The last few weeks were productive for Bionano publications, with dozens of papers and preprints describing the use of optical genome mapping (OGM) to build or analyze genomes. We posted previously about the peer-reviewed papers that describe how OGM data generated by the Bionano Saphyr® System was able to help end the diagnostic odyssey for two families affected by genetic disease. But many OGM papers are focused on genome assembly – building reference genomes for organisms for which there is no or no great reference. Bionano’s genome maps are used to place the fragmented sequence assembly into entire chromosomes or chromosome arms, with each sequence fragment in the correct order and orientation.
There is no better way to illustrate the contribution of OGM to genome assembly than with the series articles in Nature describing the progress of the Vertebrate Genomes Project (VGP) led by Erich Jarvis, an ambitious endeavor to sequence and assemble the genomes of more than 70,000 vertebrate species within 10 years. The consortium performed a thorough benchmarking of the performance of many combinations of genome sequencing and assembly methods and concluded that their standardized pipeline should consist of long-read sequencing and OGM with Saphyr and other methods to place these fragments into the correct order and orientation. Besides the lead publication describing this standardized pipeline, they also published on the marmoset genome and used a number of assembled vertebrate genomes to study the oxytocin-vasotocin ligand and receptor families.
A similar pipeline was used to assemble a high-quality bonobo genome, which enabled the team led by Evan Eichler to greatly improve the study of the genetic relationship between human, bonobo and chimpanzee. The genome assembly of the Norway rat, an important model organism, was built with OGM by a team at the Wellcome Sanger Institute, and a group of scientists from Texas A&M University improved the horse X-chromosome assembly.
Many of the high-quality reference genomes assembled using OGM are for important crops or other food sources. We saw publications on genomes of the tomato, eggplant, cereals, sorghum, trout, and on 33 varieties of rice.
We are proud that OGM is considered an essential tool to assemble error-free, complete reference genomes!