Pyrococcus horikoshii OT3^T, the first organism whose genome was analyzed at the Genome Analysis Center is a hyperthermophilic archaeon that was isolated from a hydrothermal fluid in Okinawa Prefecture in 1992 by the manned deep-sea investigation vessel "Shinkai 2000" in the DeepStar project that was carried out by the Japan Marine Science and Technology Center in collaboration with University of Maryland of U.S.

P. horikoshii OT3^T is an obligate anaerobe, harboring such characteristics as growing at temperatures between 88°C and 104°C with the optimal temperature of 98°C in the presence of sulfur, and possessing circular genomic DNA. The proteins and enzymes produced by this hyper-thermophilic archaeon have outstanding heat resistance and may, therefore, be utilized in various industrial fields such as chemistry, food, medical supplies, etc.

Analysis of the 1.74 Mb genome of this archaeon revealed the presence of only one set of genes for 16S and 23S rRNA and two genes for 5S rRNA, while it is likely to harbor 11 genes/ORFs encoding intein-containing proteins and two tRNA genes with introns. Furthermore, more than 50 % of the 2,061 genes/ORFs assigned appear to be organism-specific, some of which seem to be derived from gene duplications. These features remain to be studied further by comparing with other archaea and eubacteria.