A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

Abstract

The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.

Keywords: BAC contig coassembly; Oryza; gene density; single nucleotide polymorphism; synteny.

Fig. 1.

Ae. tauschii genome circle maps. The inner circle (#1) contains the physical maps of the Ae. tauschii chromosomes each with its short arm tip at 0 Mb. Circle #2 contains heat maps of recombination rates, circle #3 contains gene density heat maps, circle #4 contains heat maps of only genes collinear with the B. distachyon, rice, or sorghum pseudomolecules, and circle #5 shows global synteny with the rice chromosomes symbolizing 12 ancestral chromosomes. In circle #5, the active Ae. tauschii centromeres are white, inferred extinct centromeres are black, and the locations of current and inferred ancient telomeres are diagrammed by thick bars. Thirty-megabase windows sliding by 1 Mb were used in the heat map construction. The heat map units for circle #2 are cM/Mb and for circles #3 and #4 are numbers of genes and gene fragments discovered in the extended sequences per megabase of the physical maps.

Fig. 2.

Rates of structural genome evolution in the grass family. (A) Rates (k; numbers of inversions, translocations and NCIs per million years) during the evolution of grass subfamilies Panicoideae, Ehrhartoideae, and Pooideae. (B and C) Pairwise dot-plot comparisons of gene order along Ae. tauschii physical maps (B) and along sorghum pseudomolecules (C) relative to that along the rice pseudomolecules. Chromosomes and pseudomolecules on the y axis have the tips of the short arms at 0 Mb, respectively, at the top. Blue dots indicate parallel order and red dots indicate antiparallel order of chromosomes and pseudomolecules on the x and y axes. Only orthologous loci are shown for the sake of clarity.

Fig. 3.

Relationship between recombination rate and density of noncollinear genes in the Aegilops tauschii genome.