DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

126. Sequencing Microbial Genomes of Relevance to Global Climate Change

J. E. Lamerdin¹, K. Burkhart-Schultz¹, A. Arellano¹, S. Stilwagen¹, A. Erler¹, A. Kobayashi¹, M. Shah⁴, D. J. Arp², A. B. Hooper³, S. W. Chisholm⁵, G. Rocap⁶, E. Branscomb⁷, and F. Larimer⁴

¹Joint Genome Institute, Lawrence Livermore National Laboratory, Livermore, CA., ²Botany and Plant Pathology Department, Oregon State University, Corvallis, OR, ³Department of Biochemistry, University of Minnesota, St. Paul, MN, ⁴Oak Ridge National Laboratory, Oak Ridge, TN, ⁵Departments of Civil and Environmental Engineering and Biology, Massachusetts Institute of Technology , Cambridge, MA, ⁶Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program, Cambridge, MA, ⁷Joint Genome Institute, Production Sequencing Facility, Walnut Creek, CA

lamerdin1@llnl.gov

The Joint Genome Institute (JGI) has established a new program to sequence the genomes of microorganisms that may significantly impact global climate. This effort is focused initially on five microorganisms: Nitrosomonas europaea, Rhodopseudomonas palustris, Nostoc punctiforme, and two marine cyanobacteria, Prochlorococcus marinus and Synechococcus. The common theme shared by these microbes is that all are autotrophic, fairly numerous within their respective ecosystems, and contribute materially to carbon cycling or biomass production (with the exception of N. europaea). By systematic analysis of each genome, we hope to identify specialized nutrient uptake systems, pathways that contribute to or regulate nitrogen fixation, carbon cycling and photosynthesis. With this knowledge, it may be possible to maximize the carbon recycling capabilities of these organisms.

We have completed the initial data generation phase for N. europaea and P. marinus, which yielded >95% of the genomic sequence for each microbe. (Progress towards completion can be monitored through our web site: http://bbrp.llnl.gov/jgi/ microbial/). A similar level of coverage is anticipated for R. palustris by mid-March. Finishing is underway on the first two organisms, and we expect closure by Spring of 2000. The level of coverage achieved by the 'shotgun' phase is readily amenable to generating a rough inventory of the types of genes present in each organism. Preliminary analyses have been performed on N. europaea and P. marinus and the results are available on our web site. The resulting gene 'catalogues' provide the scientific user community access to the contents of unfinished sequence data in a consumable format, without the need for protracted data manipulations on their part. At this meeting, we will present some of the surprising findings that are emerging from the analyses of these two genomes.

This work was performed under the auspices of the U.S. DOE by LLNL under contract no. W-7405-ENG-48.