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Dryad

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

Cite this dataset

Huang, Zhen et al. (2023). Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates [Dataset]. Dryad. https://doi.org/10.5061/dryad.9p8cz8wkx

Abstract

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.

Funding

Fujian Normal University

FWF Austrian Science Fund, Award: J4477-B

National Natural Science Foundation of China, Award: 31722050

European Research Council, Award: 677696