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When sequences were simulated without rate heterogeneity, Blast misclassified much more sequences of the three youngest categories, affecting genes of almost all rate categories.
Among them there are two previously reported CLS_cap from two actinobacteria [ 31], and according to our phylogenetic analysis, much more sequences from actinobacteria (88 of the 148 sequenced actinobacterial species) and some other bacteria including diverse proteobacteria and others are CLS_cap (data not shown).
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"Maybe this is a hybrid species, but I'm not convinced from the genetic data that it is," says evolutionary geneticist Jerry Coyne of the University of Chicago in Illinois, who says much more sequencing would need to be done to prove H. heurippa is a hybrid.
The C-terminal quarter of the protein, while always highly charged, shows much more sequence diversity.
First, potentially much more sequence can be probed on a single RA than the 2.5 3.5 kb generally used today for MLST.
However, in the case of FIV, much more sequence information is necessary to fully understand the similar diversity of FIV and HIV.
The translated SplB (BPUM_1283) sequence is highly conserved in B. pumilus, but SplA (BPUM_1282) shows much more sequence diversity among B. pumilus, B. subtilis, and B. licheniformis (Table 2), indicating possible differences in SP lyase genetic regulation.
The resulting trees (Figure S1A, B) are not fully resolved indicated by bootstrap values below 95%, but do not contradict other reconstructions of primate phylogeny that use much more sequence data [21].
Much more sequencing is necessary for WGS.
The C2AB region is highly conserved whereas the N-terminal portion has much more sequence variation.
However, the C' and D' box are nonconserved and exhibit much more sequence-degeneracy than their C and D box counterparts.
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