Additional File 5 Phylogenetic tree of the three A genome-contained species evaluated with different sets of markers

Additional file 5 Phylogenetic tree of the three A genome-contained species evaluated with different sets of markers. A, Evaluated with all of high-quality markers with genome alignments (28,267) (left), with a set of markers (16,077) which was aligned to unique positions of A, B and C genomes (ABC-markers, middle), and markers (12,781) which were uniquely aligned to B (8,278) and C (4,503) genomes(right), respectively. All of the three figures shown that B. juncea was separated from other two species. B, Evaluated with markers aligned to A genome uniquely (3,296) (left), and 3,296 A genome specific markers plus 11,321 markers with alignment on A genome along with positions on other genome(s). B. juncea and B. rapa shown close relationship and separated from B. napus.