All plant species in nature have undergone ancient polyploidization. A major challenge in the establishment of nascent polyploids is intergenomic incompatibilities. Wheat is important cereal food through two polyploidies in nature. The first occurred 0.5-3.0 million years ago between two diploid ancestors carrying the A (T. urartu) and B (an unknown species) genomes resulting in tetraploid wheat (Triticum turgidum ssp. dicoccoides, AABB). The second took place about 9000 years ago between cultivated emmer and diploid goat grass (Aegilops tauschii, DD) to form allohexaploid common wheat. Recently our research group produced a nearly completed high-quality genome sequence of the progenitor of wheat A subgenome T. urartu. Combing with the other two high-quality reference sequences of tetraploid (emmer) and hexaploid wheat (Chinese Spring), we systematically compared three wheat A (sub) genomes at different ploidies to present the processes of gene and transposon change in A (sub)genome of T. urartu, emmer (emmer A) and Chinese Spring (TaA) from their progenitor at whole genome level and to further unravel genomic and genetic mechanisms of speciation via polyploidization in wheat. Our study supported that diploid progenitor of the A subgenome experienced frequent gene losses and duplications, resulting in a highly dynamic genome. This, on one hand, leads to a rapid loss of the syntenic trace produced by the whole genome duplication occurred ~70 million years ago in the common ancestor of grasses. On the other hand, it dramatically improved genome adaptability for extreme change, such as genomic shock incurred by polyploidization. As for transposable elements, accounting for more than 80% of the genomes, we found that allotetraploidization can dominantly activate some TE families, but triggered TE eliminations in other families. The data proved that relaxation of the negative selection of TE activity during polyploidization have high degree selectivity for TE families. Our comparative analysis at A (sub)genome among the three ploidy levels is conductive to understanding wheat’s enhanced adaptability to a wide range of climates and improved grain quality of baker’s flour contributed by A subgenome. 019188

All plant species in nature have undergone ancient polyploidization. A major challenge in the establishment of nascent polyploids is intergenomic incompatibilities. Wheat is important cereal food through two polyploidies in nature. The first occurred 0.5-3.0 million years ago between two diploid ancestors carrying the A (T. urartu) and B (an unknown species) genomes resulting in tetraploid wheat (Triticum turgidum ssp. dicoccoides, AABB). The second took place about 9000 years ago between cultivated emmer and diploid goat grass (Aegilops tauschii, DD) to form allohexaploid common wheat. Recently our research group produced a nearly completed high-quality genome sequence of the progenitor of wheat A subgenome T. urartu. Combing with the other two high-quality reference sequences of tetraploid (emmer) and hexaploid wheat (Chinese Spring), we systematically compared three wheat A (sub)genomes at different ploidies to present the processes of gene and transposon change in A (sub)genome of T. urartu, emmer (emmer A) and Chinese Spring (TaA) from their progenitor at whole genome level and to further unravel genomic and genetic mechanisms of speciation via polyploidization in wheat. Our study supported that diploid progenitor of the A subgenome experienced frequent gene losses and duplications, resulting in a highly dynamic genome. This, on one hand, leads to a rapid loss of the syntenic trace produced by the whole genome duplication occurred ~70 million years ago in the common ancestor of grasses. On the other hand, it dramatically improved genome adaptability for extreme change, such as genomic shock incurred by polyploidization. As for transposable elements, accounting for more than 80% of the genomes, we found that allotetraploidization can dominantly activate some TE families, but triggered TE eliminations in other families. The data proved that relaxation of the negative selection of TE activity during polyploidization have high degree selectivity for TE families. Our comparative analysis at A (sub)genome among the three ploidy levels is conductive to understanding wheat’s enhanced adaptability to a wide range of climates and improved grain quality of baker’s flour contributed by A subgenome. 020346