Fig. 2: Subgenome and homeologue organization in N. benthamiana.

a, The left-hand Circos plot depicts the locations of the syntenic blocks (1 Mbp) of N. tomentosiformis (blue) and N. sylvestris (red) on the N. tabacum genome, highlighting the subgenomes and their respective contribution to the subgenome structure of this species. The right-hand Circos plot similarly locates the syntenic blocks of N. tomentosiformis (blue), N. sylvestris (red) and N. glauca (purple) on the N. benthamiana LAB genome, highlighting the difficulty in assigning ancestry for subgenomes in this species, which is characterized by extensive rearrangement of blocks between individual chromosomes. The lines in the centre join syntenic regions, highlighting the fragmentation of the N. benthamiana genome. b, Dot plot showing the relationship between the LAB and QLD chromosomes (central continuous line in the far-left panel) and the fragmented syntenic relationship between the subgenomes. Comparison of the N. tabacum genome consisting of two subgenomes with clear relationships to N. sylvestris and N. tomentosiformis revealed a fragmented relationship with N. benthamiana chromosomes. c, Dendrogram highlighting the chromosome pairs and the three orphan chromosomes (annotated 9, 10 and 19). d, Retention and relocation of homeologous genes in N. benthamiana LAB and QLD genomes. Percentage values outside and within parentheses are those for LAB and QLD, respectively, and show that about half of the original homeologous pairs have lost one member.