Collaborative Research: Sequencing and Functional Genomics of Halobacterium

Institute For Systems Biology, Seattle WA

Investigators

Abstract

The focus of the project is to sequence the genome of the Archaea Halobacterium sp. NRC-1, which contains a stable 2.0 Mbp circular chromosome and two large unstable plasmids, pNRC 100 and pNRC200, 191 and 300 kb, respectively. The NRC-1 chromosome and plasmid pNRC200 have been mapped at low resolution and two BAC (bacterial artificial chromosomal) libraries, each with over 15-fold representation, have been constructed. The plasmid pNRC100 has been sequenced in its entirety. The BAC-end sequence strategy developed for more complex genomes will be used to complete the NRC-1 genome sequencing. This will circumvent sequence assembly problems resulting from the presence of a large number of repeated sequences in the Halobacterium genome. The complete genome sequence will be analyzed using sequence-analysis programs from NCBI, the University of Washington and Genetics Computer Group software packages. Genes with homologues in other organisms will be analyzed by multiple sequence alignments and phylogenetic analysis, as well as through primary literature searches. Genomic analysis will focus on the relationship of halophiles to other Archaea, as well as to eubacteria and eukaryotes, the mechanism of adaptation to high salinity, and the acquisition of new metabolic capabilities such as aerobic respiration, by an Archaeon. This research has the potential to have a significant impact in the area of biotechnology, stress biology - specifically in the area of salt tolerance, and systematic biology.