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On the basis of the small subunit of ribosomal RNA, Nanoarchaeum equitans was identified as a new phylum of Archaea. In the identification of N. equitans, difficulties were already identified because the probes normally used to amplify ribosomal RNA turned out to be ineffectual in amplifying the rRNA of N. equitans. Furthermore, its rRNA sequence was unique and singular among the Archaea although it presented some secondary structures typical of Archaea. When its genome was sequenced it became clear that N. equitans presented a truly unusual set of characters. Firstly, the large number of split genes: at least eleven proteins are split in N. equitans, i.e. a protein such as alanyl-tRNA synthetase, which is normally codified in a single gene is, in N. equitans, codified in two completely different ge nes. Coherently, six tRNA genes are split in the sense that the tRNA molecule, which is normally codified in a single gene, is codified in N. equitans in two genes codifying only half of the tRNA molecule and located in non-contiguous sites on its genome. Consistent with these first two characteristics of the genome of N. equitans
is the observation of the almost total absence of conserved operons on its genome. For instance the super-operon of ribosomal proteins, which is conserved in all the Archaea and Bacteria, is almost totally absent in N. equitans and only few fragments are present. Therefore, N. equitans seems to be the only nearly operon-less prokaryote.
All these proprieties seem to be ancestral traits and therefore N. equitans might be one of branch deeper of the archaeal domain.