Still waters run deep: Large scale genome rearrangements in the evolution of morphologically conservative Polyplacophora

<b>Background:</b> A major question in animal evolution is how genotypic and phenotypic changes are related, and whether ancient gene order is conserved in living clades. Chitons, the molluscan class Polyplacophora, retain a body plan and general morphology apparently little changed since the Palaeozoic. We present a comparative analysis of five reference quality genomes, including four <i>de novo</i> assemblies, covering all major chiton clades, and an updated phylogeny for the phylum.<b>Results:</b> We constructed 20 ancient molluscan linkage groups (MLGs) that are relatively conserved in bivalve karyotypes, but subject to re-ordering, rearrangement, fusion, or partial duplication among chitons, varying even between congeneric species. The largest number of novel fusions is in the most plesiomorphic clade Lepidopleurida, and the chitonid <i>Liolophura japonica</i> has a partial genome duplication, extending the occurrence of large-scale gene duplication within Mollusca.<b>Conclusions:</b> The extreme and dynamic genome rearrangements in this class stands in contrast to most other animals, demonstrating that chitons have overcome evolutionary constraints acting on other animal groups. The apparently conservative phenome of chitons belies rapid and extensive changes in genome.