Figure 2

Active transcripts across peanut pod development. (A) Global transcriptional analysis of peanut pod development as determined by RNA-seq and circular visualization. The tick number (× 1,000) in the outer circle represents the number of expressed transcripts in each sample. The circular tracks are, going inwards: (1) FPKM data (≥ 10 and logarithm transformed) are represented in dark-red histograms. (2) The light blue track indicates expressed TFs in 20 individual samples. (3) Inner links represent shared transcripts between paired samples. (B) Expressed transcripts (FPKM > 1) across pod development. The bars indicate the number of transcripts expressed in each sample, and the lines indicate the cumulative number of expressed transcripts. The orange line indicates the cumulative number of expressed transcripts across all samples. The blue and brown lines indicate the cumulative number of expressed transcripts in seed and shell tissues, respectively. A&S, aerial and initial subterranean pods (P0 and P1); pod expansion, P2–P5; seed filling, P6–P9; M&D, mature and desiccation stages (P9 and P10). (C) Number of specific and shared transcripts expressed in 20 samples. (D) Distribution of τ values for 165,689 transcript profiles from all samples. The distributions of τ values are also shown for expressed transcripts from seeds (green triangle curve, 127,757 profiles) and shell (sky blue solid circle curve, 133,387 profiles). τ values varied between 0 for complete housekeeping genes with similar expression level in both tissues at all stages and 1 for strictly tissue-stage-specific genes.