Fig. 6

Consensus of DEG calling and PCA of overlap of common DEGs. Venn diagram of the DEGs called between NM and M⁺ seeds by the three DEG detection programs (edgeR, NOIseq and DESeq2) using the transcriptome (a) and genome (b) approach. Principal Component Analysis of RPKM (Reads Per Kilobase per Million reads) of the 561 DEGs common to the transcriptome, ‘T’ and genome, ‘G’ (c). Samples M⁺ (circle) and NM (triangles), in black, show the results for the dehiscent and indehiscent seeds in the transcriptome approach. Samples M⁺ (circle) and NM (triangles), in white, show the corresponding results in the genome approach. The percentage variance explained by each principal component is indicated on the axes