Nature recently published the most comprehensive maize B73 reference genome to date, using Bionano optical genome mapping and hybrid scaffolding. With half of the updated assembly consisting of scaffolds over 9.6 Mbp in size, the new reference features a 240-fold increase in scaffold length relative to the recently published short-read assembly of maize cultivar PH207, as well as notable improvements in the assembly of intergenic spaces and centromeres. In addition, Bionano data directly identified new structural variations that 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 how Bionano is essential to additional assemblies of other maize varieties and other repeat-rich, large-genome plants.
Improved Assembly Contiguity with Bionano Hybrid Scaffolding
To build the improved maize assembly, a Pacific Biosciences (PacBio) assembly of 2,958 contigs was integrated with a high-quality Bionano genome map to create a hybrid assembly of 625 scaffolds. After adding bacterial artificial chromosome (BAC) reads and gap filling, the new reference has 2,522 gaps, of which Bionano maps were able to size nearly half.
Of note is the fact that the increased contiguity seen was achieved using only a single-enzyme Bionano genome map. Bionano now offers two-enzyme hybrid scaffolding capabilities, which would improve contiguity even further.
New Structural Variations Identified Directly from Bionano Data
As part of their study, researchers directly compared several Bionano optical genome maps of two additional maize lines, tropical line Ki11 and W22, to study diversity between species. Generating an entire de novo genome costs tens to hundreds of thousands of dollars, while mapping two maize lines with Bionano costs just a few thousand dollars.
With Bionano, there is no need to wait for the whole genome sequence to arrive if you want to compare the structures of two or more genomes. Bionano’s structural variation calling algorithms identify all major types of variants directly from the genome maps with a sensitivity and precision that far outperforms sequence-based structural variation calling. Read more about Bionano’s structural variation calling capabilities here:
To learn more about the maize B73 study, read the full paper published in Nature Genetics: Improved maize reference genome with single-molecule technologies.