKLWDAK A

At2g47410 NP_850474 (338) LLSSS-DDGTCRIWDAR H

At2g47990 NP_182320 (194) LVTGS-YDHTVKVWDAR B

At3g05090 NP_566246 (228) LVSGG-TEKVLRVWDPR (270) CLSGS-SDSMIRLWDLG C

At3g08850 NP_566335 (1185) QLAAGFADGSLRLYDVR A

At3g10530 NP_187664 (295) LMATSGKERKIKIWDLR B

At3g13340 NP_566453 (333) TFSTGNQDKTCRVWDIR A

At3g15354 NP_683567 (677) AFGSA--DHKVYYYDLR (599) IASSN-FDGVVQIWDVA (718) LVSSS-TDNTLKLWDLS L

At3g16650 NP_566557 (269) VLTGG-RDSVCRVWDIR (310) VITGS-HDSTIKFWDLR A

At3g18060 NP_188434 (202) FITVS-SDKKGIIYDGK (247) VLTVS-ADKSAKIWDIS D

At3g19590 NP_566644 (113) VITGS-WDKTVKCWDPR D

At3g27640 NP_566822 (186) LVSGS-RDGCFALWDLR (253) IATAGAPDSALKFWDIR (143) LLTAS-GDQTIKVWDVE B

At3g45620 NP_190148 (216) LAVGG-SDEYARVYDTR B

At3g49180 NP_190487 (278) LISGS-EDGVVCVWDPK C

At4g01860 NP_849536 (149) LLAIGCSDNSLSIWDVK (250) IVSVS-DDRSARIWEID C

At4g02730 NP_192182 (185) IVSAS-HDGSCKIWDAK (273) IVSGS-EDNCVYLWDLQ A

At4g03020 NP_192211 (287) ILSGS-DDNLCKVWDRR (333) FISNG-KDQTIKLWDIR (244) VVAGS-SDDSIYVYDLE (416) IYTGS-NDSSVYIYDLV A

At4g05410 NP_192450 (237) LATGG-VDRHVHIWDVR A

At4g11110 NP_192849 (915) LVTAS-TDNTLKLWDLK (787) YLASSDYDGIVKLWDVT L

At4g15900 NP_193325 (275) LLTGG-RDSVCRVWDIR (317) VVTGS-HDTTIKFWDLR A

At4g21130 NP_193845 (221) LATGG-VDCHVHLWDIR B

At4g28450 NP_567810 (208) LLATSASDRSITIYDLR E

At4g29380 NP_194667 (1096) FVSAS-DDSTVKVWDSR L

At4g29730 NP_194702 (288) FCSVG-DDSCLMLWDAR (381) VFGSSAEDGLLNIWDCD B

At4g29830 NP_194712 (258) IATGS-SDRTVRLWDLK D

At4g29860 NP_194715 (234) VLAGY-EDGSILLWDIR D

At4g34280 NP_195154 (598) LFATSSFDKDVKLWDLR A

At4g34460 NP_195172 (220) FISGS-CDSTARLWDTR (263) FGTGS-DDGTCRLYDIR A

At4g35050 NP_195231 (233) IFGSAGDDCQLVIWDLR A

At5g01770 NP_195797 (1186) LAAGF-ADGSVRLYDVR A

At5g08390 NP_568194 (115) FFASGSLDTNLKIWDIR (158) IVSGG-EDNVVKVWDLT (199) LLATGSADKTVKFWDLE C

At5g10940 NP_568242 (231) LLVGG-SDAFARLYDRR F

At5g12920 NP_196796 (257) IFGAG-KEGIIHIWDLR C

At5g13480 NP_196852 (264) LVSGG-KDQLVKLWDTR (306) LLTAS-KDQIIKLYDIR B

At5g14050 NP_196909 (389) LLSSG-GDGQVYVWDLR A

At5g14530 NP_196957 (129) FMSGS-LDRSVRLWDLR D

At5g15550 NP_197059 (327) LIAAGGSDPILRVWDPR (374) LLSAS-YDGKIMLWDLR A

At5g18525 NP_974804 (468) LVSSS-LDKTLRIWDLR A

At5g23430 NP_851064 (115) FFASGSLDTNLKIWDIR (158) VVSGG-EDNIVKVWDLT (199) LLATGSADRTVKFWDLE C

At5g23730 NP_568435 (161) VGASGSDDGTMQVWDPR D

At5g27570 NP_198109 (233) LASGG-NDNVVHIWDHR A

At5g49430 NP_199754 (347) LLSSS-DDGTCRIWDAR H

At5g52250 NP_200038 (182) IGASGSDDGTVQMWDPR A

At5g52820 NP_200094 (417) LLSGS-KDSTLKIWEIR A

At5g54520 NP_200263 (401) LASGS-SDGSVYMYDYK A

At5g56130 NP_200424 (81) LVATASGDKSVRLWDAR (206) FAVGS-ADSLVSLWDIS D

At5g56190 NP_851199 (328) FATGN-QDKTCRIWDTR A

At5g58230 NP_200631 (243) FGSVG-DDQYLLIWDLR (194) LLSGS-DDAQICLWDIN A

At5g58760 NP_200684 (328) LLSCG-NDHFARIWDMR (373) ILTTC-QDNRIRIWDSI B

At5g63010 NP_201106 (179) VYTGS-DDCKFSCWDIR (226) IFTGS-YDETLRVWDTR A

At5g64730 NP_568993 (117) VVSAG-FDRSLRVWDCR D

At5g66240 NP_569031 (135) FISGS-LDRTVLLWDQR D

At5g67320 NP_201533 (380) LLTGS-VDRTAVVWDVK (513) TLASASFDSTVKLWDAE K

Supplemental Figure 1. Alignment of DWD Motifs in Arabidopsis thaliana.

The following 16 conserved amino acid sequence, based on DWD proteins in

mammalian cells, was used to search for DWD proteins in Arabidopsis: [IFVL]-[IFVL]-

[AGST]-[AGST]-[AGST]-x-[DE]-x(2)-[IFVL]-x-[IFVL]-[WY]-[DE]-[IFVL]-[RK].

The alignment of the DWD motifs in the 85 Arabidopsis proteins containing this motif

is shown, along with the alignments of the DWD△R(16) domains, if present.

Conserved amino acids are shown in color. Hydrophobic amino acids are shaded in

yellow and small amino acids are shaded in gray. The WDXR submotif is shown in red

letter and the conserved D/E residues at position 7 are shown in pink. The

DWD△R(16) motif contains the first highly conserved 14 amino acids of the DWD

motif but lacks the 16th arginine/lysine. For genes with splice variants, only the

representative gene model listed at TAIR was used.

Gene ID DWD domain 1 DWD domain 2 DWD domain 3 DWD△△△△R(16) domain 1 DWD△△△△R(16) domain 2 Type Os01g03510 (203) FISVS-SDKKGLIYDGK (248) VLTVS-ADKTAKVWDIL (550) VATGS-LDTCAIVYEID D Os01g04870 (350) LLSSG-NDHYARIWDTR (395) ILTTC-QDNRIRVWDYI B Os01g08770 (295) LMATAGVDRKVKIWDLR B Os01g09252 (96) LYSGS-LDKTIKVWDLK D Os01g13730 (219) LITSA-SDRSITLYDLR E Os01g21940 (368) VITAS-SDCTVKVWDTK (233) LVSCS-VDGIIEVWDYI A Os01g28680 (160) LYSGS-DDSLCKVWDRR (205) FISNC-KDQTIKLWDIR C Os01g37120 (473) FLTGS-KDGDVKLWDAK A Os01g39380 (964) VLTAS-HDGTVKMWDVR (1005) ILAAAGRDVVAHVWDIR (923) IVSGA-DDQSVIVWDKQ (1088) IITGS-SDGLIRFWENE I Os01g44394 (127) LVSGS-WDKTLRYWDVR (41) LVATS-WDNQVRCWEIQ D Os01g51300 (256) FCSVG-DDSCLILWDAR (301) ILTGS-ADNSVRMWDRR (349) VFGSSAEDGFLNVWDHE B Os01g52640 (643) AIGSA--DHKIYCYDLR (557) IASSD-FEGIVQVWDVT (684) IVSAS-TDNSLKLWDLS L Os01g57210 (117) FASGS-SDTDLKIWDIK (159) VVTGG-EDNIVKVWDLT (201) LATGS-ADRTVKFWDLE C Os01g72220 (106) LVSGG-KDYLVKLWDAK (148) VLTAS-KDQIIKLYDIR (64) FCSCS-DDTTVKVWDFA C Os02g02380 (179) VASGS-DDRTAHVWDPR D Os02g14790 (169) VFASASGDRTARVWDVR (212) ILATGSVDKSIRVWDVR D Os02g18820 (159) LASGS-LDQEVRLWDAK C Os02g20430 (180) LMSGG-CDGAIRFWDIR (119) FVTAS-FDQYVKVWDTN D Os02g21490 (395) LTSGS-SDGCIYFYDYK A Os02g37856 (220) LFASG-LDGAVFMWDMR (264) VFAAT-KEGTVHAWDLR B Os02g49090 (387) LASGS-KDGTVKIWDDR C Os02g53140 (573) LASAS-TDSTLRLWDVK (445) VIASSDYEGIVTVWDVQ M Os02g55340 (1097) FVTAS-DDSSVKIWDTR L Os03g02440 (435) FISGC-IDGLVRIWDVR B Os03g08830 (618) IASGS-DDGRWFIWEKR N Os03g21990 (261) LLTGG-RDSVCRVWDIR (219) LFSAG-DDKQVKCWDLE (303) VVTGS-HDSTIKFWDLV A Os03g23909 (370) LAASCGLDAYARVWDLR (412) LVATGSEDNFCRIWDLR A Os03g26870 (208) VVATGNQDRTCRVWDVR A Os03g27970 (516) FVMSGDGEGSCWFWDWK A Os03g33580 (118) VITGS-WDKTIKCWDPR (261) FATGG-CDGFVNVWDGI D Os03g42770 (234) LASGG-LDRHIHLWDVR A Os03g43890 (198) LLSGS-DDAQICLWDIK (246) LFGSVGDDHNLLIWDLR A Os03g46650 (221) FVSGS-CDATVRLWDIR A Os03g47780 (8) LATAS-YDHSIKFWEAK D Os03g48090 (206) ICTGS-DDASLRIWDPR (293) VATGS-MDQKLIIWDLG (333) FVASGCIDGMVRIWDSL A Os03g49200 (177) IVTGS-RDGSFALWDLR B Os03g51550 (128) LASGS-FDETVRVWEVR (170) IVSGS-YDGLCRIWDSA (258) IVSGS-EDKCVYIWDLQ D Os03g53510 (368) LCSGH-RDGHLRLWDIR (327) VLASSSNDHTIKIWDLQ A Os04g42880 (183) LYSGS-DDCSFSCWDLR (229) LLTGS-YDEFLRVWDIR A Os04g50660 (220) LLSAG-RDKIVNVWDVR (133) LLATAGADKKVCVWDVD (427) VVTGS-KDSTVRLWDME C Os04g58130 (118) FASGS-LDTNLKIWDIR (160) VVSGG-EDNVVKLWDLT (201) LLATGSSDKTVKFWDLE C Os05g05210 (212) IVVGN-SDRSINVYDLR (253) LYSGS-DDNLCKVWDRR (300) FISNC-KDQTIKLWDVR (381) IYTGS-SDEYVYIYDVV A Os05g16660 (206) FLTGS-LDKSAKLWDTR (67) LITGS-ADQTAKLWDVQ (161) IITAG-EDATIRIWDTE D Os05g33710 (266) IYSGS-DDNLCKVWDRR (313) FISNG-KDQAIKMWDIR A Os05g46570 (130) FMSGS-LDHSVRIWDLR D Os05g49590 (981) LAFGS-ADYKIYCYDLR (896) LASTD-YDGTVQLWDAS (1023) LISAS-TDNTLKIWDLN L Os06g07540 (344) FATGN-QDKTCRVWDVR A Os06g19660 (272) LASAS-KDGMVKIWDDR C Os06g44370 (154) VVSGS-DDGTAKLWDLR (195) VFTGG-LDNDVKWWDLR (237) LLTNA-MDNELKIWDLR (111) IISAS-PDKTVRVWDVE (287) VTAGS-ADRMVYIWDTT A Os06g50880 (242) FAVAG-SDEYVRIYDSR B Os07g12320 (196) IFATGSYDRIVKLWDAR (153) LFTAG-DDALLAYWDVP B Os07g14830 (333) LASAS-DDGTVKLWELR (226) MVTCS-DDHTLKIWDTS D Os07g22220 (322) LLSGS-VDKTAIVWDTK (456) LASAS-FDSTIKLWEVE K Os07g22534 (279) LISGS˙ ˙ ˙-EDGNVRVWDTR (135) LISGS-EDGSIKVWDLL A Os07g38430 (82) LCSAS˙ ˙ ˙-DDRTLRIWDVR (148) VASGG-FDCTVRIWDVK (190) IVSGS-HDGTCKIWDAG (278) IVSGS-EDNCVYIWDLQ D Os07g40030 (127) ILSGS˙ ˙ ˙-LDRTVLLWDSR (40) LVTAC-DDESIRLYDIQ D Os07g40930 (331) IAAGG˙ ˙ ˙-SDPVLRVWDPR (377) LVSSS-FDGKVMLWDLR (289) IYSAS-WDHSVRQWDVQ A Os07g41190 (400) LLSSG˙ ˙ ˙-GDGHVYHWDLR A Os07g46620 (108) VASG˙ ˙D-DEGCIKVWDTR (277) LGSIS-HDKMLKLWDLQ C Os08g04270 (257) ILSKS-VDNEIVLWEPK (356) ILACS-EDGSIWRWDEV A Os08g21660 (206) FLTGS˙ ˙ ˙-LDKSAKLWDTR (67) LITGS-ADQTAKLWDVQ (161) IITAG-EDATIRIWDTE D Os08g31560 (331) LATGS˙ ˙ ˙-QDTTCRLWDIR A Os08g38880 (319) FATG˙ ˙N-QDKTCRIWDIR A Os09g06560 (371) LVTAG˙ ˙ ˙-LDKQVLIWDVK C Os09g12550 (167) VASGS˙ ˙ ˙-LDNEVCLWDAK C Os09g12710 (97) VATAA˙ ˙ ˙-ADKSIRLWDAR (224) FAVGS-ADSLVSLWDVK D Os09g19900 (225) VVTGS˙ ˙ ˙-EDGTARIWDCR A Os09g36900 (226) LFGSA˙ ˙ ˙GDDCKLMMWDLR (178) LLSGS-YDKKICLWDLA (317) LASSA-ADKRVMIWDVS A Os10g01540 (424) LLSGS-KDSTLKVWDIR (130) LASGS-GDTTVRFWDLS (220) FVSTS-KDGDARIWDMT A Os10g32710 (389) LLSRS-MDSTLKIWDLR (193) VLSGS-YDYTVCMYDFQ (295) ILTSS-EDGSIRLWDVS B Os10g32880 (367) LGTGT-TEAVVKIWDVK (323) FVTAS-KDNTWCFYDIP J Os10g35200 (116) FASGS-SDTNMKIWDMR (158) IVSGG-SDNSVKIWDLT (200) LATGS-ADKTVKFWDLE A Os11g03990 (283) FASCS-ADRTISIWDIR (373) LAVSS-ADHQLTIWDLS B Os11g10640 (608) IITGS-LDKTARIWDCK L Os11g38170 (424) LLSGS-KDSTLKVWDIR (130) LASGS-GDTTVRFWDLN (220) FVSAS-KDGDARIWDIT A Os11g43890 (218) LFTAS-DDCHIHIYDAK (174) LLACGSMDGTIAVYDAV (260) VATGS-SDRTVRLWDIN D Os12g06810 (55) LFTGS-RDGTLKRWEPK (228) LVSGG-TEKVVRVWDPR (270) CLSGS-SDSMIRLWDLG C Os12g42150 (283) LIASASSDGIIRIWDAR B

Supplemental Figure 2. Alignment of DWD Motifs in Oryza sativa.

Alignment of the DWD motifs of the 78 rice DWD proteins is depicted along with the alignments of the DWD△R(16) domains, if

present. Conserved amino acids are shown in color. Hydrophobic amino acids are shaded in yellow and small amino acids are shaded in

gray. The WDXR submotif is shown in red letter and the conserved D/E residues at position 7 are shown in pink. The DWD△R(16)

motif contains the first highly conserved 14 amino acids of the DWD motif but lacks the 16th arginine/lysine. Gene names are from the

TIGR Rice Genome Annotation. For genes with splice variants only the variant listed as the “Locus Name” at TIGR was used.

Supplemental Figure 3. Phylogenetic Tree for All Rice and Arabidopsis DWD Proteins.

A phylogenetic tree was constructed from 85 Arabidopsis and 78 rice DWD proteins

using CLUSTALW and MEGA3.1 by the neighbor-joining (NJ) method, using the p-

distance model. Interior branch tests were conducted to assess statistical significance of

the phylogenetic trees using 1,000 replicates. Numbers indicate % values after 1,000

replications; values below 50% are not shown. Scale bar represents the amino acid

substitutions per site for a unit branch length.

Supplemental Table 1. Rice DWD Proteins and Their Counterparts in Arabidopsis.

Rice DWD gene Arabidopsis homologue Identity (%) Similarity (%)

Os01g03510 At3g18060 67.3 81.5

Os01g04870 At5g58760 57.1 71.9

Os01g08770 At3g10530 60.3 75.6

Os01g09252 At5g51980 29.0 38.7

Os01g13730 At4g28450 69.9 81.3

Os01g21940 At1g73720 81.8 92.3

Os01g28680 At4g03020 36.2 44.6

Os01g37120 At2g46560 32.8 46.6

Os01g39380 At1g49040 69.0 82.2

Os01g44394 At1g80670 74.9 83.7

Os01g51300 At2g19520 67.6 76.4

Os01g52640 At3g15354 35.7 46.2

Os01g57210 At5g23430 41.8 58.9

Os01g72220 At5g13480 47.4 53.2

Os02g02380 At5g23730 42.4 53.5

Os02g14790 At1g29260 63.7 79.5

Os02g18820 At1g04140 49.4 60.4

Os02g20430 At1g27840 50 61.6

Os02g21490 At5g54520 51.9 66.5

Os02g37856 At5g12920 43.1 60.5

Os02g49090 At3g13290 45.1 59.6

Os02g53140 At2g32950 69.2 80.8

Os02g55340 At4g29380 51.7 66.8

Os03g02440 At5g24320 39.8 55.6

Os03g08830 At5g10940 55.3 71.3

Os03g21990 At4g15900 71.9 80.9

Os03g23909 At2g41500 55.5 68.9

Os03g26870 At1g36070 48.8 63.4

Os03g27970 At1g10580 72.8 84

Os03g33580 At3g19590 80.6 88.4

Os03g42770 At4g05410 50.5 68.3

Os03g43890 At5g58230 85 92.1

Os03g46650 At4g34460 76.9 86.9

Os03g47780 At2g22040 64.4 75.9

Os03g48090 At1g71840 53.5 71.1

Os03g49200 At3g27640 40.1 55.8

Os03g51550 At3g49660 62.3 76.3

Os03g53510 At5g50230 54.4 74.1

Rice DWD gene Arabidopsis homologue Identity (%) Similarity (%)

Os04g42880 At5g63010 54.2 69.4

Os04g50660 At5g16750 47.6 60.7

Os04g58130 At5g23430 49.4 62.0

Os05g05210 At4g03020 55.0 67.8

Os05g16660 At2g46290 70.7 80.6

Os05g33710 At4g03020 57.6 72.7

Os05g46570 At5g14530 73.8 84.3

Os05g49590 At2g46340 39.9 53.3

Os06g07540 At5g56190 58.5 73.4

Os06g19660 At3g13300 46.3 60.5

Os06g44370 At2g43770 76.2 85.5

Os06g50880 At4g38480 41.8 57.4

Os07g12320 At2g47990 43.0 61.5

Os07g14830 At2g26060 62.1 76.0

Os07g22220 At5g67320 59.8 76.1

Os07g22534 At3g49180 39.0 57.4

Os07g38430 At4g02730 55.3 69.9

Os07g40030 At5g66240 58 70

Os07g40930 At5g15550 62.1 79.7

Os07g41190 At5g14050 58.0 72.4

Os07g46620 At2g34260 50.7 65.4

Os08g04270 At3g20740 67.6 80.9

Os08g21660 At2g46280 78.7 88.8

Os08g31560 At1g78070 50.3 68.8

Os08g38880 At3g13340 63.6 78.4

Os09g06560 At3g42660 45.7 59.5

Os09g12550 At1g04140 47.0 58.1

Os09g12710 At5g56130 70.8 80.1

Os09g19900 At2g19430 36.9 50.5

Os09g36900 At4g35050 50.3 64.4

Os10g01540 At5g52820 71.9 84.6

Os10g32710 At2g20330 64.5 76.9

Os10g32880 At1g04510 70.0 82.6

Os10g35200 At5g08390 41.8 56.3

Os11g03990 At2g19540 65.7 77.8

Os11g10640 ND ND ND

Os11g38170 At5g52820 72.3 84.8

Os11g43890 At4g29830 69.8 85.2

Os12g06810 At3g05090 67.2 78.7

Os12g42150 At1g65030 49.4 64.0

Each rice DWD protein was analyzed using BLAST search to find its Arabidopsis

homologue. Arabidopsis homologue means the protein which shows the highest

similarity with each rice protein. After the homologues were selected, rice and

Arabidopsis homologues were analyzed under ‘EMBOSS Pairwise Alignment

Algorithms’ at EMBL-EBI (http://www.ebi.ac.uk/emboss/align/index.html; Rice et al.,

2000) to acquire the identity and similarity values to covers the whole length of both

sequences. Bold letters in Arabidopsis homologues indicate the proteins which are

included in Arabidopsis DWD list. ND, not determined.

Supplemental Table 2. Oligonucleotide Sequences of the Primer Pairs Used in RT-PCR

Experiments and to Confirm the Presence of the Transgene.

Forward Primer Reverse Primer

ASUS1 5’-GAGAAAAGACTCGGAACCAG-3’ 5’-AGGGGAATCTCCCAACAGCC-3’

ADH 5’-CATGAACAAGGAGCTGGAGC-3’ 5’-CAGAGAAGAAAACCAAAAGCGATGG-3’

CHS 5’-CACATGTGTGCTTACATGGC-3’ 5’-CAACAGTGAGACCTGGTCCG-3’

RBCS 5’-TCCATCACAAGCAACGGCGG-3’ 5’-CCGGTGAAGCTTGGTGGCTT-3’

ACO2 5’-AAGGAGCCACGGTTCGCAGC-3’ 5’-CCCCACACTTTAAAACACACC-3’

RPN6a 5’-AAGGCACGATAGATCTGCAGA-3’ 5’-TCGAGGGTAGCCGAGTAGAT-3’

ACTIN2 5’-TTGACCTTGCTGGACGTGAC-3’ 5’-TTCTGTGAACGATTCCTGGACC-3’

PRL1 5’-CTGCCACAACATGCTTTCGC-3’ 5’-CGCCTAATCTCCTTTGGTGG-3’

At3g45620 5’-ATGGCGAGACCGAGACGAAG-3’ 5’-TCAGCTTACAGTACATTCTC-3’

At4g35050 5’-ATGGCGGCAGAAGAGGGTAA-3’ 5’-TCATTTCTGGTTTTCATTGG-3’

At1g65030 5’-ATGAGTATCATCGCAGGCTC-3’ 5'-TTATTCTGAGTCCTCATGCT-3'

At4g29830 5’-ATGAAACTCGCAGGTCTGAA-3’ 5’-TCATGAGTAATCATAGAGCG-3’

At2g19430 5’-ATGTACGGAGACGCTACAAA-3’ 5’-TTACAATGAACTGCTACGAA-3’

At1g04140 5’-ATGACGGAATCTATCTGGTT-3’ 5'-CTAACGCATAGGTCTGCACC-3'

Supplemental Methods: Identifying Arabidopsis and Rice DWD Proteins.

We first retrieved all annotated Arabidopsis WD40 proteins from The Arabidopsis

Information Resource (www.arabidopsis.org) and from the, National Center for

Biotechnology Information (http://www.ncbi.nlm.nih.gov/). We compiled a total of 297

WD40 proteins in Arabidopsis after counting splice variants as a single protein. WD40

regions of these proteins were confirmed by querying the Pfam database with the

“protein search” function (http://www.sanger.ac.uk/Software/Pfam/) and the conserved

domain database at NCBI with BLAST (Marchler-Bauer et al., 2005). WD40 regions

from each protein were then searched for the sequence ([IFVL]-[IFVL]-[AGST]-

[AGST]-[AGST]-x-[DE]-x-x-[IFVL]-x-[IFVL]-[WY]-[DE]-[IFVL]-[RK]) manually.

We also searched for Arabidopsis DWD proteins using this sequence as the pattern

input for the MyHits program and confirmed most of our positives but did not find any

additional DWD proteins (http://myhits.isb-sib.ch/cgi-bin/pattern_search, Pagni et al.,

2004).

To identify rice DWD proteins we first retrieved all rice WD40 proteins identified

using Pfam Profile search from The Institute for Genomic Research (http://rice.tigr.org/)

and all rice proteins annotated as containing WD40 repeats from the National Center for

Biotechnology Information (http://www.ncbi.nlm.nih.gov/). We compiled 223 WD40

proteins in rice after counting splice variants as a single protein. WD40 regions of the

proteins were checked against the Pfam and NCBI conserved domain databases

(Marchler-Bauer et al., 2005). WD40 regions from each protein were then searched for

the 16 residue DWD motif as in Arabidopsis.

Supplemental References

Marchler-Bauer, A., Anderson, J.B., Cherukuri, P.F., DeWeese-Scott, C., Geer, L.Y.,

Gwadz, M., He, S., Hurwitz, D.I., Jackson, J.D., Ke, Z., Lanczycki, C., Liebert,

C.A., Liu, C., Lu, F., Marchler, G.H., Mullokandov, M., Shoemaker, B.A.,

Simonyan, V., Song, J.S., Thiessen, P.A, Yamashita, R.A., Yin, J.J., Zhang, D.,

and Bryant, S.H. (2005). CDD: a Conserved Domain Database for protein

classification. Nucleic Acids Res. 33: D192-196.

Rice, P., Longden, I., and Bleasby, A. (2000). EMBOSS: the European Molecular

Biology Open Software Suite. Trends Gen. 16: 276–277.