Short description
(English)
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We want to assess and compare the overall genome sequence composition of five Triticeae species with respect to transposable element (TE) and gene content and test the usefulness of the obtained sequences for molecular marker production. The genomes of five Triticeae species, including barley, rye and diploid wheat, will be sampled by 454 whole genome shotgun sequencing. Using the latest Titanium technology, each 454 run should provide 5-10% of a genome equivalent. These sequence data will allow to identify and quantify differences in the TE composition of the five genomes. Because all Triticeae have very similar genome sizes, the results will shed light on the differential evolution of the repetitive fraction and the dynamic processes of TE amplification and deletion which keep genome size in an equilibrium. Additionally, we expect to sample about 10,000 genes from each of the species. From these sequences, we can estimate the total gene content as well as the size of specific gene families in the five genomes. By comparison with the rice genome, we also expect to identify numerous conserved non-coding sequences, allowing a first quantitative assessment of these sequences of unknown function.
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Partners and International Organizations
(English)
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AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GR, HR, HU, IL, IS, IT, LT, LV, NL, NO, PL, PT, RS, SE, SK, TR, UK
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Abstract
(English)
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We performed 454 sample sequencing on the donors of the A, B and D subgenomes of hexaploid wheat as well as rye. The resulting sequences represented an approximately 2.5-4% coverage of the genomes. We have determined the contribution of different transposable element (TE) families to the genomes and found strong differences in TE compositions between the four species. We have also assembled high-quality sequences for chloroplasts and ribosomal DNAs (rDNAs) for all the species, none of these organelles had been sequenced so far. Through a collaboration with the International Barley Sequencing Consortium, we have also received sequences from wild and cultivated barley, which were included in the analysis. Additionally, we are currently constructing consensus sequences for the most abundant TE families in the five species (including barley). We used the chloroplast genomes to construct robust phylogenies for the Triticeae to determine their precise relationships and for molecular clock analyses to obtain precise divergence time estimates of Triticeae species. We estimate that barely diverged from the other Triticeae approximately 10 million years ago (MYA) while rye diverged from the different wheat species about 4 MYA. The different wheat subgenomes diverged, according to our estimates, during the past 2.5-1.7 million years. Additionally, we could identify Aegilops speltoides (B genome) as the organelle donor of modern hexaploid wheat.
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