Sequencing and mapping statistics.

Paired-end Illumina sequencing was carried out as described in Materials and Methods, and reads were mapped to the P. tetraurelia MAC reference genome using the BWA short-read aligner. The genome coverage is the fraction of the genome covered by at least 1 read. The depth of coverage with the PGM DNA is on average 165×. The depth of coverage with the lambda-phage DNA is on average 75× for the part of the genome that is covered. The PGM reads that were not aligned contain Paramecium mitochondrial and rDNA sequences, contaminating bacterial sequences as well as sequences present only in the MIC genome. In addition, a large proportion of the unaligned lambda-phage reads are from bacterial contaminants with AT-rich genomes; this DNA was not eliminated by the cesium chloride density gradient separation step of the phage library construction [28].