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Summary: We sequenced and analyzed the subtelomeric regions of 1356 macronuclear “nanochromosomes” of the spirotrichous ciliate Oxytricha trifallax. We show that the telomeres in this species have a length of 20 nt, with minor deviations; there is no correlation between telomere lengths at the two ends of the molecule. A search for open reading frames revealed that the 3′ and 5′ untranslated regions are short, with a median length of ∼130 nt, and that surprisingly there are no detectable differences between sequences upstream and downstream of genes. Our results confirm a previously reported purine bias in the first ∼80 nucleotides of the subtelomeric regions, but with this larger data set we curiously detected a 10 bp periodicity in the bias; we relate this finding to the possible regulatory and structural functions these regions must serve. Palindromic sequences in opposing subtelomeric regions, although present in most sequences, are not statistically significant. [Copyright &y& Elsevier]

Ciliates, microbial eukaryotes, have been important experimental organisms for >100 years, contributing to the discovery and understanding of self-splicing RNA, telomere biochemistry and transcriptional regulation by histone modification. We have completed a pilot sequencing project of the Oxytricha trifallax macronuclear (MAC) genome. When complete, this genome sequence, along with the emerging Tetrahymena thermophila and Paramecium tetraurelia sequences, will provide an important resource for basic eukaryotic cell biology, molecular evolution and the related apicomplexan parasites, such as Plasmodium spp. [Copyright &y& Elsevier]