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Figure 1. 

Mitogenome assembly graph and possible connections (black lines) mediated by repeats for (a) M. notabilis, (b) M. mongolica, (c) M. alba-ZS5801, and (d) M. alba-ZZB. Each colored segment is labeled with its name and coverage. The boxes represent the different mitogenome conformations mediated by each pair of repeats and the probability of being supported.

Figure 2. 

The mitogenome map of Morus species. (a) M. notabilis, (b) M. mongolica, (c) M. alba-ZS5801, and (d) M. alba-ZZB. Genes belonging to different functional groups are color-coded.

Figure 3. 

Repeat sequences in the Morus mitogenomes. (a) Type and number of dispersed repeats and tandem repeats, (b) type and number of simple sequence repeats (SSRs).

Figure 4. 

Relative synonymous codon usage (RSCU) in the four Morus mitogenomes. (a) M. notabilis, (b) M. mongolica, (c) M. alba-ZS5801, and (d) M. alba-ZZB respectively.

Figure 5. 

Schematic representation of the distribution of MTPTs between plastome and mitogenomes for (a) M. notabilis, (b) M. mongolica, (c) M. alba-ZS5801, and (d) M. alba-ZZB. The MTPTs on the plastid IR regions were counted only once. Different colors of ribbons represent different identities. The length of each MTPT and the genes it contains can be found in Supplemental Table S6.

Figure 6. 

Phylogenetic trees of Rosales estimated using RA × ML from 25 PCGs of the mitogenomes. Numbers above the branches represent ML bootstrap/Bayesian posterior probability (BS/PP), ML bootstrap values with lower than 50 are indicated by the dash.