a, Syntenic analysis of Tu genome with the D subgenome of Ta, and the genome of Aet. Each syntenic block contains five or more genes, with sequence similarity of 80% or more. b, Comparison of Tu genome with BACs of T. turgidum (Tt) and Ta. BAC KF282630 from chromosome 4 of the A subgenome of Tt contained two inserted fragments (blue arrows) that are composed of Copia RLC_WIS_B elements, which were not detected on the corresponding Tu4 region. BAC JQ354543 from chromosome 3 of the A subgenome of Ta lacked the Gypsy RLG_Jeli element (blue arrow), which was found on the corresponding region of Tu3. c, Comparison of the Tu genome with Ta7A scaffolds from TGACv119. The dot plots on the top show comparison of two largest TaA scaffolds to corresponding parts of Tu7 chromosome. The diagonal lines on the dot plots show fine co-linearity. The lower part shows validation of the sequence assembly of Tu7 by BioNano maps. The Tu7 sequences were digested into in silico consensus maps, and the consensus maps corresponding to the two Ta7A scaffolds (green bar) are compared against their corresponding BioNano genome maps (blue bar). Each vertical line on the green/blue bars indicates a restriction enzyme cutting site (Nt.BspQI), and vertical lines between green bars and blue bars indicate alignments among these sites. The blue bars highlighted with red vertical line demonstrate that two BioNano genome maps (for example, 3912 and 6183) overlap with one another (they all have alignments on the overlapping region), although the two maps are not merged together owing to lack of coverage on the overlapping region. The high consistency of alignments between consensus maps and BioNano genome maps confirm the high quality of Tu genome assembly. Therefore, the insertion/deletion events in the dot plots should be sequence variations between the two A genomes from Ta and Tu, rather than assembly errors. d, Comparison of Tu7 with all Ta7A scaffolds from TGACv1 at nucleotide levels. *Nucleotide: minimum cutoff of DNA sequence alignments between Tu7 and Ta7A. †ML, minimum length (bp) to align.