None of these genes were up-regulated in the EE-IE and IE-LE comparisons and the majority were down-regulated during development, when comparing IE with LE.
In both the EE vs. IE and IE vs. LE comparisons a set of GO classes linked to amino acid transport were identified as changing significantly during development.
We observed enrichment in transporter activity genes both in the EE-IE and IE-LE comparisons, with the presence of amino acid transporters being amongst the most significant.
On the other hand, between the EE-IE and IE-LE comparisons, we observed a continuity of expression in the majority of common genes (340 out of 435 changed in the same direction, with 322 showing an up-regulation during development).
In the IE-LE comparison, the morphogenesis and appendage development genes showed significant changes in expression levels.
In particular the expression of the ACYPI007803 gene, which encodes for the enzyme phenylalanine 4-monooxygenase responsible for the synthesis of Tyr in the pea aphid (EC 1.14.16.1), significantly increased in the IE-LE comparison (log2 difference of 3.36 for the IE-LE comparison).
For the IE-LE and LE-L1 comparisons, the analysis revealed three GO classes involved in the cuticle formation process.
For example, the highest number of common genes is found at the intersection between the IE-LE and LE-L1 comparisons, with 604 genes (Additional file 1: Table S1D).
At least one enzyme-coding gene showed significant differential expression for 43, 74 and 90 pathways in the EE-IE, IE-LE and LE-L1 comparisons, respectively (Additional file 5: Table S5).
It is worth noting that, out of these 604 genes common to the IE-LE and LE-L1 comparisons, 516 showed expression changes in opposite directions in the two comparisons and, among those, 366 were up-regulated between IE and LE and down-regulated between LE and L1.
The expression of this gene was relatively low in the early (EE) and intermediate (IE) embryo stages, compared to other genes, but it increased significantly between IE and L1 (2.37 and 2.91 log2 differences for the IE-LE and LE-L1 comparisons, respectively).
