Protocol

Plant Cytogenetics

Volume 1429 of the series Methods in Molecular Biology pp 103-117

Date:

Optical Nano-mapping and Analysis of Plant Genomes

  • Ming-Cheng LuoAffiliated withDepartment of Plant Sciences, University of California Email author 
  • , Karin R. DealAffiliated withDepartment of Plant Sciences, University of California
  • , Armond MurrayAffiliated withDepartment of Plant Sciences, University of California
  • , Tingting ZhuAffiliated withDepartment of Plant Sciences, University of California
  • , Alex R. HastieAffiliated withBioNano Genomics
  • , Will StedmanAffiliated withBioNano Genomics
  • , Henry SadowskiAffiliated withBioNano Genomics
  • , Michael SaghbiniAffiliated withBioNano Genomics

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Abstract

Application of optical mapping based on BioNano Genomics Irys® technology (http://​www.​bionanogenomics.​com/​) is growing rapidly since its debut in November 2012. The technology can be used to facilitate genome sequence assembly and analysis of genome structural variations. We describe here the detailed protocol that we used to generate a whole genome BioNano map for Aegilops tauschii, the D genome progenitor of hexaploid wheat (Triticum aestivum). We are using the whole genome BioNano map to validate sequence assembly based on the next-generation sequencing, order sequence scaffolds, and ultimately build pseudomolecules for the genome.

Key words

BioNano genome map Optical mapping Physical map