The axolotl is an odd creature. It never really grows up and stays in its larval stage throughout life. It looks like an anime character. It regenerates limbs effortlessly. And it has the largest genome ever assembled: 32 gigabasepairs – that’s ten times the size of a human genome.
Where do you even start to assemble such a monstrously large genome? You take 3 easy steps:
Step 1, you use Bionano’s high throughput Saphyr to build 2 complete maps of the genome, based on separate labeling of two sequence motifs.
Step 2, you use these maps to anchor sequence contigs generated from 32x PacBio coverage using a custom built assembler, error corrected with 7x Illumina short reads.
Step 3, you use the Bionano maps to resolve 4,828 chimeric contigs. And to be honest, that happens automatically as part of step 2.
Sounds easy enough, right?
To test the completeness of the assembly on an organism with a poorly characterized genome like this remarkable little salamander’s, you check for the presence of aligning non-exonic ultra conserved elements (UCEs). A remarkable 98.5% of non-exonic UCEs that are conserved across vertebrates align to this axolotl assembly.
Here at Bionano, we are proud to see our technology used to push the boundaries of genome assembly. Read the Nature paper here, and if you have an even larger genome you would like to assemble, don’t hesitate to get in touch!