Gene collinearity along the pseudomolecules of tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, subgenomes AABB) and diploid Aegilops tauschii (genomes DD) was employed to confirm these rearrangements and to analyze the breakpoints. The exchange of distal regions of chromosome arms 4AS and 4AL due to pericentric inversion Inv(4AS;4AL)1 was detected, and breakpoints were validated with an optical Bionano genome map. Both breakpoints contained satellite DNA. The breakpoints of reciprocal translocation T(4AL;7BS)1 were also found. However, the breakpoints that generated paracentric inversion Inv(4AL;4AL)1 appeared to be collocated with the 4AL breakpoints that had produced Inv(4AS;4AL)1 and T(4AL;7BS)1. Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 either originated sequentially, and Inv(4AL;4AL)1 was produced by recurrent chromosome breaks at the same breakpoints that generated Inv(4AS;4AL)1 and T(4AL;7BS)1, or Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 originated simultaneously. We prefer the latter hypothesis since it makes fewer assumptions about the sequence of events that produced these chromosome rearrangements.
Dot-plots. a Dot-plots comparing the 14 wild emmer wheat pseudomolecules with the seven pseudomolecules of Ae. tauschii. Each dot consists of a sequence of three or more collinear genes. The plots are oriented with the tips of the short arms to the left (x-axis) and bottom (y-axis). Large gaps in the profiles are centromeric regions. The correspondence of alignments with the synteny blocks in Fig. 2a is indicated. b–d Details of synteny between wild emmer wheat pseudomolecule 4A and Ae. tauschii pseudomolecules 4D, 5D, and 7D, respectively. The correspondence of alignments with the synteny blocks in Fig. 2a is indicated in each figure. The antiparallel alignment (b) indicates a pericentric inversion starting with an interstitial breakpoint in present-day 4AL and ending with a breakpoint at the tip of the present-day 4AS delimiting block 1 (inset). The distal portion of 4AL consists of an inverted terminal portion of 5AL (including an additional distally located inversion) (blocks 4 and 5) (c), followed by a portion of 4AL (block 6) (b), and ending with an inverted terminal portion of 7BS (block 7) (d).