Data for: Genome assemblies of the simultaneously hermaphroditic flatworms Macrostomum cliftonense and Macrostomum hystrix

The free-living, simultaneously hermaphroditic flatworms of the genus <em>Macrostomum, </em>are increasingly used as model systems in various contexts. In particular, <em>M. lignano</em>, the only species of this group with a published genome assembly, has emerged as a model for the study of regeneration, reproduction, and stem-cell function. However, challenges have emerged due to <em>M. lignano</em> being a hidden polyploid, having recently undergone whole-genome duplication and chromosome fusion events. This complex genome architecture presents a significant roadblock to the application of many modern genetic tools. Hence, additional genomic resources for this genus are needed. Here we present such resources for <em>M. cliftonense</em> and <em>M. hystrix</em>, which represent<em> </em>the contrasting mating behaviors of reciprocal copulation and hypodermic insemination found in the genus. We use a combination of PacBio long-read sequencing and Illumina shot-gun sequencing, along with several RNA-Seq datasets, to assemble and annotate highly contiguous genomes for both species. The assemblies span ~227Mb and ~220Mb and are represented by 399 and 42 contigs for<em> M. cliftonense</em> and<em> M. hystrix,</em> respectively. Furthermore, high BUSCO completeness (~84-85%), low BUSCO duplication rates (8.3-6.2%), and low k-mer multiplicity indicate that these assemblies do not suffer from the same assembly ambiguities of the<em> M. lignano</em> genome assembly, that can be attributed to the complex karyology of this species. We also show that these resources, in combination with the prior resources from <em>M. lignano, </em>offer excellent foundations for comparative genomic research in this group of organisms.