Supplemental Figure 1. Comparison of Tiller Bud Formation between the Wild Type and d27. (A) and (B) Longitudinal sections of shoot apex in wild-type

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1 A B Supplemental Figure 1. Comparison of Tiller Bud Formation between the Wild Type and d27. (A) and (B) Longitudinal sections of shoot apex in wild-type (A) and d27 (B) seedlings at the four leaf stage. Arrows indicate tiller buds and numbers 1, 2, 3 represent the first, second and third tiller bud, respectively. Bars = 15 µm.

2 attcccaccacaaccaagatgccctctccatgccatttggtctcttctctctccctcctt 6 gcaaattgcatgaccctctctctctctctccacttctctctataaaccttcctctctccc 12 ataacttctttccattttcaacctacaaatatactaatctctctctagctagtcttcacc 18 tacaaatctctctctctctctctctctctctctcttcatggagaccaccacgcttgtgct 24 M E T T T L V L GCTTCTTCCTCATGGCGGCGCCGGCGGCGTACGGCCGGCGGCAGCGGCAACGGCGAAGCG 3 L L P H G G A G G V R P A A A A T A K R AAGCTACGTGATGAGGAGGTGTTGCTCGACGGTGAGGGCGGTCATGGCGAGGCCGCAAGA 36 S Y V M R R C C S T V R A V M A R P Q E GGCGCCGGCGTCGGCGCCGGCCAAGAAGACGGAGACGGCGGCGATGATGTCGACGGTGCA 42 A P A S A P A K K T E T A A M M S T V Q GACGGAGACGGCGGCGGCGCCGCCGGCGACGGTGTACCGGGACAGCTGGTTCGACAAGCT 48 T E T A A A P P A T V Y R D S W F D K L CGCCATTGGTTACCTGTCCAGGAACCTTCAAGAAGCTTCTGGGCTAAAGAATGAAAAGGA 54 A I G Y L S R N L Q E A S G L K N E K D TGGCTACGAGAGCCTGATAGATGCCGCCCTAGCCATCTCAAGAATCTTCAGTCTGGATAA 6 G Y E S L I D A A L A I S R I F S L D K ACAAAGCGAGATTGTGACCCAAGCTCTTGAAAGAGCACTTCCAAGCTACATCCTCACAAT 66 Q S E I V T Q A L E R A L P S Y I L T M GATCAAGGTGATGATGCCACCTTCAAGATTTTCCAGGGAGTACTTTGCTGCATTCACCAC 72 I K V M M P P S R F S R E Y F A A F T T GATATTTTTTCCTTGGTTGGTTGGGCCGTGTGAGGTTATGGAATCTGAAGTTGAAGGAAG * * * * 78 I F F P W L V G P C E V M E S E V E G R GAAAGAGAAAAACGTGGTATATATCCCCAAATGCAGATTTCTGGAAAGTACAAATTGTGT 84 K E K N V V Y I P K C R F L E S T N C V TGGTATGTGCACAAACCTTTGCAAGATTCCATGCCAGAAGTTCATCCAAGATTCACTTGG 9 G M C T N L C K I P C Q K F I Q D S L G CATGAAGGTCTACATGTCTCCCAATTTTGAAGACATGAGCTGTGAGATGATATTTGGACA 96 M K V Y M S P N F E D M S C E M I F G Q GCAACCTCCTGAAGATGACCCTGCATTGAAGCAGCCATGCTTCCGGACAAAATGCGTCGC 12 Q P P E D D P A L K Q P C F R T K C V A AAAGCAGAATCATGGTGTGAATTGCTCCATCTGAtctgaaagaaattatcaatagataga 18 K Q N H G V N C S I tttcaaatcagtaaaatgccttaagctccatttcctttattcctttggaaaaaaaattag 114 caccatcattgtttttgcccacaacaccagcatgtttggaacatacactcttcattgtaa 12 tccaaaagtaatctaagaggaaatgaaaggcccaacagtaaccattttaaggta 1254 Supplemental Figure 2. D27 cdna Sequence and Its Deduced Amino Acid Sequence Blue letters indicate 5 - and 3 -untranslated regions (UTRs). Red asterisks indicate the 4- bp deletion in d27-zf82. Red letters indicate the premature termination site.

3 Supplemental Figure 3. Multiple Sequence Alignment of the Deduced Amino Acid Sequence of D27 with Its Homologs. D27 was used as query to search possible homolog genes in other organisms against NCBI non-redundant protein sequences database with an E-value cut-off level of 1e-1 by BLAST, and 38 hits were identified. Homology analysis against TIGR plant transcript assemblies using the mrna sequence of D27 showed that D27 shares high identities with 13 deduced proteins. Multiple alignment was performed with the ClustalX (2.) software. Am: Acaryochloris marina; At: Arabidopsis thaliana; Cr: Chlamydomonas reinhardtii; Fv: Fragaria vesca; Gm: Glycine max; Lp: Lactuca perennis; Me: Manihot esculenta; Mt: Medicago truncatula; Ol: Ostreococcus lucimarinus; Os: Oryza sativa; Ot: Ostreococcus tauri; Pp: Physcomitrella patens; Ps: Picea sitchensis; Pt: Phaeodactylum tricornutum; Sm: Selaginella moellendorffii; Sy: Synechococcus sp. PCC 7335; Ta: Triticum aestivum; Te: Thermosynechococcus elongates; To: Taraxacum officinale; Tv: Triphysaria versicolor; Vv: Vitis vinifera; Zm: Zea mays; Zo: Zingiber officinale

4 Supplemental Figure 3 (Continued)

5 Supplemental Figure 3 (Continued)

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8 GR24 Shiokari d27 d1 H 2 O Supplemental Figure 4. Germination of O. minor seeds 5 days after treatment with root exudate extracts of Shiokari, d27, d1, water (negative control) or GR24 (positive control).

9 Supplemental Table 1. PCR-based molecular markers developed in this study. Name Forward sequence Reverse sequence C189 5'-TAAGTTCTACATCGACCCCA-3' 5'-CACATGAAGAGCTGGAAACG-3' RM26 5'-CCCATGCGTTTAACTATTCT-3' 5'-CGTTCCATCGATCCGTATGG-3' P1 5'-CAAACAGAACATCAGGCCGAG-3' 5'-TGTACCAGGTGTCTCCGCCAC-3' P2 5'-GCTTGCAGTAGGGTGGATCG-3' 5'-CAAGATATTTGGTGCATGACTC-3' P3 5'-TTCCTCGTCTCCAGCAACTC-3' 5'-CGAATAGACCGAGTATGGTTG-3' P4 5'-TGTGAAAAATCCAGCAGCCC-3' 5'-GGGACGGTTTGGGTCTTTGG-3' P5 5'-CTTGTTGGATAGAGGATTAG-3' 5'-ATGCCATGGCATGGCATCGG-3' P6 5'-ACATGGCAGACGATGAACACTG-3' 5'-CGATTAGCAGGCAAGGAGGA-3' P7 5'-CTAACTGGCACAGATGGAGC-3' 5'-ATGCCCACTAAGTCCTAAAGC-3'

10 Supplemental Table 2. Primer sequences used for D27 analyses. Experiment Primer name Sequence RACE Real-time PCR In-situ hybridzation Protein expression Subcellular localization 5 D27 5 Nested D Nested D D27 3 Nested D27 D27EF D27ER UbiF UbiR D27IF D27IR D27PF D27PR D PF D PR GFPF GFPR D27F D27R 5'-CTTCAGATTCCATAACCTCACACGGCCC-3' 5'-CGAACCAGCTGTCCCGGTACACCG-3' 5'-AGCAGCACAAGCGTGGTGGTCTCC-3' 5'-GAAGCGAAGCTACGTGATGAGGAGGTG-3' 5'-GATGCCACCTTCAAGATTTTCCAGGG-3' 5'-TCTGGGCTAAAGAATGAAAAGGA-3' 5'-AGAGCTTGGGTCACAATCTCG-3' 5'-GCCCAAGAAGAAGATCAAGAAC-3' 5'-AGATAACAACGGAAGCATAAAAGTC-3' 5'- AAGGATCCCGCTTGTGCTGCTTCTTCCTC-3' 5'- AAGGTACCCATCTTCAGGAGGTTGCTGTCC-3' 5'- AAGAATTCATGGAGACCACCACGCTTGT-3' 5'- AAGGATCCTCAGATGGAGCAATTCACACC -3' 5'- AAGAATTCATGGAGACCACCACGCTTGT -3' 5'- AAGGATCCTCCTTCAACTTCAGATTCCATAAC -3' 5'- AAAAAAGCTTATGGTGAGCAAGGGCGAG-3' 5'-AAAAGCGGCCGCTTTACTTGTACAGCTCGTC -3' 5'- AAGGATCCATGGAGACCACCACGCTTGTGC-3' 5'- AAAAGCTTGATGGAGCAATTCACACCATGATTC-3'