The genome of strain PCVAL only differs in 4 nucleotides in length from strain PCIT [16], involving five short indel events of one (4 cases) or two nucleotides (1 case). Additionally, 23 nucleotide substitutions were detected. Transitions represent

43.5% (10/23) of the total substitutions. Although the number of mutations is too small to be representative and, therefore, it is difficult to draw clear conclusions, it is noteworthy that all indels plus 87% of the detected substitutions between both strains are located in the coding fraction of the genome, in spite of its low coding density. One of the detected indels affects the start codon of aroC, involved in the biosynthetic pathway of aromatic amino acids, which Ilomastat concentration is then changed to a GTG start codon. Two other short deletions yield the loss (AT) and recovery (T) of the reading frame of ilvD, needed for the synthesis of isoleucine and valine. The non-inactivating character of these mutations on genes involved in biosynthetic pathways of essential amino acids without an ortholog in the genome of M. endobia, corroborates their importance for the bacterial partnership. The other two indels, as well as 20 out of 23 of the observed substitutions, were located at the 3′ end of rplQ, which suggests that this region could be a mutational

hot-spot. To confirm this point, we analyzed the original P. citri DNA samples used in the genome sequencing experiments by PCR amplification of the

rplQ and flanking ITS Temsirolimus in vitro regions, as well as new DNA samples obtained from individual insects cultivated in Almassora (Spain) and from environmental colonies collected in Murcia (Spain). Although all three samples were obtained from different plant hosts and separated by more than 300 Km, they were identical. Since we have no direct availability of the PCIT strain, it is feasible that the Spanish and American populations differ. M. endobia genomes comparison The alignment of both genomes of M. endobia showed that the genome of strain PCVAL is 65 nucleotides shorter than that of PCIT, and allowed the identification of 262 substitutions. PAK6 Among them, 90.1% were G/C↔A/T changes, with only 18 A↔T changes and 8 G↔C changes, which is additional indirect evidence of the mutational bias towards A/T already observed in the codon usage analysis (Additional file 2). As expected for a neutral process, the mutational bias affected both strains equally, being the changes G/C↔A/T evenly distributed (50.4% A/T in strain PCIT and 49.5% in PCVAL). Regarding the genome distribution of the polymorphisms, 47% of them (123) map onto IGRs, and 4.5% (12) onto 10 pseudogenes. The 139 substitutions detected in the coding fraction affect only 111 out of the 406 orthologous genes. Among these substitutions, 77 are synonymous (dS = 0.0011 ± 0,0001), and 62 non-synonymous (dN = 0.0005 ± 0,0000), with a ω = 0.44, suggesting the action of purifying selection.