These sequences vary slightly between pseudogenes, for example is more typically LQAEEI to KNRG for msp3 pseudogenes from A. marginale subspecies centrale, but the locations can readily be identified by alignment. Comparing pyrosequencing data to all the known msp2 and msp3 genes showed that all msp2 pseudogenes with the best match in the heterologous strain below 92% variable region identity were detected as absent (−) and all msp3 pseudogenes with below
97% variable region identity were detected as absent (−) ( Table 1). Since the Mosaik alignment parameter −mmp allows a 5% error in aligning reads, we conservatively estimate that variant genes are detected as absent if they have <90% identity, but may not be detected as absent if they have >90% identity. In this study we examined the presence or absence of the pfam01617 buy RAD001 superfamily including genes encoding OMPs 1 through 15, OPAG1-3 and MSP4  and ; proteins identified by surface cross-linking including their encoding
genes AM366, 712, 779, 780, 854, 1011, 1051 ; and type 4 secretion system genes AM030, 097, 810, 811, 812, 813, 814, 815, 1053, 1312, 1313, 1314, 1315, 1316 . Numbering refers to annotations of the St. Maries, Idaho strain, CP000030. find more To be defined as conserved in A. marginale in Table 4 no segment of the genes was detected as absent in any comparisons of pyrosequenced data from each of 10 U.S. strains of A. marginale with the fully sequenced genomes of Florida and St. Maries, Idaho strains. Pyrosequencing data was previously obtained for A. marginale strains Puerto second Rico, Mississippi and Virginia and in the present study for A. marginale strains Florida, Florida-relapse, Florida-Okeechobee, St. Maries-Idaho, South Idaho, Oklahoma and Washington-O. The average genome coverages were 40×, 12×, 63×, 59×, 76×,
47×, 117×, 37×, 96×, and 108× for the ten strains, respectively, when compared to the completed genome from the Florida strain. Since we did not have current access to the Mississippi strain and coverage was lower for this strain, we also verified that no gene was determined as not conserved solely because of absence in this one strain. The number of high confidence differences between strains (Table 3) was analyzed using Roche/454 gsMapper software to generate the 454HCDiffs.txt file. The base differences and their locations were extracted with the unix grep command and imported into Excel 2008 (Microsoft, Redmond, WA). The number of differences and their respective frequencies (the percentage of different reads versus total reads that fully span the difference location) were tabulated. Finally, for coverage and SNP analyses in Fig. 4 and Table 5, the BAM files generated by Mosaik were processed by samtools version 0.12 to generate pileups. Pileups for genes of interest were extracted to determine coverage for each nucleotide position comparing to both the Florida and St. Maries strains. Final coverages for each gene of interest were graphed using Excel 2008.