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  • Then there were 9: Bionano Data Featured in 9 Recent Nature Articles

Now updated with more wheat!

Bionano’s optical genome mapping technology is an essential part of genomic research and now, the proof is in the papers. Bionano’s ability to image extremely high-molecular-weight DNA has been featured in nine Nature, Nature Communications and Nature Genetics publications, including papers on global food crops such as rice, barley, quinoa, maize, spinach, apple and asparagus, as well as the domestic goat. The collection of research presented in these nine papers clearly shows the ability of Bionano technology to not only improve reference genome assembly, but to identify large biologically significant structural variations missed by sequencing-based methods alone.

The order and orientation data added by Bionano helped these papers make it into high impact journals. If you too would like to publish your research in Nature journals, you now know who to call!

 

Better Rice with Genome Maps

The indica rice species is a staple of diets around the world. Recently, researchers set out to build a reference for this critical genome, this time integrating Bionano genome mapping with other short-read-based sequencing data. By utilizing Bionano, researchers corrected short-read-based assembly errors, identified structural variations missed by other methods and greatly improved contiguity.

The result? The most complete indica rice Shuhui498 (R498) assembly to date with greater than 99% coverage of the genome.

Read the full paper published in Nature Communications: Sequencing and de novo assembly of a near complete indica rice genome

 

Barley Benefits from Bionano 

Barley is a staple in nearly every culture. Historically, repetitive elements in the Barley (Hordeum vulgare L.) genome have made it impossible for short-read sequencing technologies to efficiently build a high-quality reference genome for the species. Enter Bionano genome mapping.

By scaffolding highly contiguous Bionano genome maps with the short-read sequence assemblies, researchers increased the contiguity of the barley reference genome from N50 of 79 kb to N50 of 1.9 Mb. This study clearly demonstrates how Bionano data is essential to the construction of reference genomes.

Read the full paper published in Nature: A Chromosome conformation capture ordered sequence of the barley genome

 

Improved Assembly for Delicious, and Highly Nutritious Quinoa

Quinoa has been cultivated for over 7,000 years and remains a key crop in many parts of the world due to its ability to grow on marginal land not suitable for other crops. Using a combination of Bionano optical genome mapping, chromosome-contact maps, and PacBio long-read sequence, researchers have assembled a high-quality, chromosome-scale quinoa (Chenopodium) reference genome that will help enable more active breeding programs for this versatile crop.

By scaffolding sequence assemblies with Bionano genome maps, researchers created an assembly of 3,486 scaffolds, with a scaffold N50 of 3.84 Mb, marking a substantial improvement over the previously published quinoa draft genome sequence.

Read the full paper published in Nature: The genome of Chenopodium quinoa

 

Improved Assembly for Genetically Diverse Maize

The most complete maize B73 reference genome to date was recently built using Bionano optical genome mapping and hybrid scaffolding in combination with single-molecule real-time sequencing (SMRT). The new reference features a 52-fold increase in contig length relative to the previous maize reference, as well as notable improvements in the assembly of intergenic spaces and centromeres. Additionally, Bionano optical genome mapping directly identified new structural variations short-read-based sequencing methods missed.

The improved maize B73 assembly will help researchers further understand the genetic diversity in maize, an important part of the global food economy, and demonstrates that additional assemblies of other maize varieties and other repeat-rich, large-genome plants are feasible.

Read our earlier and more extensive Bionano U post, or the full paper published in Nature: Improved maize reference genome with single-molecule technologies.

 

Highly Repetitive Spinach Reference Sees Improvement

Spinach is cultivated in over 60 countries around the world and its production has increased tenfold in the past 40 years. Recently, researchers scaffolded sequencing data with Bionano genome mapping data to produce a high-quality genome assembly of a Chinese spinach cultivar (Sp75). Researchers generated transcriptome data of 120 cultivated and wild spinach accessions as well.

Spinach is a crop with a highly repetitive genome. The previous reference assembly was limited in its ability to serve as a reference for research studies, as it represented only half of the genome and contained many short-assembled fragments. The updated assembly will serve as a basis for comparative genomic studies and, together with the transcriptome variation data, provides a valuable resource for research and improvement of this vital vegetable. 

Read the full paper published in Nature Communications: Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

 

New Apple Reference is Both Golden and Delicious

Researchers recently assembled, de novo, the most comprehensive apple (Malus domestica Borkh.) genome to date using Bionano optical genome mapping and hybrid scaffolding in conjunction with short and long-read-sequencing. To produce the high-quality apple reference genome, researchers scaffolded sequence assembly data with long-range Bionano genome maps to assemble a Golden Delicious doubled-haploid tree.

The new apple genome shows 50x contiguity improvement over a recent assembly built using the sequencing technologies alone and enables analysis of structure, transposable elements, epigenetic regulation of transcription, and fruit development like never before. 

Have a look at our much more detailed summary in a previous Bionano U post, or read the full paper published in Nature Genetics: High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

 

G.G.G.O.A.T (Greatest Goat Genome of All Time)

Using a combination of Bionano genome mapping data and short-read sequencing data, researchers have produced the greatest goat genome of all time. The high-quality assembly of the domestic goat also happens to be the most contiguous de novo mammalian assembly to date.

By scaffolding sequencing assemblies with Bionano optical genome maps, researchers created an assembly which shows a ~400-fold improvement in contiguity over the previous version and better resolves repetitive structures longer than 1kb. This study demonstrates the ability of optical genome mapping to improve on the highly fragmented, draft genome assemblies that often result from the use short-read sequencing technologies alone.

Read the full paper published in Nature Genetics: Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

 

How Male Asparagus Came To Be

How well do you know the origin and evolution of the Y-chromosome in asparagus? Sex chromosomes evolved from autosomes many times in eukaryotic evolution, and little was known about the sex determination mechanism in asparagus.

Bionano maps helped bring clarity by building a contiguous assembly of the entire megabase-size non-recombining region on the Y, allowing the researchers to identify and test candidate sex determining genes.

Read the full paper published in Nature Communications: The asparagus genome sheds light on the origin and evolution of a young Y chromosome

 

Making sense of hexaploid wheat, one diploid genome at a time

Rounding out our series of high profile papers on edible organisms is this recent publication in Nature. An international research team reports the genome sequence of Aegilops tauschii, the diploid progenitor of the D genome of hexaploid wheat and a key genetic resource for the crop plant. Using a variety of technologies including ordered-clone genome sequencing, whole-genome shotgun sequencing, and Bionano optical genome mapping, the researchers show that compared to other sequenced and larger plant genomes, the Ae. tauschii genome contains “unprecedented amounts of very similar repeated sequences.” The genome also features a greater number of dispersed duplicated genes versus other sequenced genomes and “chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes,” the researchers say.

Read the full paper in Nature here: Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

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