Additionally, LY2874455 cost 60 indels were detected between both M. endobia strains, with a mean size of 5.4 nucleotides, although there is a great variance, between 1 and 75 nucleotides. Results showed 58.3% (35/60) of the indels affect homopolymers of A (22/39), T (12/36) and, less frequently, G (5/37) and C (3/35), which is consistent with the higher proportion of A and T homopolymers. This fact may be related with the above-mentioned A/T mutational bias. Although artifacts due to sequencing errors cannot be ruled out, given
that PCVAL genomes were assembled based on 454 sequencing data, there are several pieces of evidence that indicate that the observed indels may be real. First, although homopolymers can be found both in coding and non-coding regions, most indels affect the non-coding parts of the genome. Second, even when A/T homopolymers are quite abundant in the M. endobia genome (844 cases equal to or bigger than 6 nucleotides), Geneticin concentration only a small fraction of them are affected by indels (29
cases, representing 3.4%). Finally, the coverage of the affected regions was always higher than 27X, and the PCVAL reads polymorphism was almost null. The remaining indels affect microsatellites of 2 to 8 nucleotides with a small number of copies. Forty-seven indels (78.3%) map onto intergenic regions, pseudogenes (2 in ΨpdxB, 1 in ΨprfC) or the non-functional part of shortened genes (dnaX), and only 13 indels (21.7%) map onto coding regions. Most of these are located on the 3′ end of the PDK4 affected gene, causing enlargement or shortening of the ORFs compared with the orthologous gene in other γ-proteobacteria. Thus, glyQ
(involved in translation) and ptsI (participating in the incorporation of sugars to the intermediary metabolism) are enlarged in strain PCVAL, while rppH (involved in RNA catabolism) is shortened in this strain without affecting described functional domains. Conversely, the shortening of fis (encoding a bacterial regulatory protein) in PCVAL, and of yicC (unknown function) and panC (involved in the metabolism of cofactors and vitamins, a function that is incomplete in M. endobia) in PCIT, affect some functional domains, although their activity might not be compromised. Finally, amino acid losses without frameshift were observed in PCVAL (relative to PCIT) for the loci holC (encoding subunit chi of DNA polymerase III), rluB (involved in ribosome maturation), surA (encoding a chaperone involved in proper folding of external membrane proteins), and pitA (encoding an AG-881 in vivo inorganic phosphate transporter).