Methodologies for In Vitro Cloning of Small RNAs and Application for Plant Genome(s)

Figure 7

Annotation of biological processes targeted by abundant copy (>5 copies) candidate siRNAs of developing ovules in cotton. To better visualize the specific and overlapping putatively targeted proteins at 0 to 10 DPA ovules, Cytoscape [43] was used to generate genetic interaction networks of putative targets at different DPA stages of ovule, where each node (DPA) and its edges (targeted proteins) were colored. The interaction networks were depicted using Cytoscape’s “spring embedded layout algorithm” for both full protein target dataset and protein groups targeted by only abundant copy candidate siRNAs, importing the “simple interaction format (SIF) files” into Cytoscape. SIF files were created based on specific and overlapping target protein information for 0–10 DPA ovule stages [33].