Skip to main content
Dryad

Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly

Zhu, Tingting, University of California, Davis, University of California, Davis, https://orcid.org/0000-0003-3141-1884
Wang, Le, University of California, Davis, University of California, Davis
Rimbert, Hélène, University of Clermont Auvergne, University of Clermont Auvergne
Rodriguez, Juan, University of California, Davis
Deal, Karin, University of California, Davis
De Oliveira, Romain, University of Clermont Auvergne, University of Clermont Auvergne
Choulet, Frédéric, University of Clermont Auvergne, University of Clermont Auvergne, https://orcid.org/0000-0003-1788-7288
Keeble-Gagnère, Gabriel, AgriBio
Tibbits, Josquin, AgriBio, Agriculture Victoria Services (Australia)
Rogers, Jane, International Wheat Genome Sequencing Consortium, University of Wisconsin–Eau Claire
Eversole, Kellye, International Wheat Genome Sequencing Consortium, University of Wisconsin–Eau Claire, https://orcid.org/0000-0002-8784-4913
Appels, Rudi, AgriBio, Agriculture Victoria Services (Australia)
Gu, Yong, Agricultural Research Service
Mascher, Martin, Institute of Plant Genetics and Crop Plant Research, Institute of Plant Genetics and Crop Plant Research, https://orcid.org/0000-0001-6373-6013
Dvorak, Jan, University of California, Davis, University of California, Davis
Luo, Ming-Cheng, University of California, Davis
Rodriguez, Juan C., University of California, Davis
Deal, Karin R., University of California, Davis
Keeble‐Gagnère, Gabriel, Agriculture Victoria Services (Australia)
Gu, Yong Q., Institute of Plant Genetics and Crop Plant Research, https://orcid.org/0000-0002-2575-4744
Luo, Ming‐Cheng, University of California, Davis, https://orcid.org/0000-0002-9744-5887
yooheez@gmail.com
Published May 06, 2021 on Dryad. https://doi.org/10.25338/B8K917

Cite this dataset

Zhu, Tingting et al. (2021). Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly [Dataset]. Dryad. https://doi.org/10.25338/B8K917

Abstract

This dataset contains a single whole-genome optical map file (.CMAP) for bread wheat (Triticum aestivum) cv Chinese Spring (CS). The methods for constructing this optical map and the properties of this map are described below. The definition of the CMAP format is documented in https://bionanogenomics.com/wp-content/uploads/2017/03/30039-CMAP-File-Format-Specification-Sheet.pdf. 

The extracted ultra-high-molecular weight DNA molecules of CS were labeled with the DLE-1 enzyme (Bionano Genomics, San Diego, CA, USA) and were then stained with the Bionano PrepTM DLS Kit (Bionano Genomics, San Diego, CA, USA). A consensus optical map was de novo assembled with the Assembler tool of the Bionano Solve v3.3 package using significance cutoffs of P < 1 × 10-11 to generate draft consensus contigs, P < 1 × 10-12 for draft consensus contig extension, and P < 1 × 10-16 for final merging of the draft consensus contigs. A recipe of “nonhaplotype”, “noES”, and “noCut” was chosen. The initial optical map was then checked for potential chimeric contigs.

Images of DLE-1-labeled CS DNA molecules > 150 kb and equivalent to about 136x genome coverage were collected and assembled into a whole-genome optical map. The map contained 726 contigs with an N50 of 55.01 Mb and a total length of 14.41 Gb.