A 4-Gigabase Comparative Physical Map Of Aegilops tauschii, The Wheat D-Genome Progenitor, Opens The Window Into The Evolution Of Gene Content and Meaning Of Genome Size In Grasses

We constructed a 4-Gb physical map of the Ae. tauschii genome anchored on a 7,185-marker genetic map with the aid of a 10K Ae. tauschii Infinium iSelect single nucleotide polymorphism (SNP) oligonucleotide array. To enhance the comparative value of the map, we extended the mapped SNP markers with Roche 454 and Illumina whole genome shotgun reads and discovered 17,093 genes and pseudogenes in the extended sequences. We used the physical map to assess synteny and genome evolution rates in grasses and showed that the rates were fast in the entire subfamily Pooideae including B. distachyon and used this evidence to suggested that the small B. distachyon genome probably evolved from a larger progenitor genome. Sequencing of bacterial artificial chromosome (BAC) clone contigs and modeling of gene space evolution in the grass family indicated that the increase in size of the Ae. tauschii genome was accompanied by gaining about 8,000 (21%) duplicated genes, which increased its genome size from 28,000 genes prior to the Brachypodiae-Triticeae divergence to 36,000 genes. The contraction of the B. distachyon genome was accompanied by the loss of about 3,000 genes, reducing the gene number from 28,000 to 25,000. Using the physical map, we found 24.5% of the Ae. tauschii genes to be recently duplicated, confirming the gene number increase in the Ae. tauschii genome. We showed that the duplicated genes are nonrandomly distributed along the Ae. tauschii chromosomes. They are preferentially located in distal, high recombination regions in Ae. tauschii chromosomes and their densities along chromosomes correlate with recombination rates.