Fig. 3: Evolutionary and chromosome synteny analyses of the rye genome.

a, Phylogeny and divergence time estimate of rye, as investigated with a gene tree constructed using 2,517 single-copy orthologous genes conserved between Weining rye and 11 other grass genomes. Os, rice; Sb, S. bicolor; Si, S. italica; Zm, Z. mays. b, Probable evolutionary scenario of rye chromosomes according to the AGK model proposed by Murat et al.³¹. The rye chromosomes (1R–7R) are presented with a color code to show different segments from the ancestral grass chromosomes (AGK1–AGK12), which are referenced by the 12 chromosomes of rice (Os1–Os12). Chromosome 3R was derived from AGK1 or Os1, and a segment of this chromosome was translocated to 6RL. Chromosome 1R evolved from a nested insertion of AGK10 or Os10 into AGK5 or Os5, and 2R evolved by a nested insertion of AGK7 or Os7 into AGK4 or Os4. Chromosome 4R evolved by fusions of AGK11 or Os11 with the segments from AGK2 or Os2, AGK3 or Os3, AGK6 or Os6 and AGK8 or Os8, and 5R evolved by a fusion between AGK9 or Os9 and AGK12 or Os12 and acquisition of a segment from AGK3 or Os3. Chromosome 6R was mainly derived from AGK2 or Os2 and further fusions with the segments from AGK1 or Os1 and AGK6 or Os6. Lastly, 7R evolved mainly from AGK8 or Os8, with additional fusions of the segments from AGK3 or Os3, AGK4 or Os4 and AGK6 or Os6. c, Chromosome synteny between rye and the three subgenomes of common wheat (TaA, TaB and TaD). Syntenic chromosomes (or chromosomal segments) are labeled with the same color.