I worked my way through Chambers three times from beginning to end, checking each word for possible anagrams and storing the results in loose-leaf files.
The method of editing dynamic MLC leaf sequence files has been published previously [ 29].
Using a fold change of >1, false discovery rate (FDR) of <1e-05 as a cutoff to identify differentially expressed genes, 842 contigs were up-regulated in the stigma compared to the ovary and leaf (Additional file 2 and Additional file 3).
The examples for these include GO 0009628 (response to abiotic stimulus), GO 0016051 (carbohydrate biosynthetic process), and GO 0000271 (polysaccharide biosynthetic process), which is clearly seen in leaf (Additional file 8), but not in root (Additional file 9).
In all, 447 homologs were identified in the leaf (Additional file 2: Table S6) and 145 homologs (Additional file 2: Table S7) in the root, these were further analysed in MapMan.
Additionally, both sulphate and ABC transporters showed inducible higher expression levels in the leaf (Additional file 2: Table S8, Fig. 3) and root (Additional file 2: Table S9, Fig. 3).
Some groups of genes in the hybrid were expressed at levels between midparent and SRG200 (0 < d/a < 1) under sufficient N condition, but had more genes expressed at levels outside the SRG200 range under low N condition (d/a >1), e.g. gene expression (GO 0010467) in leaf (Additional file 8), and carbohydrate metabolic process (GO 0005975) in root (Additional file 9).
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While "GO 0046148_pigment biosynthetic process" showed no significant change in root, "GO 0009765_photosynthesis, light harvesting" was enhanced in this organ and both of them were repressed in leaf (Additional file 3: Table S3a).
We found a total of 12,822 transcripts with different expression between root and leaf (Additional file 1: Figure S1).
