Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates

The slow-evolving invertebrate amphioxus has an irreplaceable role in
advancing our understanding into vertebrate origin and innovations. Here
we resolve the nearly complete chromosomal genomes of three amphioxus
species, one of which best recapitulates the 17 chordate ancestor linkage
groups. We reconstruct the fusions, retention, or rearrangements between
descendants of whole genome duplications (WGDs), which gave rise to the
extant microchromosomes that likely existed in the vertebrate ancestor.
Similar to vertebrates, the amphioxus genome gradually establishes its 3D
chromatin architecture at the onset of zygotic activation and forms two
topologically associated domains at the Hox gene cluster. We find that all
three amphioxus species have ZW sex chromosomes with little sequence
differentiation, and their putative sex-determining regions are
nonhomologous to each other. Our results illuminate the unappreciated
interspecific diversity and developmental dynamics of amphioxus genomes
and provide high-quality references for understanding the mechanisms of
chordate functional genome evolution.