If you remember Paramecium from high school biology, you remember cilliates. These single-celled creatures are eukaryotes that are vaguely related to plants, but only to the same degree that animals are related to fungi: the plant and cilliate lineages split shortly after eukaryotes developed, and they've largely gone their separate ways since. A sequencing consortium has now announced the completion of one of the genomes of a related cilliate, Tetrahymena thermophila, the thing on the right that looks vaguely like a microscopic and furry avocado (it's in PLoS, so you can read for free). That genome is a very strange place indeed.
For starters, note that I wrote "one of the genomes" above: that was not a typo. These things have two genomes, one of which (stored in the micronucleus) is exchanged during sexual reproduction, but not used otherwise. The day-to-day activities of Tetrahymena is run from the genome in the macronucleus. The two genomes are related, however: to make the macronuclear genome, the one in the micronucleus is processed. All repetitive sequences, such as transposons, are first chopped out. The large micronuclear chromosomes are then cut into 250-300 smaller chromosomes, which are then amplified up to somewhere in the area of 50 copies each. When dividing asexually, these excess copies allow the macronucleus to get by without the usual cell division process of lining up and splitting the chromosomes. Instead, random chance ensures that most progeny wind up with at least a few copies of every chromosome. All these unusual features made sequencing it a unique challenge, but one that's revealed some interesting things.
One of the odd things is the use of codons for translating RNAs into proteins. Tetrahymena is one of many organisms that use some of the typical stop codons to code for an amino acid. It also one of the ones that uses a different stop codon, in combination with the structure of the RNA, to encode a special metal-complexed amino acid. By combining these two features, it can be said that Tetrahymena doesn't really have any stop codons; it only stops translating when the context of the RNA tells it to. Another big surprise came in terms of the number of genes there are to translate: 27,000, or roughly double the number in flies, and close to the human count. Why so many? Researchers suggest that it's because Tetrahymena is a generalist. As the press release put it, "Whatever this unicell touches with its hairlike projections, it will try to eat." Aside from having a lot to digest, it's very much at the mercy of its environment, so its genome has to carry all the tools needed to adjust to changing conditions in whatever pond it finds itself in.
The other nice thing about having the Tetrahymena genome done is that it gives us a broader perspective on what things are common to all eukaryotes. It's especially interesting in this case, because some are proposing that eukaryotes got their start living a lifestyle very much like Tetrahymena, as unicellular predators. If this "eukaryotic raptor" proposal gains traction, this genome sequence may turn out to be very significant for the perspective it provides on eukaryotic origins.