Common Wheat Chromosome 5B Composition Analysis Using Low‐Coverage 454 Sequencing

The sequencing of individual chromosomes of common wheat is in progress. The molecular size of wheat chromosome 5B is nearly 870 Mb (5BL = 580 Mb and 5BS = 290 Mb). We produced the first low coverage 454-sequencing of the long and short arms of wheat chromosome 5B (110,793 and 39,695 reads, which compose 8 and 6% of total 5BL and 5BS length, respectively) and calculated the ratios of the different families of repetitive sequences, including transposable elements (TEs), satellite repeats (Afa, pSc119.2 , 5S rDNA and 45S rDNA), and microsatellites, as well as direct and inverted repeat motifs. The TEs accounted for 70% of the total analyzed nucleotide sequences. The content of the Cereba retrotransposon family differed between the two arms of chromosome 5B. Comparing the reads of chromosome 5B with the data from chromosome 5A, we found the retrotransposons Fatima and Sakura and DNA transposon Jorge were prevalent in 5B. The hypothetical coding sequences accounted for 2.0% of the short arm and 2.07% of the long arm. Using in silico mapping, we identified the regions of synteny with rice and Brachypodium chromosomes (1,073,526 and 1,767,298 bp aligned, respectively), and the result was consistent with the data from the expressed sequence tag (EST) mapping of wheat 5B chromosome to the genomes of these grasses. Thus, these results show that low coverage survey sequencing can provide useful information about the composition and evolution of wheat chromosome 5B. T he common wheat (Triticum aestivum L., 2n = 6x = 42) is an allohexaploid composed of three differ ent genomes (AABBDD) that originated from T. urartu Thum. (AA), an Aegilops species related to the Sitopsis section (presumably Ae. speltoides Tausch) (BB), and Ae. tauschii Coss. (DD). Triticum aestivum is a relatively young polyploid derived from two successive interspecific crosses dated approximately 0.5 million years ago and 8,000 to 10,000 yr ago. Bread wheat has a large genome of 17,000 Mb, which mainly consists of repetitive DNA sequences of different origin, and 90% of the genome is reiterative, 80% of which is composed of TEs (Paux et al., 2006; Choulet et al., 2010; Brenchley et al., 2012). For these reasons, sequencing the wheat genome is a challenge, for which the international scientific community has established the International Wheat Genome Sequencing Consortium. To solve the problem of polyploidy in the wheat genome, the