Tracking karyotype dynamics by flow cytometry reveals <i>de novo</i> chromosome duplications in laboratory cultures of <i>Macrostomum lignano</i>

The flatworm Macrostomum lignano is a versatile invertebrate model organism with a growing molecular toolbox. Genome assembly and detailed karyotyping revealed that M. lignano is a hidden polyploid species with a recent whole-genome duplication. Its karyotype consists of six small and two large chromosomes (2n=8), with the large chromosomes originating from the fusion of duplicated ancestral chromosomes. However, 2n=9 and 2n=10 karyotypes with duplicated large chromosomes were also observed in animals from both laboratory cultures and field samples, prompting us to further investigate this phenomenon. To this end, we optimized a flow cytometric approach that enables easy and rapid studies of tens or even hundreds of animals simultaneously to gain insight into the karyotype polymorphisms present in a culture and consistently tracked karyotype dynamics in multiple cultures over a period of 26 months. We demonstrate that de novo duplications of the large chromosome in M. lignano can spontaneously appear under laboratory conditions and can become dominant in laboratory cultures. Since uncontrolled chromosomal duplications can complicate genetic studies in laboratory model organisms, we propose an approach to easily control the karyotype of experimental cultures by regularly karyotyping M. lignano subcultures using flow cytometry and replacing cultures with de novo chromosome duplications as needed.