Comparison of Oxytricha macronuclear genome assemblies.

The 2-telomere contigs have both 5′ (CCCCAAAACCCC; with degenerate bases—see Materials and Methods) and 3′ (GGGGTTTTGGGG; with degenerate bases) telomeric repeats. Note that 2-telomere contigs are mostly complete nanochromosomes but may also be alternatively fragmented nanochromosomes with one or more additional missing ends and that multitelomere contigs may be either alternatively fragmented nanochromosomes or nanochromosomes with internal telomere-like repeats. Raw read coverage is calculated from LAST (default parameters; version 159; contig telomeres were masked) matches (≥70 bp long and ≥90% identical) to the assemblies. Read coverage was calculated for the total high quality PE sequence data set and one of the three lanes of SE sequence data. Of the PE reads 13% were telomere bearing, as opposed to 4.7% of the SE reads.