Supplementary Figure 1: Features of Euplotes genomes.

(a) Comparison Euplotes genomes in comparison with the genomes of other representative eukaryotes. The tree was constructed based on the sequences of 18S rRNA genes, and archaeal 16S rRNA gene (from Pyrococcus furiosis) was used as an outgroup. *number of contigs with telomeric repeats at both ends. (b) Distribution of telomeric repeat lengths in E. crassus (red) and E. focardii (black) macronuclear genomes. The X axis indicates the observed telomeric repeat number and the Y axis their frequencies. As expected, Euplotes genomes consist of gene-sized chromosomes capped by telomeres. The length of terminal repeats slightly varies; however, most chromosomes in both organisms have a double-stranded telomere length of 3.5 repeats (c) Sequence logo of subtelomeric regions at the 3’ end of E. crassus nanochromosomes. 1000 randomly selected chromosome sequences with telomeric repeat GGGGTTTTGGGGTTTTGGGGTTTTGGGG were chosen for constructing the logo. The logo detects a conserved position-specific sequence motif associated with telomeric repeats. Abundance of high-quality telomeric sequences allowed an unbiased screen for motifs and patterns associated with telomere function. A previously described TCAA motif (Baird S. E. & Klobutcher L. A., Genes Dev 3, 585-597, 1989; Klobutcher, L. A. et al., Proc Natl Acad Sci USA 78, 3015-3019,1981) was readily detected with Weblogo (Crooks, G. E. et al, Genome Res 14, 1188-1190, 2004) in the subtelomeric region due to its conserved position relative to the telomere repeats. An analysis of sequences in the vicinity of telomeres with a pattern discovery suite MEME (Bailey, T. L. et al., Nucl Acids Res 34, W369-373, 2006) did not reveal additional common motifs.