Testing of Long Wheat Sequence Contigs Quality by using Physical and Genetic Maps

Wheat physical maps developed within IWGSC are an important resource for characterization of genome structural organization. This resource can also be used to evaluate the quality of wheat pseudomolecules assembled using novel analytical technology developed by NRGene together with IWGSC. We present the results obtained by in silico mapping of individual fingerprinted MTP BACs to pseudomolecule sequences and comparing the resulted positions with physical maps. In case of reliable long BAC scaffolds (up to 20 Mbp), obtained by using LTC analytical system and whenever possible confirmed by genome zipper, RH- , deletion bin and/or linkage maps), this comparison can prove local ordering of sequence contigs within sequence scaffolds of corresponding length. With taking into account pseudomolecule sequences of evolutionary related species, estimated parallel BAC clone overlaps, this cross-talk approach can assist in further improving of genetic and physical maps as well as assembled pseudomolecules. We found that up to 90% of MTP BAC-clones can be effectively mapped on pseudomolecule sequences and in the vast majority of cases our physical contigs are collinear with the corresponding pseudomolecules. We found only several inconsistency cases; most of them seem to be caused by errors in physical maps. Yet, we also found a few inconsistency cases where we believe that the problem is in the sequence assembly rather than in the physical contigs (due to presence of parallel BAC clone overlaps). The high quality of the NRGene sequence assembly is also confirmed by the remarkable similarity of the pseudomolecules of the A and B chromosomes of the hexaploid and tetraploid wheat.