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An additional 694 probes were shared between methods.
We next examined specific chloroplast sequence polymorphisms that were shared between ORSC and O. sativa (Fig. 4; Additional file 13: Table S6A).
Approximately half of all genes changing in each comparison were shared, with an additional unique set of genes specific to each time point.
It is worth noting, however, that cutoRNAs were abundant in the species-specific secondary metabolic gene clusters, where they were shared between genes with obvious functional relationships (Additional file 1: Table S1 and below).
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An additional advantage of using cross-assembly is that the sequences of biological entities, which are shared between specific samples, are simultaneously assembled.
To facilitate the understanding of pathways (and pathway clusters) that are shared between, or selectively ascribed to, specific gene lists, additional visualizations were developed for Metascape.
PCR primers specific to the family member but which can be shared by the three homoeologues of the same gene were designed and used for quantitative expression studies using qRT-PCR (Additional file 2).
Although the majority of functional groups are shared between several stages, some of these clusters show specific functional categories enrichment (Additional file 6).
A series of specific shared repeats (See Table 2 and Additional file 7, Figure S7) substantiate the scenario depicted in the next section: r15 is shared only by TRGJ5 and TRGJ3, just like r21 is shared by TRGJ3 and TRGJ4.
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