design: High-quality macronuclear DNA was isolated using a modified sucrose gradient ultracentrifugation protocol (https://doi.org/10.1371/journal.pgen.1002984). Briefly, Paramecium cells were lysed in a non-ionic detergent buffer and mechanically homogenized on ice to release macronuclei, which were purified via sucrose cushion ultracentrifugation (35,000 rpm, 1 h, 4C; SW40Ti rotor). Purified macronuclei were lysed in SDS/proteinase K buffer and incubated overnight at 55C. DNA was extracted using phenol:chloroform:isoamyl alcohol, followed by dialysis against Tris-EDTA buffer. The recovered DNA was concentrated using centrifugal filter units (30 kDa MWCO; Amicon Ultra-2, Millipore), quantified by spectrophotometry, and quality-checked by agarose gel electrophoresis.  Sequencing libraries were made using TruSeq Nano DNA High Throughput Library Prep Kit (96 samples, illumina, 20015965) in combination with IDT for Illumina  TruSeq DNA UD Indexes v2 (96 Indexes, 96 Samples, illumina, 20040870) according to the kit reference guide (illumina, Part # 15041110 Rev. D June 2015). Pooled DNA libraries were sequenced paired-end on a shared NextSeq1000 P2 Reagent Kit (300 cycles; illumina, 20100985) on an illumina NextSeq1000. The quality of the sequencing run was assessed using illumina Sequencing Analysis Viewer (illumina version 2.4.7) and all base call files were demultiplexed and converted into FASTQ files using illumina bcl2fastq conversion software v2.20. All steps from DNA QC to sequencing data generation and data utility were performed at the Next Generation Sequencing Platform, University of Bern, Switzerland.