99. The primer sequences were designed using PerlPrimer v1.1.14 [http://perlprimer.sourceforge.net] OICR-9429 manufacturer and are described in table 1. All primers were synthesized by MDV3100 purchase integrated DNA Technologies and were purified by standard desalting. PCR products were sequenced to confirm specificity of the primers and all amplified a single, specific target. Data were analyzed by the Opticon Monitor 3 software (Bio-Rad) which uses the ΔCT method. The average copy number
of integrated phage was compared to the expected number based on published sequence data and the difference was statistically analyzed with a two-tailed t-test. The correlation tests between the three WO phages and wRi were performed using the Pearson Product Moment Correlation test. When determining the relative copy number for each of the phage types, it was assumed that integrated prophage sequences would amplify with the same efficiency as sequences from mature virus particles. Sequence
analysis Annotated genomes of Wolbachia strains wMel [GenBank:NC_002978]  and wRi [GenBank:NC_012416] , and phage strains WOCauB2 [GenBank:AB478515] , and WOVitA [GenBank:HQ906662]  were retrieved . The phage regions [WRi_005250-005970] (WORiB) and [WRi_006570-WRi_007250] (WORiC) from the wRi genome were used for whole phage genome alignments. The region [WD0562-WD0646] from the wMel genome was used for WOMelB genome alignments. Whole genome comparisons were performed using the Mauve plug-in v.2.2.0  for Geneious v5.4.4 . The predicted amino acid sequences for the large terminase subunit and baseplate assembly gene W were used for phylogenetic analysis. Proteins were aligned buy INCB018424 using the ClustalW multiple alignment algorithm implemented in Geneious v5.4.4. . Model selection was performed using Prottest 2.4  with Akaike’s information criterion (AIC)
used to select for an appropriate evolutionary model for each data set [terminase (JTT+I+Γ+F) and baseplate assembly protein W (JTT+Γ)] prior to analysis. The evolutionary history was inferred for both genes using the maximum likelihood method. Phylogenetic Methane monooxygenase trees generated by PHYML used 1000 bootstrap replicated datasets and estimated gamma distribution and proportion of invariable sites . Results Presence and activity of WO prophages in Wolbachia of D. simulans When lytic viruses replicate and lyse host cells, they do so through an enzymatic process involving a two component cell lysis system of a holin and lysozyme . To date, there is no direct evidence that the WO phages of wRi are capable of enzymatic lysis of bacterial hosts. Therefore, the term “”lytic”" is not used here to describe phage or phage DNA detected in excess of the integrated prophage genomes. Instead, replicating WO is referred to as a mature, extrachromosomal, or active phage. WO phages in wMel and wRi have been classically referred to as WO-A, WO-B, and WO-C [4, 10].