Sequence composition, organization, and evolution of the core Triticeae genome

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Abstract
Summary: We investigated the composition and the basis of genome expansion in the core Triticeae genome using Aegilops tauschii, the D‐genome donor of bread wheat. We sequenced an unfiltered genomic shotgun (trs) and a methylation–filtration (tmf) library of A. tauschii, and analyzed wheat expressed sequence tags (ESTs) to estimate the expression of genes and transposable elements (TEs). The sampled D‐genome sequences consisted of 91.6% repetitive elements, 2.5% known genes, and 5.9% low‐copy sequences of unknown function. TEs constituted 68.2% of the D‐genome compared with 50% in maize and 14% in rice. The DNA transposons constituted 13% of the D‐genome compared with 2% in maize. TEs were methylated unevenly within and among elements and families, and most were transcribed which contributed to genome expansion in the core Triticeae genome. The copy number of a majority of repeat families increased gradually following polyploidization. Certain TE families occupied discrete chromosome territories. Nested insertions and illegitimate recombination occurred extensively between the TE families, and a majority of the TEs contained internal deletions. The GC content varied significantly among the three sequence sets examined ranging from 42% in tmf to 46% in trs and 52% in the EST. Based on enrichment of genic sequences, methylation–filtration offers one option, although not as efficient as in maize, for isolating gene‐rich regions from the large genome of wheat.