Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps
2019
Wild emmer (
Triticum turgidumssp. dicoccoides ) is the progenitor of all modern cultivated tetraploid wheat. Its genome is large (> 10 Gb) and contains over 80%
repeated sequences. The successful whole-genome-
shotgunassembly of the wild emmer (accession Zavitan) genome sequence (WEW_v1.0) was an important milestone for wheat genomics. In an effort to improve this assembly, an
optical mapof accession Zavitan was constructed using Bionano Direct Label and Stain (DLS) technology. The map spanned 10.4 Gb. This map and another map produced earlier by us with the Bionano9s Nick Label Repair and Stain (NLRS) technology were used to improve the current wild emmer assembly. The WEW_v1.0 assembly consisted of 151,912
scaffolds. Of them, 3,102 could be confidently aligned on the
optical maps. Forty-seven were chimeric. They were disjoined and new
scaffoldswere assembled with the aid of the
optical maps. The total number of
scaffoldswas reduced from 151,912 to 149,252 and N50 increased from 6.96 Mb to 72.63 Mb. Of the 149,252
scaffolds, 485
scaffolds, which accounted for 97% of the total genome length, were aligned and oriented on genetic maps, and new WEW_v2.0 pseudomolecules were constructed. The new pseudomolecules included 333
scaffolds(68.51 Mb) which were originally unassigned, 226
scaffolds(554.84 Mb) were placed into new locations, and 332
scaffolds(394.83 Mb) were re-oriented. The improved wild emmer genome assembly is an important resource for understanding genomic modification that occurred by domestication.
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