Gene Expression Profiles in Physic Nut Seeds Figure 4. Overview of expression profiles of central metabolism pathway genes in developing physic nut seeds. A: Profiles of plastid glycolysis metabolic pathway genes. B: Profiles of cytosol glycolysis metabolic pathway genes that are highly expressed at the filling stage. C: Profiles of oxidative pentose phosphate pathway (OPPP) genes. D: Profiles of C3–C4 intermediary metabolism pathway genes. All expression data were transformed to the log2 scale for plotting the profiles. Lines in different colors indicate the expression patterns of different genes in the metabolic pathway. Genes shown in this figure are listed in Table S2. doi:10.1371/journal.pone.0036522.g004 (Figures 5E and S5). The expression of several fatty acid synthesis genes, from early development to the point where the dry weight of seeds peaks, has been analyzed by Xu et al. [26]. In accordance with their observations, we found that expression of the b- ketoacyl-ACP synthase I (KASI) gene increased before those encoding KASII and KASIII. In contrast, the expression of genes encoding glycerol-3-phosphate dehydrogenase, glycerol-3-phos- phate acyltransferase, 1-acylglycerol-3-phosphate acyltransferase, acyl-CoA: diacylglycerol acyltransferase, phosphatidate phospha- tase, which are involved in TAG assembly, did not match the profiles for genes involved in FA synthesis (Figures 5D and S5) as observed in several oilseed plants [40].This supports the suggestion that TAG accumulation may not require coordinated expression of acyltransferase transcripts and/or may involve post-transcrip- tional regulation [40]. Seed Storage Protein and Late Embryogenesis-abundant Protein Genes The storage proteins in seeds are important sources of amino acids in animal feed. We examined the gene models that showed similarity to known genes encoding seed storage proteins and their expression patterns in developing physic nut seeds. The draft of the physic nut genome reveals five 11S globulin (Legumin), three 7S globulin (Vicilin), two Vicilin-like and eight 2S albumin genes (Figure S6). The expression patterns of these storage protein genes were examined and compared to those of late embryo abundant (LEA) protein genes [42]. The expression level of 11S globulin genes and 2S albumin genes were highest at S6, while those of 7S globulin genes and most LEA protein genes were highest at S7 (Figures 5F and S6). These results indicate that expression levels of 11S globulin genes and 2S albumin genes peak before those of 7S globulin genes and LEA protein genes in developing physic nut seeds. Transcription Factors Function in Storage Compound Biosynthesis and Accumulation in the Seeds At least 114 transcription factor (TF) genes were co-expressed with seed storage reserve synthesis genes during seed matura- tion, including orthologs of identified TFs that play important roles in seed reserve synthesis in Arabidopsis [11,20], such as LEC1 (JC_C100019577), LEC1L (JC_C100016264), FUS3 (JC_C100015987), LEC2 (JC_C100026639), WRI1 (JC_C100004962 and JC_C100015563), ABI3 (JC_C100033915), ABI4 (JC_C100020647) and ABI5 (JC_C100013731). Several of these TFs are embryogenesis- related genes, such as PEI1 (JC_C100018497), AtMYB118 (JC_C100013351), bHLH95 (JC_C100022524) and AGL15 (JC_C100012112) (Table S3). In the physic nut developing seeds, the LEC1, WRI1L, and ABI5 genes were expressed from PLoS ONE | www.plosone.org 5 May 2012 | Volume 7 | Issue 5 | e36522