Since Euplotes exhibits frequent translational frameshifting, a gene predictor which can predict such frameshifts, EuGene, was employed. The macronuclear genome of Euplotes crassus strain DP1 was assembled. Contigs bound by telomeric repeats, representing full-length nanochromosomes (30,392) comprising 62 Mb were selected for gene prediction. RNA-seq data was mapped to the nanochromosomes, and then genes predicted with EuGene with its frameshift plugin.