Supplemental Data

Files in this Data Supplement:

• Supplemental Table 3 - Supplemental Table 3. Biochemical pathways regulated by light in both rice and Arabidopsis. Two sample enzymes for each pathway are given, with one rice gene and one Arabidopsis gene as examples. These two genes were from a best-matched homologous pair. Light-induced gene expression changes in fold are in parenthesis after each gene name. Pathways and Arabidopsis genes in each pathway were identified following the AraCyc pathway database (Mueller et al., 2003), while rice genes were identified based on homology to Arabidopsis genes.
• Supplemental Figure 1 - Supplemental Figure 1. RT-PCR verification of microarray data. W light and dark conditions are selected for verification. Gene name and expression ratio from microarray for each gene are shown. Actin is selected as a control for both rice and Arabidopsis. A total of 6 pairs of corresponding genes from rice and Arabidopsis are tested and shown.
• Supplemental Figure 2 - Supplemental Figure 2. (A) and in Arabidopsis (B).
• Supplemental Figure 3 - Supplemental Figure 3.Organ-specific light-regulated expression in Arabidopsis. (A) Expression profiles of four Arabidopsis genes with similar light regulation. From left to right: At4g04840, pilin-like transcription factor; At5g60890, ATR1, a receptor-like kinase; At2g44840, ethylene response element binding protein; At1g64230, E2 ubiquitin-conjugating enzyme. (B) Expression profiles of four Arabidopsis genes with light regulation only in cotyledons. From left to right: At1g22400, UDP-glucose glucosyltransferase; At4g00520, acetyl-CoA thioesterase; At5g50250, chloroplast RNA-binding protein cp31; At1g53700, auxin response transcription factor (ARF6). (C) Expression profiles of four Arabidopsis genes with light regulation only in root. From left to right: At3g18130, protein kinase C-receptor; At5g05410, DRE binding protein (DREB2A); At1g21450, SCARECROW-like 1; At3g56400, WRKY family transcription factor. (D) Expression profiles of four Arabidopsis genes with antagonistic light regulation in cotyledons and roots. From left to right: At4g16920, disease resistance protein (TIR-NBS-LRR class); At1g72940, disease resistance protein (TIR-NBS class); At5g02270, ABC transporter family protein; At5g48000, cytochrome p450 protein. Bars in each graph of (A) through (D) correspond to the log₂-transformed expression ratios of W light compared with dark.
• Supplemental Figure 4 - Supplemental Figure 4. Residual check for the calculation of Pearson correlation between reciprocal best-matched gene pairs. Both normal quantile plot and a plot between residuals and fitted values are shown for(A) expression values before transformation and (B) log₁₀-transformed expression values. Transformed expression values had a close-to-normal distribution with no obvious patterns or bias.
• Supplemental Table 1 - Supplemental Table 1. Expression of 37,132 rice genes in response to light exposure. Expression intensities (without logarithm transformation) for each light and dark condition are shown. A Pvalue of a two-tailed t test and log₂-transformed light versus dark ratio are calculated for each gene in each comparison.
• Supplemental Table 2 - Supplemental Table 2. Expression of 25,676 Arabidopsis genes in response to light exposure. Expression intensities (without logarithm transformation) for each light and dark condition are shown. A P value of a two-tailedt test and log₂-transformed light versus dark ratio are calculated for each gene in each comparison