Genome Analysis of Hypertherophilic Archaea, Pyrococcus horikoshii OT3
Yutaka KAWARABAYASI*a,b, Yuhko OHFUKUa, Hiroshi HORIKAWAa, Mituhiro SAWADAa, Yuji HAIKAWAa, Koji JIN-NOa, Yumi HINOa, Saori YAMAMOTOa, Mitsuo SEKINEa, Sin-ichi BABAa, Hiroki KOSUGIa, Akira HOSOYAMAa, Yoshimi NAGAIa, Mari SAKAIa, Keiko OGURAa, Rie OTSUKAa, Hidekazu NAKAZAWAa, Tomomichi FUNAHASHIa, Toshihiro TANAKAa, Yutaka KUDOHa, Jun YAMAZAKIa, Norihiro KUSHIDAa, Akio OGUCHIa, Ken-ichi AOKIa, Takio YOSHIZAWAa, Yoshinobu NAKAMURAa, and Hisasi KIKUCHIa
a National Institute of Technology and Evaluation, Shibuya, Tokyo, Japan
b National Institute of Bioscience and Human-Technology, Tsukuba, Ibaraki, Japan
We finished the determination of entire nucleotide sequence of Pyrococcus horikoshii OT3 and analysis of the genomic organization.
Pyrococcus horikoshii OT3 is a hyperthermophilic archaeon isolated from a hydrothermal vent at Okinawa Trough. It grows optimallY at 95℃ and survives over 100℃ and possesses 1.89 Mbp long genome DNA.
The genome sequencing of P. horikoshii OT3 will provide us with many information about evolution and origin of life. Moreover the information about proteins deduced from these genome sequence is expected to introduce the new industrial trial. Then the big genome project of P. horikoshii OT3 was organized by MITI and started at 2 years ago.
To determine the entire nucleotide sequence of this archaeon we selected the following strategy:
1. We constructed the fosmid library of P. horikoshii OT3 genome DNA.
2. We ordered the clones of this library and mapped these clones on genome.
3. These ordered fosmid clones were sequenced by shotgun sequencing method.
4. We filled the remaining gaps.
We successfully constructed the fosmid contigs covering over 90% of P. horikoshii OT3 genome, collected the about 1000 raw sequencing data from each shotgun clones. We used the Phred-Phrap and Sequencher for assembling and editing these data. The nucleotide sequence of regions which was not covered by fosmid clones is determined by shotgun clones directly constructed from long PCR fragment or genomic DNA fragment. It is very important that our nucleotide sequence has very high accuracy in comparison with other microbial genome sequence.
The about 2000 deduced ORFs with 100aa or over are assigned on the P. horikoshii OT3 whole genome. 20% of these all ORFs are annotated by homology analysis, 30% have homology just with the hypothetical proteins deduced from the nucleotide sequence of already finished microbial genomes and 50% have no significant homology with any proteins listed in database. The codon-usage of P. horikoshii is different from other microorganisms. These features show the originality of P. horikoshii OT3.
We will discuss other characteristic features of this hyperthermophilic archaeon genome and the comparison with other archaea genomes in this meeting.
