Fig. 5

Verifying the quality of the cpDNA library. a Verify the cpDNA library’s quality using the sequencing results. The scaffold fasta file is constructed from the sequencing result by SPAdes and A5-miseq software. Collinearity analysis to verify the clones of the cpDNA sequence integrity from soybean circular cpDNA library (conform to Fig. 2b3). The reference genome of soybean chloroplast (NCo 07942.1) is entirely covered with the four scaffolds by the MUMmer software. Only five gaps/insertions with an average size of 21.6 bp were visible and located at specific points in the Referee-genome’s IRa and IRb. LSC and SSC refer to the large and small single-copy regions, respectively, and IRa and IRb are the two inverted repeats. b Diagrammatic representation of the circular cpDNA traits in soybeans. Gap-filling by PCR was performed after screening/assembling the four scaffolds from the scaffold fasta file. The CPGAVAS2 software can annotate and view the soybean circular cpDNA from the cpDNA libraries. From the center going outward, the first circle shows the forward and reverse repeats connected with red and green arcs, respectively. The second circle shows the tandem repeats marked with short bars. The third circle shows the microsatellite sequences identified using MISA. The fourth circle is drawn using draw gene map and shows the gene structure on the soybean circular cpDNA. The genes are colored based on their functional categories