The main goal of this proposal is to develop a meaningful basis by which to measure field isolate variability in Mycoplasma hyopneumoniae that can correlate to virulence and/or protection from vaccination. In order to do this, we will sequence the genome of multiple field isolates of M. hyopneumoniae and then assess the genetic variability in well-known, but poorly understood gene family members such as P97 – P102 along with less well-known lipoproteins on the cell surface. Our collection of single-colony, cloned isolates includes recent and older isolates from the Midwest of the United States, one isolate from Belgium and two isolates from Australia. Genome libraries were prepared and sequencing was performed at the University of Washington High Throughput Genomics Unit on the Illumina platform and at the University of Iowa Genomics Division on the 454 FLX platform. The sequence data has been assembled using the Illumina data, and we are currently analyzing the assembled genomes for amino acid variability in the P97-P102 gene families and in the 53 surface lipoproteins to complete the objectives.