ABSTRACT
The bread wheat genome poses specific technical challenges for whole-genome sequencing because of the very high content of LTR TEs and the high levels of similarity between the homologous gene sets on the three genomes. Different approaches have been attempted to circumvent these difficulties. These include whole-genome sequencing of the diploid genomes of wild relatives or focusing only on the assembly of genic regions from the hexaploid wheat genome. WGS sequences have been produced using Illumina mate pairs and paired-end reads for the A and D genomes of the diploid-related wild species T. urartu and Ae. tauschii (Jia et al. 2013; Ling et al. 2013). Contiguous sequences with scaffold N50 values ranging from 57.8 kb to 63.7 kb were assembled and gene spaces containing 34 879 genes for the A genome of T. urartu and 43 150 genes for the D genome of Ae. tauschii were characterized. The data have provided useful information about these two species and for bread wheat in the context of the use of the diploid genomes in breeding programmes (Parry and Hawkesford 2012). There are, however, two main drawbacks to using the diploid-related wild species as surrogates for the hexaploid. First, the A, B and D sub-genomes of T. aestivum have evolved independently from their ancestral, diploid genome donors and have experienced domestication and selection episodes in a polyploid context since the first hybridization event 0.5-0.8 MYA. Second, there is no existing diploid species carrying a B genome. The closest relative is believed to be the wild species Ae. speltoides that contains a different S genome. Comparisons between the diploid genomes that were carried out as part of the chromosome-based survey sequencing project confirmed that there were significantly more differences between genic sequences of Ae. speltoides and the B genome of wheat than between the A and D genome comparators and thus, the results from diploids should be used with caution to interpret the bread wheat genome (The International Wheat Genome Sequencing Consortium 2014).
