Fig. 1

Schematic of sub-assembly of chloroplast genome from PE RAD-seq. a Illustration of RAD-seq method. b Pipeline for sub-assembly of cpDNA from PE RAD-seq. This pipeline, SACRing, was divided into 4 steps, and step 3 and 4 were highlighted in top and bottom boxes with a purple dashed line, respectively. The detail of assembly was enlarged with the boxes with a grey dashed line. c Illustration of cluster analysis based on the result of SACRing