*2.3. Intracellular Gene Transfer (IGT) in Trifolium*

The extent of IGT among the three genomic compartments was analyzed in *T. pratense* by BLAST (Figure 4; Table 3). The amount of DNA shared between the two organelle genomes was very low (0.3 kb). The organelle genomes shared considerable DNA with the nuclear genome and GC content of shared DNA reflected the compartment of origin (45.8% for mitogenome and 35.1% for plastome). In general, BLAST hits between nuclear and organelle genomes were very short and had high sequence identity (Table 3).

**Figure 4.** Shared DNA among three different genomic compartments in *Trifolium pratense*. Size of each genome is presented below the bar. Values on arrows represent the amount of shared DNA. Round end of arrow represents query sequence and pointed end represents subject sequence in BLAST analyses.

**Table 3.** BLAST hit statistics for shared DNA between nuclear and organelle genomes in *Trifolium pratense*.


A long contiguous region (348.5 kb) was identified from chromosome 4 of *T. repens* (position: 72,476,623–72,825,180) that shared substantial DNA with the mitogenome of *T. meduseum* (Figure S3). This sequence had a high GC content (44.3%) compared to the entire chromosome 4 (33.2%).
