Optical Nano-mapping and Analysis of Plant Genomes

Ming-Cheng Luo; Karin R Deal; Armond Murray; Tingting Zhu; Alex R Hastie; Will Stedman; Henry Sadowski; Michael Saghbini

doi:10.1007/978-1-4939-3622-9_9

Optical Nano-mapping and Analysis of Plant Genomes

Methods Mol Biol. 2016:1429:103-17. doi: 10.1007/978-1-4939-3622-9_9.

Authors

Ming-Cheng Luo¹, Karin R Deal², Armond Murray², Tingting Zhu², Alex R Hastie³, Will Stedman³, Henry Sadowski³, Michael Saghbini³

Affiliations

¹ Department of Plant Sciences, University of California, One Shields Ave., Davis, CA, 95616, USA. mcluo@ucdavis.edu.
² Department of Plant Sciences, University of California, One Shields Ave., Davis, CA, 95616, USA.
³ BioNano Genomics, 9640 Towne Centre Drive, Ste. 100, San Diego, CA, 92121, USA.

PMID: 27511170
DOI: 10.1007/978-1-4939-3622-9_9

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.

Keywords: BioNano genome map; Optical mapping; Physical map.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosome Mapping / methods*
Genome, Plant*
Genomics / methods*
High-Throughput Nucleotide Sequencing / methods*
Nanotechnology / methods*
Optics and Photonics
Sequence Analysis, DNA / methods*
Triticum / genetics*