Conservation of animal genome structure is the exception not the rule

Species from diverse animal lineages, including molluscs, annelids, echinoderms, hemichordates, and cephalochordates, have retained groups of orthologous genes on the same chromosomes for over half a billion years since the last common ancestor of bilaterians. Though there are notable exceptions, it has been proposed that the conservation of chromosome-scale gene linkages is the norm among animals. Here, by examining interchromosomal rearrangements in 64 chromosome-level genomes across 15 bilaterian phyla and at least 52 classes, we show that, though striking, cases of genome structure conservation are exceptionally rare. The ubiquity of massive genome rearrangements suggests that, in general, chromosome-scale gene linkages are of minimal importance to animal genome function.

This project includes gene models for 14 genome assemblies annotated in this study, with files available for coding sequences (*.fasta), protein sequences (*.faa), and gene annotations in GTF format (*.gtf), as detailed below. Additionally, a spreadsheet containing all accession numbers and genome metadata for 64 bilaterian genomes and 3 cnidarian genomes is provided as a Supplemental Dataset.

- Amphiscolops sp. MND2022 (acoel worm; phylum Xenacoelomorpha)- Antedon bifida (crinoid; phylum Echinodermata)- Carcinoscorpius rotundicauda (horseshoe crab; phylum Arthropoda)- Convolutriloba macropyga (acoel worm; phylum Xenacoelomorpha)- Emplectonema gracile (ribbon worm; phylum Nemertea)- Gordius sp. MW1 (horsehair worm; phylum Nematomorpha)- Hypsibius dujardini (water bear; phylum Tardigrada)- Ophiura sarsii (brittle star; phylum Echinodermata)- Schizocardium californicum (acorn worm, phylum Hemichordata)- Schmidtea mediterranea (planarian; phylum Platyhelminthes)- Strigamia acuminata (centipede; phylum Arthropoda)- Styela plicata (tunicate; phylum Chordata)- Trichinella spiralis (nematode; phylum Nematoda)- Trididemnum miniatum (tunicate; phylum Chordata)