Establishing genetically controlled, closed colonies of an ascidian

Recent technological advances have made many "non-model" organisms accessible for experimental studies. However, inbred reference strains are not available for many of these, a situation that potentially affects experimental reproducibility. Although ascidians, Ciona intestinalis (type A, or C. robusta), are widely used for developmental biology, development of reference strains has not been successful. As an alternative way to improve reproducibility, we have established and maintained ascidian colonies through intra-population breeding every year from 2016 to 2020, and monitored genomic variants of these colonies. This method does not reduce genetic variation, but instead monitors and manages it in these colonies in an easy and cost-effective way. Furthermore, we recently upgraded these genetically isolated, closed colonies, which had been annually re-established, and have maintained them since 2021 with only intra-population breeding and occasional back-cross using cryopreserved sperm. Genetic variants that we have uncovered will facilitate new experimental designs using this species, and our genetically-controlled colonies will undoubtedly improve experimental reproducibility and traceability. Our method will provide a realistic solution for performing reproducible experiments using non-model organisms.