10-year project generated comprehensive and highly-complex barley genome, two times larger than the human genome
SAN DIEGO, CA – April 26, 2017 – Bionano Genomics®, Inc., a company focused on genome structure analysis, today highlighted results from a study demonstrating how combining sequencing technologies with Bionano optical mapping generated the most complete and accurate barley genome assembly. The results of the study, “A chromosome conformation capture ordered sequence of the barley genome,” will be published tomorrow in the April 27 issue of prestigious peer-reviewed journal, Nature.
The paper describes the hierarchal use of several genome technologies, including initial sequencing of bacterial artificial chromosomes (BACs) by Illumina followed by optical mapping by Bionano to construct super-scaffolds composed of merged assemblies of individual BACs, which increased the contiguity as measured by the N50 value from 79 kb to 1.9 Mb. Scaffolds were then assigned to chromosomes using a POPSEQ genetic map, followed by chromosome-conformation capture sequencing performed by researchers in Germany to generate three-dimensional proximity information.
The new reference assembly showed high frequency of repetitive elements such as duplicated genes, including five full-length amy1 genes, four of which share more than 99.8 percent identity at the nucleotide level, including introns. The amy1 genes are significant because they code for amylase proteins important to the malting process but before now had not been able to be quantified or fully understood regarding their structural variability. Furthermore, the reference assembly can now for the first time be used to assess genetic diversity in modern elite barley varieties with the goal of introducing beneficial alleles from exotic genepools to counteract genetic erosion. The long-term goal of the new reference barley genome assembly is to breed a barley crop that can maintain high yields in a changing environment to safeguard global food security.
Additional details are available in a press release issued by the study’s lead researchers at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany.
Erik Holmlin, PhD, CEO of Bionano, commented, “Full assembly of the barley genome marks a significant milestone for plant breeders and researchers as it reveals detailed information on the location, structure and function of its genes and provides useful knowledge for breeding programs to boost crop improvement. Before now, no one has ever assembled a genome this large – the barley genome is almost two times larger than the human genome – and complex with such high accuracy. Bionano optical mapping provided hybrid scaffolding to accurately orient the hundreds of thousands of contigs to assemble the entire genome with assured proper placement. This paper serves as another example of how NGM is an essential complementary genomic tool for researchers to combine with next-generation sequencing technologies to reveal the true structure of chromosomes, especially genomes with high frequency of repetitive elements.”
Nils Stein, researcher at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany, commented, “The Bionano optical mapping information that was used for this project provided a crucial element in studying the barley genome. Through its unique capability to visualize the complex structures of the genome, we were able to enhance, and validate key findings that the other sequencing techniques provided. Optical mapping using Bionano has certainly demonstrated its power and value in the field of better understanding complex and large plant genomes, key elements that we experienced here.”
About Bionano Genomics®
Bionano Genomics, Inc. provides the Irys and Saphyr systems for next-generation mapping (NGM), which is the leading solution in physical genome mapping. NGM offers customers whole genome analysis tools that reveal true genome structure and enabling researchers to capture what’s missing in their data to advance human, plant and animal genomic research. NGM uses NanoChannel arrays to image DNA at the single-molecule level with average single-molecule lengths of about 350,000 base pairs, which leads the genomics industry. The long-range genomic information obtained with NGM detects and deciphers structural variations (SVs), which are large, complex DNA segments involving repeats that are often missed by sequencing technologies and which are a leading cause of inaccurate and incomplete genome assembly.
As a stand-alone tool, NGM enables the accurate detection of SVs, many of which have been shown to be associated with human disease as well as complex traits in plants and animals. As a complementary tool to next-generation sequencing (NGS), NGM integrates with sequence assemblies to create contiguous hybrid scaffolds for reference-quality genome assemblies that reveal the highly informative native structure of the chromosome. NGM also provides the additional ability to verify, correct and improve a NGS-generated genome assembly.
Only Bionano provides long-range genomic information with the cost-efficiency and high throughput to keep up with advances in NGS.
NGM has been adopted by a growing number of leading institutions around the world, including: National Cancer Institute (NCI), National Institutes of Health (NIH), Wellcome Trust Sanger Institute, BGI, Garvan Institute, Salk Institute, Mount Sinai and Washington University. Investors in the Company include Domain Associates, Legend Capital, Novartis Venture Fund and Monashee Investment Management. For more information, please visit www.BionanoGenomics.com.
