Furthermore a similar approach might be applied to detect other symbionts such as Sodalis glossinidius (secondary symbiont of Glossina) and the primary symbiont Candidatus Sodalis pierantonius str. SOPE of the weevil Sitophilus orizae. Both symbiont genomes exhibit more than 20% of repetitive DNA rendering them appropriate candidates for repeat-based PCR analysis [16, 17]. However, we anticipate that such a method reaches its limit when dealing with symbiont genomes, which have become highly streamlined in the course of tight host-symbiont coevolution. Methods Drosophila and Glossina strains plus

hybrid samples Drosophila specimens included members of New world and Old world Selleckchem 8-Bromo-cAMP clades (Additional file 2). Representatives of the new world clade were Drosophila paulistorum semispecies AM, RG-7388 mouse CA and OR, together with Wolbachia-infected (Dw + ) and -uninfected (Dw – ) D. willistoni (see Additional file 2 for details). The Old world clade was represented by Wolbachia-infected D. melanogaster (Dm +) and Wolbachia-infected (Ds +) and uninfected (Ds -) D. simulans (Additional

file 2). Additionally, the tsetse fly species Glossina swynnertoni and G. morsitans morsitans (genus Glossina, superfamily Hippoboscoidea) and hybrids from D. paulistorum (A/O) and Glossina (Gs/Gm) were included (Additional file 2). Detailed descriptions of establishing hybrid samples check details can be found in [11, 12]. Drosophila strains are permanently maintained in the Laboratory of Genome Dynamics in Vienna, Glossina colonies are kept at the Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria. Analysis of complete and draft Wolbachia genomes for candidate marker loci and primer design Dichloromethane dehalogenase Candidate multicopy marker regions were identified by running

nucmer and repeat-match from the MUMmer 3 package [18] on the wMel genome (Wolbachia, endosymbiont of Drosophila melanogaster; GenBank reference NC_002978). Searches were performed with the megablast algorithm using default settings against 14 Wolbachia genomes present in GenBank (see Table 1; http://​www.​ncbi.​nlm.​nih.​gov) and other analyses were performed using Geneious 5.6.6 software (Biomatters, New Zealand). Diagnostic wsp-, IS5-, ARM- and 12S rRNA-PCR Primer pairs for diagnostic wsp-PCR were taken from [19] and the corresponding PCR set-up is described in [11]. Primers and PCR profile for IS5 can be found in [9]. We designed the following primer set targeting ARM: ARM-F 5’-TTCGCCAATCTGCAGATTAAA-3’ and ARM-R 5’-GTTTTAAACGCTTGACAA-3’. Both primers are positioned in the flanking regions of the VNTR-105 locus in wMel [9, 13], and produce an amplicon of 315 bp constant size. Composition of the locus is shown in Figure 1. Diagnostic ARM-PCR was performed in 20 μl reactions containing 1x reaction buffer, 3.0 mM MgCl2, 0.4 μM of forward and reverse primer, 35 μM dNTPs, 0.