Subgenomic asymmetry of ptDNA/mtDNA integration during tetraploid domestication and allohexaploid processes. A) The schematic diagram for calculating the DI for NUPTs/NUMTs. The letters near each node/tip indicate the number of NUPTs/NUMTs in each evolution node. The dashed line indicates the split time point (here, the time of tetraploid domestication). B and C) Comparing the DI of NUPTs between A- and B-subgenomes based on B) 4-factors and C) 3-factors tree topology levels. Whether the DI in A-subgenome is significantly different from that in B-subgenome is tested using the χ2 test. In these 2 tree topology levels, IWGSC RefSeq 1.0 (CS) was used as the representative common wheat genome (T. aestivum). Comparison of the DI of NUPTs/NUMTs between A- and B-subgenomes based on D) 4-factors and E) 3-factors tree topology levels, using different resources of hexaploid wheat genomes. The significant results of the χ2 test are shown as **P < 0.01 and *0.01 < P < 0.05. F) The ratio of species-specific and homo-NUPTs/NUMTs between A- and B-subgenomes based on the pairwise comparison of T. dicoccoides (before domestication) and T. durum (after domestication) (χ2 test, P < 0.05). G) The ratio of specific NUPTs/NUMTs between A- and B-subgenomes (n = 13 for each) based on the pairwise comparison of T. durum (before hexaploidy) and different resources of T. aestivum (after hexaploidy). P values were calculated based on the pairwise Mann–Whitney U test (P < 0.01).
