3.2 | Whole-genome duplication, phylogenetic evolution, and genome synteny
To clarify whole-genome duplication in Pse. libanotica , synonymous substitutions (Ks) were calculated in Pse. libanotica ,D. glomerat , and B. distachyon . The peak Ks at 0.20 which occurred after the divergence peak at 0.05 between Pse. libanotica and D. glomerat and 0.05 between Pse. libanotica and B. distachyon (Figure 2B), indicating a whole-genome duplication event occurred in the common ancestor of Poaceae. To explore the phylogeny and divergence of the St genome, a unique set of gene families was identified in 14 Poaceae plants based on available genomic resources (Figure 2A). Sorghum bicolor andZea mays were C4 plants and diverged firstly in the phylogenetic tree, followed by Oryza sativa , Brachypodium distachyon,and Dactylis glomerat . Triticeae species were clustered into one monophyletic group (A. tauschii , H. vulgare , S. cereale , T. aestivum , T. durum , T. dicoccoides ,T. urartu ). The Pse. libanotica diverged ~10.7 million years ago (Mya) after H. vulgare(~11.9 Mya), the S. cereale and the genusTriticum separated ~9.6 Mya.
Orthologous gene in Pse. libanotica , T. aestivum , T. urartu , H. vulgare , and D. glomerat were analyzed to illustrate chromosome collinearity and derivation (Figure S4).Pse. libanotica exhibited conserved chromosome homoeologous collinearity with A genome, B-subgenome, D-subgenome and H genome, and varied with D. glomerat. Interestingly, the 4St in Pse. libanotica and the 4A chromosome of T. urartu displayed highly consistency, nevertheless, a pericentric inversion was observed in the 4A chromosome, and a 4AL (long arm)-5AL-7BS (short arm) translocation in the common wheat. However, the St genome and the D. glomeratdisplayed chaotic chromosome collinearity. The 2St and 3St chromosomes mainly matched to the 1 and 5 chromosomes of D. glomerat , the 5St had syntenic to the 3 and 4 chromosomes of D. glomerat , and the 7 St was syntenic to the 3 and 7 chromosome groups of D. glomerat(Figure S4). Thus, gene order and location varied among Poaceae species after divergence, conserved among diploid Triticeae species, and partly rearranged during polyploidization of Triticeae.