Comparative Analysis of Triticum urartu Genome with other Grass Genomes

Triticum urartu is the wild progenitor of the A subgenome of bread wheat (T. aestivum, Ta), which is an allopolyploid (2n = 6x = 42) containing three homoeologous subgenomes (A, B and D). Ample genetic studies have shown the value of T. urartu for investigating the structure, function and evolution of polyploid wheat genomes. Recently，we have generated a high-quality genome sequence of T. urartu by combining BAC-by-BAC sequencing and PacBio-based whole genome shotgun sequencing. More than forty thousand protein-coding genes have been predicted, and more than 80% of repetitive DNA were annotated. Comparative analysis of Tu genes with those from other grass genomes revealed about six thousand Tu specific genes. GO analysis revealed that these genes were involved mainly in the response to chemicals and endogenous stimuli. Further, we identified intact Gypsy and Copia retrotransposons and estimated their possible insertion times. The peak burst time for Gypsy and Copia retrotrasposons were more and less than 1 MYA, respectively, indicating that the two events occurred at different times. To study the evolution of chromosomal construction of Tu, we compared T. urartu genome to the major grasses (Brachypodium, rice, sorghum and wheat) and reconstructed the chromosomal evolution of T. urartu. Generally, our results provide a good basis for studying of Triticeae genomes and for the genetic improvement of wheat.