In particular, since the genomes of Symbiodinium and Perkinsus are available and are really do not appear to be too much for divergent from Apicomplexa compared with Vitrella and Chromera (at least as drawn in Figure 1A of this paper), I wondered what insight was new here and what was a rehashing of old data (with, of course, the addition of two new species).
In contrast, bighorn and domestic are much less divergent which allows for successful direct alignment of reads: over 76% of our quality filtered reads mapped to the reference genome.
RS-82 is similar to other tick defensins, while the remaining are much more divergent; RS-531, for example, was found to be most similar to a wheat defensin.
Although exact quantification of genetic distances without subjective alignment decisions was difficult, intron sequences were clearly much more divergent than exon sequences for all automated or manual alignments considered.
However, the one step method is divergent for heavy damping.
For instance, Goodenia and Musa are highly divergent for atp1 but only moderately divergent for cox1.
See reply to reviewers 1 and 2; briefly, alignments of homologs detected by HHpred are often much more divergent than traditional alignments of homologs detected, for instance, by psi-blast, which does not rely on secondary structure.
However, sequences of the 5' halves were much more divergent, with pairwise comparisons yielding sequence identities of 70% or less for some isolates.
The much more divergent foraminiferal SSU rDNA was only identified later, after primers specific for the group were developed [ 11].
We have previously observed that the HD1/HD2 alleles of some red yeasts are much more divergent than the correspondent PR genes [ 24], and therefore less suitable for comparisons involving more distantly related species.
