Supplementary Material for: Comparison of mealybug <i>(Planococcus lilacinus)</i> and fruit fly genomes: isolation and analysis of conserved sequences and their utility in studying synteny in the mealybug

By using ligation-mediated PCR products from mealybug DNA as tester and biotinylated fly DNA as driver, we recovered a fraction of the tester that remains hybridized to driver following high-stringency washing conditions. This fraction is expected to contain mealybug sequences conserved in the fly (MCF). Reciprocal experiments enabled the isolation of fly sequences conserved in the mealybug (FCM). Coding sequences among MCF show amino acid identities &gt;40% with fly proteins, allowing a reliable identification of orthologs. Three sequences from the fly cytogenetic positions 98–99 were hybridized onto mealybug chromosomes and the results identified differences in synteny between the two species. Taken together, our results present a method for direct isolation of sequences conserved between an ‘orphan’ (mealybug) genome and a ‘reference’ (fly) genome and showed that these sequences can be used to study chromosome synteny in the mealybug.