Wolbachia mCGH of Five Supergroup A Strains

Using microarray-based comparative genome hybridizations (mCGH), the genomic content of Wolbachia pipientis wMel from Drosophila melanogaster was compared to the Wolbachia from D. innubila (wInn), D. santomea (wSan), and three strains from D. simulans (wAu, wRi, wSim). Cy3- and Cy5-labeled probes were synthesized from a pool of three distinct GenomiPhi amplifications to reduce bias. One flip-dye experiment (two hybridizations) was performed with each of three independent pools, yielding a total of six hybridizations/strain. With 4-8 printed replicates per slide this yielded 24-48 replicated spots per gene to compare across the study. Ratios were normalized using iterative log mode centering. The geometric mean ratio was calculated for all good spots in each flip-dye experiment.