Plant Genome Research

Progress in plant genome research is vital to understanding natural evolution and feeding the world. The size and highly repetitive nature of plant genomes make building quality reference genomes a challenge for short-read sequencing technologies. Bionano Saphyr™ offers hybrid scaffolding and structural variation discovery capabilities that are essential for driving progress.

Short-read technologies typically fail to span long repeat regions or disambiguate different copies of interspersed repeats, resulting in limited contig length, introduction of chimeric joins and other assembly errors. Unlike next-generation sequencing (NGS), which algorithmically infers structural variations from fragmented DNA data, Bionano optical genome mapping directly observes long DNA molecules by linearizing and imaging DNA in its native state using massively parallel NanoChannels.

De novo Saphyr genome maps can be integrated with sequence assembly to order and orient sequence fragments, identify and correct potential chimeric joins in the sequence assembly, and estimate the gap size between adjacent sequences.

Bionano hybrid scaffolding considerably reduces the number of contigs found in the initial NGS assembly and improves contiguity up to 1000 times over NGS-based approaches alone.

The combination of Bionano maps with sequencing data improves assembly accuracy and quality while reducing the need for deep sequencing coverage. This improved contiguity significantly lowers costs associated with assembling reference genomes.

Saphyr also offers unparalleled sensitivity for large structural variations from 500 bp to megabase pair lengths.

  • 99% sensitivity for homozygous insertions/deletions larger than 500 base pairs
  • 95% sensitivity for heterozygous insertions/deletions larger than 500 base pairs
  • 95% sensitivity for balanced and unbalanced translocations larger than 50,000 base pairs
  • 99% sensitivity for inversions larger than 30,000 base pairs
  • 97% sensitivity for duplications larger than 30,000 base pairs

Saphyr detects all types of structural variants down to 5% Variant Allele Fraction. Saphyr provides this performance typically with a false positive rate of less than 2%. Saphyr also detects repeats, copy number variants, and complex rearrangements.

See below for publications, white papers and other resources regarding Bionano genome mapping in plant genome research.

Use Cases

  • Large-scale breeding– identify areas of biological interest for crossbreeding and massively screen previous crosses in existing plant species
  • Evolutionary biology – see the complete picture of how genomes have evolved and been reorganized
  • Gene discovery– call structural variations to identify variants of interest and elucidate their effect on genes within a plant species
  • Reference genome assembly– perform de novo assembly and scaffold assemblies generated by sequencing-based systems
Bionano genome maps help researchers assemble the most accurate plant reference genomes


Dr. Hastie reviews Bionano Saphyr's genome assembly capabilities at the VGP Genome10k tech talk


    Case Studies
  • This Case Study highlights Scientists at the USDA and Cold Spring Harbor Laboratory who know that better breeding of maize to feed a growing population will depend on an accurate reference assembly. They tackled the previously intractable crop with a combination of PacBio® Sequencing and BioNano Genomics®genome maps, leading to the first-ever high-quality reference assembly.

      White Papers
    • This white paper explains how Bionano whole genome imaging can make any sequence assembly up to 100 times more contiguous by scaffolding sequence contigs, and more exact by correcting errors. The new two-enzyme hybrid scaffold pipeline introduced here improves both aspects. It creates functional genomes at a low cost, no matter what your sequencing strategy is.


    This website stores cookies on your computer. These cookies are used to collect information about how you interact with our website and allow us to remember you. We use this information in order to improve and customize your browsing experience and for analytics and metrics about our visitors both on this website and other media. To find out more about the cookies we use, see our Privacy Policy.