Bionano Genomics was thrilled to be a part of this year’s International Plant & Animal Genome (PAG) conference in San Diego. As a company we look forward to PAG each year as we get to see numerous examples first-hand of researchers incorporating Bionano optical maps as a powerful tool for building the very best reference genomes possible. For PAG XXVII, we found over 30 posters and workshop talks that explicitly featured Bionano data and as in years past, it is not uncommon to see a Bionano map pop up on the screen in any given session you might attend.
A key take-away from the year’s event was how Bionano maps have become a foundational technology for many groups working to scale genome assembly well beyond a single representative platinum reference genome. We heard from groups that are collecting multiple (beyond) platinum reference genomes to assemble a more “pan genome” view for various important crop species, to even more auspicious endeavors like the Vertebrate Genomes Project that are seeking to assemble the more than 66,000 genomes of extant vertebrates.
To highlight some of the work we have been doing internally at Bionano, we presented 2 posters this year:
- Novel Method for Isolating High-Quality UHMW DNA from 10 mg of Freshly Frozen or Liquid-Preserved Animal and Human Tissue including Solid Tumors
- Bionano Hybrid Scaffold Assemblies Provide High Contiguity and Accuracy
We hosted a workshop session featuring several scientists who are using Bionano maps to further their research.Our workshop was kicked off by Mark Borodkin, Chief Operating Officer at Bionano Genomics, who previewed some of the exciting things we will release in 2019. Mark discussed a new sample prep kit for blood and cells (launching this spring) that dramatically reduces the time and effort to isolate extremely high quality, high molecular weight DNA (3-hour workflow, 12 samples/day). Also discussed were Saphyr instrument improvements that will dramatically increase throughput and yield that would allow economical incorporation of our maps in the pan genome efforts of even very large genomes like wheat. To support this huge new influx of raw data being collected, Bionano is developing an on-demand bioinformatics pipeline to supplement on-site compute capabilities and provide a relief valve to ensure that the bioinformatics backend will keep pace with the Saphyr instrument raw throughput. And finally, Mark discussed how our software tools are being improved this year to detect low allelic events to capture extremely rare structural variants. Taken together these improvements will enable the easiest, most cost-effective, high-depth genome maps, and detection of rare structural variants of all types.
Victor Llaca, from Corteva Agriscience, Agriculture Division of DowDuPont, discussed his group’s efforts to implement a fast-response, high-throughput reference genome pipeline that takes advantage of improvements in PacBio, 10X Chromium and Bionano technologies to assemble high-quality sequence scaffolds up to the entire length of chromosomes. Victor shared how using long-range contig scaffolding assembled with our direct-label (DLS) optical maps, enables mis-assembly correction, gap closing, gap sizing and the unscrambling of complex regions. The end result are research-ready reference genomes with high levels of contiguity and precision in a wide range of organisms.
Klaus-Peter Koepfli from the Center for Species Survival at the Smithsonian Conservation Biology Institute, National Zoological Park discussed his team’s efforts to develop and apply data derived from whole genome sequences to the management of ex situ populations of the endangered black-footed ferret and the critically endangered dama gazelle. De novogenome assemblies were generated for both species using several technologies, including Bionano mapping. The highly contiguous assemblies of these 2 species provide critical references for mapping of sequences from additional individuals addressing a variety of conservation genomic questions. The Bionano maps are also revealing novel insights in the genomes of species which have undergone severe population bottlenecks like the black footed ferret that could help future conservations efforts.
Helene Berges of the French Plant Genomic Center (CNRGV), INRA discussed how they are extensively using Bionano to improve the quality of the assemblies of complex plant genomes. Plant genomes exhibit high degrees of diversity and complexity based on their genome size, high percentage of repetitive regions and elements, varying ploidy levels as well as high levels of intra-species variability (e.g. maize species share ~20% genomic identity with each other). Helene’s group is using Bionano to assemble several extremely high-quality Sunflower reference genomes, taking one assembly from 0.5Mb to a staggering 175Mb scaffold N50. These assemblies are then being used to study structural variation between different genotypes. These comparative analyses are very useful for studying plant evolution and provide insight into a possible “core genome” that is maintained across all the reference assemblies. They are also using Bionano maps as a quick way to identify regions of high divergence between species as a fast and efficient method to narrow down the genome based on a QTL of interest for detailed study with other technologies.
Olivier Fedrigo from The Rockefeller University outlined the mission of the Vertebrate Genome Project (VGP) and laid out in his presentation the various challenges the consortia faces as it seeks to deliver high quality assemblies of ~66,000 vertebrate species. To reach this goal, the VGP uses a combination of 4 genome data types: Pacific Biosciences long reads, 10X Genomics linked reads, Bionano optical maps, and Arima Genomics Hi-C chromosomal crosslinked reads. Olivier shared details of the assembly pipeline the VGP has developed to incorporate these 4 datatypes as well as the first results of Phase 1 (of 4) that includes the first 15 vertebrate genomes that meet the VGP quality standard (4 mammals, 4 birds, 1 reptile, 1 amphibian, and 5 fishes).
On the last day of the conference, Bionano Genomics was represented at the Vertebrate Genome Project workshop where Alex Hastie, Director of Bionano Customer Solutions, provided an overview of the Bionano Genomics platform, capabilities and workflow. Alex also briefly discussed how our algorithms work to create de novo assembled maps and our on-going effort to better enable haplotype phased assemblies which is highly desired by the VGP consortia members.
To everyone who attended the conference, stopped by our booth or presented Bionano data, we are extremely grateful to you for helping make PAG XXVII so exciting and reaffirming our commitment every year to make our tools more powerful, more affordable and easier to use. We can’t wait to see what you show us next year at PAG XXVIII.