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This unique indel is heterozygous.
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This Group II Gammaproteobacteria clustering is also supported by the phylogenetic study by Gao et al. [ 42] based on 36 protein data as well as the existence of the unique indel within the RNA polymerase β-subunit (RpoB).
Adding in the unique indels does not significantly change this calculation.
Only 12% of the unique InDels for each strain were within the coding sequence.
Unique indels were shorter than expected overall, but the most significant differences between observed and expected length were found among those unique indels located outside genes, rather than within gene elements (p = 0.007 0.009, Table S2.1A (see Additional file 1)).
The ratio of these unique indels to unique SNVs is higher in DT40 (0.130) than in the L2 and Silkie genomes (0.0919 and 0.0864, respectively).
When examining the distribution of the unique InDels for each strain along the chromosomes, some (chrXVII, X, XI, XV) showed an enrichment of variants (Additional file 11: Figure S4C).
Because we used two reciprocally monophyletic pairs of Portiera genomes (two from B. tabaci biotype B and two from biotype Q), we were able to apply a simple parsimony assumption to predict that these unique indels represent recent mutations (i.e., the derived state).
There are no nonsynonymous SNPs in strain 309 in the 730 kb region carrying the mutation tiny (ti) and there is only one unique indel among the 163 ORFs in this region.
Unique indel loci were selected for PCR-based primer design.
Strain FGSC 1303 contains only one unique indel and no unique SNPs in the 1 Mb region between pyr-1 and ace-4.
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