FIGURE 2.

The assembly graph of multipartite T. esculentum mitochondrial genome. The marama mitochondrial genome is composed of 5 circular molecules, which were built based on 16 primary long scaffolds. 4 of them shown here including H, I, J, O are long repeats, which are present in two copies in the marama mitogenome. The scaffolds are assembled together by the PacBio long reads across the gaps. Connections between two adjacent scaffolds were quantified by PacBio reads and the counts are shown as numbers in black. Recombination on repeats causes the existence of different connections between the same scaffolds, which are shown (within black boxes) in the dashed boxes and also quantified by PacBio reads. The numbers next to the black boxes represent their counts. According to the connections shown in the dashed boxes, the 16 scaffolds can also be assembled into two long rings, as shown in Figure 3. The PacBio long reads data confirmed that these two structures co-exist in the experimental individual and they are close to the same frequency.