Supplemental Figure 1 Phylogenetic analysis of transcription factor genes
The phylogenetic trees were constructed by the neighbor-joining method. The clades for one-to-one
orthologs are marked with red closed circles, and the clades for many-to-many orthologs are marked
with black closed circles. The nodes representing segmental duplications are labeled with open circles
in rice (red circles) and Arabidopsis (green circles). The clades with gene expansion in the
many-to-many and lineage-specific expansion categories are shaded as green (rice) and orange
(Arabidopsis). The transcription factor genes identified in the KOME database are labeled as cDNA.
The number at each node is the bootstrap value in percentage. Only the node with a bootstrap value of
60 or higher is labeled. The number below the line represents the number of substitution per site.
Supplemental Figure 2 The phylogenetic tree of the liguleless clade of the SBP gene family.
The tree was constructed using the neighbor-joining method. MZLG1: LIGULELESS gene in maize;
OsLG: the ortholog of MZLG1 in rice.
9632.m04490
88
98
9634.m04348
9630.m00762
At1g02065
ZmLG1
100
OsLG
SPL8, Pollen sac development
Ligule development
Supplemental Figure 3 Clusters of tandem duplicated transcription factor genes in rice.
The locus name of each gene is abbreviated. For example, 00395 on chromosome 1 (Chr1) refers to
locus 9629.m00395. Centromeres are shown as black boxes.
Supplemental Figure 4 Clusters of tandem duplicated transcription factor genes in Arabidopsis.
Supplemental Figure 4 Clusters of tandem duplicated transcription factor genes in Arabidopsis.
Supplemental Figure 5 The phylogenetic tree of the GRAS family.
The tree was constructed using the neighbor-joining method based on the alignment of the full-length
amino acid sequences. Only two clades were shown here.
A. LAS/LS/MOC1 clade.
LAS
(LATERAL SUPPRESSOR) in Arabidopsis, Ls (Lateral suppressor) in tomato and two rice duplicate
genes, including MOC1 (MONOCULM 1), formed a monophyletic clade. B. GAI/RGA clade. Five
Arabidopsis genes (GAI, RGA, RGL1, RGL2 and RGL3) and OsGAI/SLR1 in rice, D8 in maize,
RHT-1Da in wheat, SLN1 in barley form a monophyletic clade.
A.
B.
Supplemental Figure 6 The phylogenetic tree of the SPT/ALC clade of the BHLH gene family.
A. This is a section of the unrooted phylogenetic tree of the group 15 of the BHLH family, which was
constructed using the neighbor-joining method from the alignment of the full-length amino acid
sequences. The Arabidopsis duplicate genes SPT (SPATULA) and ALC (ALCATRAZ) are orthologs of
two rice duplicate genes 9634.m00622 and 9630.m05571.
B. Gene structure of 9634.m00622 with a
retrotransposon insertion. The triangle indicates the insertion site of a TOS17 retrotransposon in the
fifth exon of the predicted gene. Exons and introns are shown as black and white boxes,
respectively.
A
B
Supplemental Figure 7 The phylogenetic clades of the Homeobox and MYB families
The trees were constructed by the neighbor-joining method from the alignment of the full-length
amino acid sequences. Only the relevant clades of the trees wee shown here.
A. HD-ZIPIII
subfamily of the HD-ZIP family. Five rice genes and five Arabidopsis genes form three orthologous
groups. REV/IFL1 (REVOLUTA/INTERFASCICULAR FIBERLESS 1), PHV (PHAVOLUTA), and PHB
(PHABULOSA) in Arabidopsis, and RLD1 (ROLLED LEAF1) in maize were functionally
characterized. B. CPC-like group of the MYB-related family. Five Arabidopsis genes including CPC
(CAPRICE), TRY (TRIPTYCHON) and two rice genes formed a monophyletic clade. C. A clade of the
unrooted tree of the GL2 (HD-ZIP IV) subfamily of the HD-ZIP family. The Arabidopsis gene GL2
(GLABRA2) and the rice gene 8350.m05180 formed a one-to-one orthologous relationship.
A
B
C