Fig. 2

Syntenic relationships and genomic rearrangements between the genomes of Bgh isolates DH14 and RACE1. a Circos diagram illustrating the syntenic relationships between the genomes of DH14 and RACE1. Based on the corresponding N50 values, the 8 and 11 largest scaffolds/contigs from the DH14 and RACE1 genomes and the corresponding aligning scaffolds/contigs were chosen for visualization. Syntenic regions were identified based on whole-genome alignment, and aligning regions (≥2 kb, similarity ≥75%) are connected with lines. The surrounding circles represent from the outside: on the right DH14 scaffolds (pink) and on the left RACE1 contigs (blue), with all unaligned regions (≥ 1 kb) indicated as white gaps; gene density (green) and TE density (blue) calculated in 10 kb sliding windows; locations of all genes predicted to code for SPs; locations of isolate-specific genes coding for SPs (dark red) or any other proteins (black) and isolate-specific additional gene copies/paralogs coding for SPs (pink) or any other proteins (grey). The arrowheads indicate observed alignment breaks of at least two large-scale genomic rearrangements (green and brown arrowheads, respectively). Scaffolds or contigs marked with “T” indicate presence of telomeric repeats. b Visualization of sequence identity to RACE1, gene and TE density along the two largest DH14 scaffolds. The top panel shows the sequence identity to the aligning RACE1 contigs obtained from the whole-genome alignment, with bars colored according to the involved RACE1 contig as indicated next to the graph. The two lower panels show the gene density (green) and TE density (blue) in DH14 calculated in 10 kb sliding windows along the DH14 scaffolds. c Detailed synteny between RACE1 tig00005299 and DH14 scaffold_35 visualized with SyMap [87]. Local inversions within the otherwise syntenic region are highlighted by green boxes, while grey lines connecting the RACE1 and DH14 contigs represent the syntenic alignments and black marks on the contigs indicate the positions of annotated genes