The planarian
Schmidtea mediterranea
is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of
S. mediterranea
and high-quality chromosome-scale assemblies of its three close relatives,
S. polychroa
,
S. nova
, and
S. lugubris
. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus
Schmidtea
and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in
Schmidtea
and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.
Planarians are model systems for stem cells and regeneration. This study provides new genome assemblies of the model species
S. mediterranea
and 3 relatives and uses comparative genomics of planarians to reveal that synteny is not an evolutionary constraint in flatworm genome evolution.