Genome of Paramecium caudatum, kajaani clone 1 (KAJ-01)
This study presents the macronuclear genome sequence and annotation of Paramecium caudatum strain Kajaani clone 1 (KAJ-01). P. caudatum is a unicellular ciliate widely used as a model organism in studies of cell biology, symbiosis, and environmental adaptation. Like other ciliates, Paramecium exhibits nuclear dimorphism, possessing a germline micronucleus and a somatic macronucleus responsible for gene expression during vegetative growth.  The KAJ-01 clone was established as a stable genetic background for the generation and maintenance of transgenic lines, where introduced constructs remain stably maintained over multiple cell divisions. In contrast, transgenes introduced into other Paramecium strains, including commonly used P. tetraurelia strains and other available P. caudatum isolates, are frequently lost after relatively few vegetative divisions.  High-fidelity long reads were generated using Pacific Biosciences (PacBio) sequencing to assemble the macronuclear genome. The resulting assembly contains chromosome-scale contigs corresponding to macronuclear chromosomes, which are gene-rich and typically capped by telomeric repeats. The genome assembly was subsequently annotated to identify protein-coding genes and other genomic features.  The datasets deposited in this study include raw PacBio HiFi sequencing reads, the assembled macronuclear genome sequence, chromosome-level contigs, and structural genome annotations. These resources provide a genomic reference for the KAJ-01 clone of Paramecium caudatum and support future studies on ciliate genome organization, genome rearrangements, and the development of stable transgenic systems in ciliates.