Amphioxus reference genome

Amphioxus is a marvelous animal. As basal chordata, it is an important model organism for evolutionary biologists interested in characterization of the common ancestor of all vertebrates. I find amphioxus interesting because of its strange genome, the SNPs and variable indels are covering about 9% of its genome.

How comes that individuals with that different genome still have same body plan and how comes that they still can mate with each other? When I say, that I am fascinated by diversity of life, this is what I have in my mind, rather than wondering about beaks and feather colours of tropical birds.

I am putting together a new reference genome using long read sequencing.