Figure 3

Expression dynamics during pod development. (A) DETs between libraries pairwise. The DETs were filtered using the three criteria as follows. (1) The FPKM of transcripts in the paired samples should be at least 1. (2) All DETs were identified by both DEGseq and GFOLD software programs. (3) The FPKM in one sample was at least twofold higher (up-regulation) or lower (down-regulation) than the FPKM in the other sample. Concentric circles were drawn to show DETs between paired samples using the Circos program. The ‘a’ and ‘e’ tracks represent up-regulated genes in the given sample compared with other samples. The ‘b’ and ‘f’ tracks represent down-regulated genes in the given sample compared with other samples. The ‘c’ and ‘d’ tracks represent all DETs (including up-regulated and down-regulated genes) in the given sample compared with other samples. Different colors in ‘a’, ‘b’ and ‘c’ tracks indicate the corresponding samples. The data-set used for this figure was supplied in Table S4. (B) Heatmap of tissue-stage-specific genes. Red, high expression; cyan, low expression. A list of these maker transcripts was provided in Table S5. (C) Average expression levels of transcripts expressed in one or multiple samples. (D) PCA was applied to 20 samples representing 11 developmental stages. Red squares represent seed, and light triangles represent shell. The two black solid circles represent P0 and P1. (E) PCA was applied to all expressed transcripts, and six trends were determined to together explain ~ 94% of the total expression variance across 20 samples. Contribution of each component is indicated on top left. Green represent P0 and P1 stages, Light brown presents seed, and stages are indicated by corresponding numbers (2–10). Orange represents shell, and stages are also indicated by numbers (2–10).