Figure 1

Schematic illustration of macronuclear nanochromosomes and their micronuclear sequences. (A) Macronuclear nanochromosomes, transcribed during vegetative growth. (B) Macronuclear nanochromosomes, silenced during vegetative growth. (A,B) Total length of nanochromosome is indicated in brackets. DNA sequences are shown in green, telomeres are red. Black bars below nanochromosomes indicate the coding region of each gene, partly interrupted by introns and flanked by non-coding sequences. Blue bars above nanochromosomes show the positions of qRT-PCR fragments. Numbers show the order of PCR fragments, for primer sequences see Additional file 5. (C) Micronuclear sequences of the actin I, mdp2 and the 1.1 kb gene. Macronuclear-destined sequences (MDS) in green are interrupted by micronucleus-specific internal eliminated sequences (IES) in yellow and partly flanked by further micronucleus-specific sequences (orange). MDSs of the actin I gene are found in a scrambled disorder in micronuclei and anlagen (3-4-5-6-7-8-10-(-2)-(-1)-9) and are reorganized into the correct order (1-2-3-4-5-6-7-8-9-10) upon differentiation [19]. Total length of sequence is indicated in brackets. Blue bars above DNA sequence indicate positions of qRT-PCR fragments. Letters show order of PCR fragments, for corresponding primer sequences see Additional file 6.