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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Research » Publications at this Location » Publication #132695
Title: THE FIBROBACTER SUCCINOGENES STRAIN S85 GENOME SEQUENCING PROJECT

Author
item NELSON, K - TIGER, ROCKVILLE, MD
item AMINOV, R - TIGER, ROCKVILLE, MD
item FORSBERG, C - UNIVERSITY OF GUELPH
item MACKIE, R - UNIVERSITY ILLINOIS
item Russell, James
item WHITE, B - UNIVERSITY ILLINOIS
item WILSON, D - CORNELL UNIVERSITY
item MULLIGAN, S - TIGER, ROCKVILLE, MD
item TRAN, K - TIGER, ROCKVILLE, MD
item MORRISON, M - OHIO STATE UNIVERSITY

Submitted to: Symposium on Rumen Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 6/15/2002
Publication Date: 4/4/2004
Citation: Nelson, K., Aminov, R., Forsberg, C., Mackie, R.I., Russell, J.B., White, B.A., Wilson, D.B., Mulligan, S., Tran, K., Morrison, M. 2004. The fibrobacter succinogenes strain s85 genome sequencing project. Symposium on Rumen Microbiology. p. 41.

Interpretive Summary:

Technical Abstract: The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria (hereafter referred to as the Consortium) was established in 2000, and our overarching objective is to generate and exploit genomics-based information to better understand the genetics, physiology and ecology of bacteria underpinning ruminal fiber degradation. We report here the progress to date with the Fibrobacter succinogenes S85 genome project. The random sequencing phase of the project was completed in January 2002, from 75,461 sequences with an average edited length of 641 bp. There were 266 assemblies, for a total of 3.916 Mbp, approximately 0.5 Mbp larger than the genome size predicted from physical maps. Of the initial 179 sequencing gaps identified, no less than 120 were closed with editing and the first round of closure sequencing reactions. The sequence data has been searchable since July 2001, at www.tigr.org. From the preliminary gene list, we have identified 24 genes encoding endoglucanases and cellodextrinases from families 2,3,5,8,9,10,13 and 32. Another 23 genes have been identified as encoding xylanases and related enzymes. Many of these genes had not been previously identified in clone libraries propagated in E. coli. Furthermore, we have yet to identify any exo-acting cellulase (from family 6 or 48), nor is there a processive endoglucanase apparent in the genome sequence data available. Both type I and type II secretion systems are present, in addition to Pil-proteins, including Pil-T1 homologs that coordinate twitching motility in other gram-negative eubacteria. There is currently no evidence for chemotaxis gene homologs in the genome sequence. Whole genome annotation by the Consortium should begin in late March or early April.