and red light in wild type and pif3 mutant. Gene_id in right panel indicates Arabidopsis gene name; numbers in the section of gene/ gene family are the same with the order of 32 genes; U in the section of type indicates unique genes, P in the section of types of genes indicates predominantly light-induced gene family members, NP in the section of type indicates not predominantly light- induced gene family members, and indicates ‘‘not analyzed’’; photomorphogenic in the section of severity of phenotype is a targeted phenotype related to phytochrome signaling pathway. Data of the phenotypes for 32 genes in this figure came from Khanna et al. [3]. Found at: doi:10.1371/journal.pgen.1000164.s006 (0.66 MB JPG) Figure S7 Representation of Co-expressed Gene Clusters in Figure 4 using Cytoscape Software. Co-expression analysis of 72 genes in 13 biochemical/metabolic pathways or reactions related to mutants identified in this study identifies 10 gene clusters in Figure 4. Circles indicate steps in pathways identified by functional analyses in rice. Ten colored lines indicate 10 gene clusters in Figure 4. Eleven colored boxes indicate 11 different pathways used in this figure. Weak gray boxes indicate reactions for two unknown genes. Weak gray lines indicate the steps not analyzed for co- expression analysis. Blue box indicates methyl-erythritol phos- phate (MEP); purple box, Nitrate assimilation pathway; yellow box, the reaction by carbonic anhydrase; pink box, ABA biosynthesis pathway; dark gray box, Photorespiration pathway; sky blue, Vitamin C biosynthesis pathway; red box, Carotenoid biosynthesis pathway; orange box, Ammonia assimilation path- way; green box, Chlorophyll biosynthesis pathway; lime box, Vitamin E biosynthesis pathway; white box, Photosynthetic light reaction pathway; and weak gray box, reactions by unknown genes. Numbers in each pathway indicate the order of reactions in the pathway. Found at: doi:10.1371/journal.pgen.1000164.s007 (0.38 MB JPG) Figure S8 Phenotype of mcs Mutant in MEP pathway. Found at: doi:10.1371/journal.pgen.1000164.s008 (0.19 MB JPG) Figure S9 Scheme for co-segregation analysis of T-DNA insertions and observed phenotypes on a large scale. Genomic DNAs were isolated from progenies showing phenotypic variation. Amplification of the hph gene was used to check for T-DNA insertions. p1, forward primers, in front of the T-DNA insertion site; p2, reverse primers, behind the T-DNA insertion site; p3, forward primer for identifying the hph gene; p4, reverse primer for identifying the hph gene. Upper PCR bands were produced as a result of amplifications with p1 and p2; lower PCR bands were produced as a result of amplifications with p3 and p4. Found at: doi:10.1371/journal.pgen.1000164.s009 (0.12 MB JPG) Figure S10 Expression Analysis of Rice Candidate Genes Involved in the Chlorophyll Biosynthesis Pathway Carried Out Using Publicly Available Multiplatform Array Data. Published BGI/Yale light vs. dark microarray datasets were used to check the consistency of the gene expression patterns of candidate genes in this pathway [49] (Table S6). In addition, 23 Affymetrix microarray datasets were used to compare the gene expression levels of the genes in the pathway in many different tissues and at different developmental stages (Table S6). ‘‘Two channel array’’ indicate the data from NSF45K and BGI/Yale arrays; ‘‘one channel array’’ indicates the data from the Affymetrix array. ‘‘Step’’ indicates the corresponding position in the chlorophyll biosynthesis pathway marked in Figure 1. 1a, 1b, and 1c indicate the genes encoding the three subunits of magnesium chelatase, respectively. Gene family members in each step are represented as 21, 22, etc. Unique means genes without gene family members; Functional Analysis of Singleton and Gene Families Predominant indicates a gene family member that is predomi- nantly expressed in the light; and Not Predominant indicates a gene family member that is not the predominantly expressed gene family member in the light. An asterisk (*) indicates the existence of consistency between the gene expression patterns derived using the NSF45K and the BGI/Yale microarrays. Data in the left panel were generated by using log2 ratios from the two two-channel arrays and data in the right panel were generated using log2 transformed signal intensities from the single-channel array data. Red color in the left panel indicates light-responsive gene expression and green indicates dark-responsive expression. Yellow color in the right panel indicates a high level of gene expression and blue, a low level of gene expression. The yellow box highlights the rice light vs. dark microarray data using the NSF45K and BGI/Yale arrays. The red box highlights gene expression data from seedling leaf, seedling shoot, and young leaf derived using the Affymetrix array. Found at: doi:10.1371/journal.pgen.1000164.s010 (0.47 MB JPG) Table S1 Complete Dataset from Light vs. Dark Experiments Carried out with the Rice NSF45K Microarray. Oligo_id is the name of the NSF 45K oligo; Locus_id is the TIGR version 5 gene model based on gene locus; FDR is adjusted p-value; log2 (Light/ Dark) is log2 fold change value of average normalized spot intensity in the light over average normalized spot intensity in the dark; Avg_light intensity is average normalized spot intensity in the light; Avg_dark intensity is average normalized spot intensity in the dark; std_light is standard variation in the normalized intensity in the light of all replicates and std_dark is variation in the normalized intensity in the dark of all replicates. The numbers of ESTs in nineteen tissues such as callus, root, leaf, seedling, sheath, phloem, shoot, stem, flower, panicle, anthers, pistil, endosperm, immature seed, seed, suspension, mixed, unknown, and whole are prepared. Sum of total ESTs is the summation of ESTs related to a corresponding oligo. Full length cDNA is the cDNA accession number available in Knowledge-based Oryza Molecular biological Encyclopedia (KOME, http://red.dna.affrc. go.jp/cDNA/). GO_id indicates the GO identifier accessible at AmiGO (http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?- session = 7122b1203889484). Found at: doi:10.1371/journal.pgen.1000164.s011 (8.19 MB XLS) Table S2 Microarray Data Used for Figure 2. Gene_id is a simplified gene identifier; U indicates unique gene; P indicates predominantly light-induced gene family member; R indicates not predominantly light-induced gene family member; Redundancy of gene sequences is marked as U (Unique) or R (Not predominant); Predominant expression within a gene family is marked as P (Predominant); Knockout lines which were analyzed in this study are described and PFG indicates Plant Functional Genomics Laboratory in POSTECH, South Korea; Phenotypes related to light response are described; Co-segregation of observed pheno- types and T-DNA insertion is indicated as Yes or NO; Oligo_id is the name of the NSF 45K oligo; locus_id is the TIGR version 5 gene models based on gene locus; annotation indicates the putative function of the gene; NSF45K_light_vs_dark is the average log2 (natural light/dark) value derived using the NSF45K array data; BGI far-red_light_vs_dark is the average log2 (far-red light/dark) value derived using the BGI/Yale array data; BGI white_ light_vs_dark is the average log2 (whole seedling treated with white light/dark) value derived using the BGI/Yale array data; BGI root white light_vs_dark is the average log2 (root treated with white light/dark) value derived using the BGI/Yale array data; BGI shoot white light_vs_dark is the average log2 (shoot treated PLoS Genetics | www.plosgenetics.org 16 August 2008 | Volume 4 | Issue 8 | e1000164