Fig. 4

Chloroplast repeat scaffolding. Each subfigure is a common chloroplast genome structure with its associated order of oriented contigs (coloured arrows). The green and the blue sequences of arrows are IR and DR, respectively. The purple and the red ones are single-copy regions. Contig \(s\) is the starter, and the right side black arrow determines the contigs’ order. Contigs \(a_0\), \(a_1\), \(b_0\), \(b_1\), \(c_0\), \(c_1\) and \(d_0\), \(d_1\) are two occurrences of four contigs \(a\), \(b\), \(c\) and \(d\), respectively. Each coloured dashed line links two occurrences of the same contig. a The order of the occurrences is reversed, and their arrows are oppositely oriented. Visually, an IR produces parallel dashed lines. b The order and the orientation of the occurrences is preserved, revealing a DR. c A chloroplast genome can contain the two types of repeats. Here, we will retain the hierarchical problem succession \(\mathcal {IRP}\)–\(\mathcal {DRP}\)–\(\mathcal {SCP}\) (\(h_2\)) since the IR contains more contigs than the DR