*4.5. Shared DNA among Di*ff*erent Genomic Compartments*

Shared DNA was evaluated in *Trifolium pratense* because this is the only species examined with completed sequences from all three genomic compartments. The mitogenome (MT039389) and plastome (MT039393) in this study were utilized and the nuclear genome was available as a chromosome-scale reference draft (LT990601- LT990607) [43]. Shared DNA among the genomes was evaluated in MegaBLAST with a word size of 28 and an e-value of 1e−6. For nuclear and organelle genome comparisons, each organelle sequence was used as the query against a subject database comprising the nuclear genome. For the comparison of organelle genomes, the plastome was used as the query and the mitogenome was the subject. BLAST hits with sequence identity higher than 90% were retained. Overlapping regions between hits were excluded from the estimations of shared DNA.

To search for putative large-scale IGT (> 100 kb) events, shared DNA analysis was conducted as described above but in this case the largest mitogenome (*T. meduseum*) and other published nuclear genomes of *Trifolium* (Table S1) were utilized. BLAST hits between the mitogenome and a long stretch of the nuclear region of *T. repens* were visualized by Circoletto [68].
