Coding properties of macronuclear DNA molecules in Sterkiella nova (Oxytricha nova)

The DNA in the macronucleus of the stichotrichs like Sterkiella nova (formerly Oxytricha nova) occurs in short molecules ranging from ∼200 bp to ∼20,000 bp. It has been estimated that there are ∼24,500 different sized DNA molecules in the macronucleus. Single genes have been assigned to ∼130 different sized macronuclear molecules in various stichotrichs (12 in Sterkiella nova) and hypotrichs, suggesting that each of the ∼24,500 different sized molecules encodes a different gene. To test this proposition we sequenced 31 macronuclear molecules picked randomly from a plasmid library of macronuclear DNA and analyzed them for potential gene content. The open reading frames (ORFs) in three short molecules encode amino acid (aa) sequences that do not match sequences in GenBank. They may or may not encode genes. Twenty-eight of the 31 molecules contain ORFs encoding aa sequences with significant matches to sequences in GenBank. Six molecules contain more than one ORF with a significant match to GenBank. These results indicate that almost all, if not all of the ∼24,500 different molecules encode one or more genes, yielding an estimate of ∼26,800 genes in the macronucleus of S. nova.