Genome assemblies of the simultaneously hermaphroditic flatworms Macrostomum cliftonense and Macrostomum hystrix.

Abstract

The free-living, simultaneously hermaphroditic flatworms of the genus Macrostomum, are increasingly used as model systems in various contexts. In particular, M. lignano, 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 M. lignano 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 M. cliftonense and M. hystrix, which represent 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 M. cliftonense and M. hystrix, 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 M. lignano 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 M. lignano, offer excellent foundations for comparative genomic research in this group of organisms.