Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs
(A) A cartoon of a blastn output between orthologous genes in rice, sorghum, and two maize homeologs. The colored rectangles (blue, orange, purple) represent high-scoring sequence pairs (HSPs), or regions with high sequence similarity to each other. Sorghum is the reference sequence (Sb09). The top two panels show the syntenous exon sequence (highlighted in blue) between rice (rice chromosome 5, or Os05) and sorghum (sorghum chromosome 9, or Sb09); the second and fourth panels demonstrate the location of the deletion in maize homeolog Zm chromosome 8 (Zm08) to its sorghum ortholog (purple). As can be seen, the deletion is evident when the Zm08 sequence (circled) is compared to the orthologous sequence of Zm06 (orange) and rice (blue) when all HSPs are aligned on sorghum. The GEvo alignment output for these data may be found at http://genomevolution.org/r/3em. (B) A ClustalW alignment of the rice, sorghum, and maize homeologs from Figure 5A. The purple sequence in the unfractionated maize homeolog (Zm06) indicates the location of the direct repeat sequence that originally flanked the deletion in the fractionated homeolog (Zm08). (C) A diagram representing the mechanism of intra-chromosomal recombination, based on the flanking sequence highlighted in (B). Direct repeats come together to form a circle, which is then recombined away, leaving a solo repeat in its place.