A Genome-Wide Comparison of Structural Variation in Triticum urartu Genome

Triticum urartu is the wild progenitor of the A subgenome of bread wheat (Triticum aestivum). We generated a high-quality genome sequence of T. urartu by BAC-by-BAC sequencing, and predicted about forty thousand protein-coding genes and more than 80% of repetitive DNA. The evolutionary relationships between wheat and several other genome-sequenced grasses, including Brachypodium, sorghum and rice, had been reported. Brachypodim diverged with wheat about 32-39 MYA and sorghum about 45-60 MYA. Between them, rice split to wheat about 40-54 MYA. Comparisons between T. urartu genome and other whole-genome sequenced grasses presented syntenic orthologues of all T. urartu chromosome segments in Brachypodium, rice and sorghum. These provide precise sequence framework for understanding the structural variations in T. urartu. Except for two chromosomes, which evolved from a single ancestor chromosome, most T. urartu chromosomes are chimera of multiple chromosomes of ancestor genome. The most commonly observed is an insertion of one chromosomal segment into centromeric region of another. This happened on chromosome 1, 2, 4 and 7 of T. urartu. One exception, chromosome 5, was shaped by fusions of three ancestor chromosomes. Our study allowed the localization of accurate fusion positions on wheat chromosomes. The comparisons also presented multiple chromosome segments in other three grass genomes whose syntenic orthologues were not detected in T. urartu. The studies are helpful to understand the causes of the fragment losses identified in wheat genome. In summary, our study revealed the comprehensive understanding of precise chromosomal structure variations of T. urartu.