Final Report: Complete Sequencing of the 2.3Mbp Genome of the Hyperthermophilic211 Archaeon Pyrbaculum Aerophilum, January 1, 1998-December 31, 1998

摘要

Pyrobaculum aerophilum is a hyperthermophilic archeon discovered from a boiling211u001emarine water hole at Maronti Beach, Italy that is capable of growth at 110 C. 211u001eThis microorganism can grow aerobically, unlike most of it's thermophilic 211u001erelatives. Due to the tolerance to oxygen, it is possible to grow this microbe in 211u001ethe presence of air, i.e. on plates. Therefore, it is a good candidate a model 211u001eorganism for studying archaeal biology and thermophilism. Sequencing the entire 211u001egenome of this organism will provide a wealth of information on the evolutionary 211u001eand phylogenetic relationship between archaea and other organisms as well as the 211u001ebiology of thermophilism. We have constructed a physical map that covers 211u001eestimated 2,3 Megabase pair genome using a 10X fosmid library. The map currently 211u001econsists of 96 overlapping fosmid clones. We have completed sequencing the entire 211u001egenome using in random shotgun approach with the supplement of oligonucleotide 211u001eprimer directed sequencing. Total 16,098 random sequences corresponding to 211u001eapproximately 3.5X genomic coverage were obtained by sequencing from both ends 211u001ewith vector-specific primers the 2-3 kbp genomic DNA fragments cloned into 211u001epUC18/19 vector after shearing have been assembled into a number of contigs using 211u001ePhrap program developed by Dr. Phil Green at University of Washington, Seattle. 211u001eGaps and regions of low quality base calls have been a total of 2,300 directed 211u001esequencing and reassembly. Our current full length genomic sequence still suffers 211u001efrom low data quality: only approximately 99% of the nucleotide sequences are 211u001eaccurate. This is mainly due to the low redundancy (3.5 fold) in random 211u001esequencing. We plan to perform 2-3,000 more directed sequencing to polish the 211u001esequence to 99,99% accuracy. Final polishing of the sequence data and annotation 211u001eis currently being performed by UCLA team and Caltech sequencing core facility.