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We found qualitative differences in the assemblies of whole-animals versus tissues.
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There were some differences in the assembly statistics of different PADs (Table 1).
These repetitive and virtually identical regions are notoriously difficult to assemble and therefore the observed changes may represent differences in the assembly rather than differences in the target genomic DNA sequence.
These may reflect differences in the assembly mechanisms of the virions.
Although we cannot exclude the possibility of subtle differences in the assembly or dynamics of actin and microtubules between wild-type and mutant strains, it seems that the actin- and microtubule-cytoskeletons were unrelated to Sep4 fibers.
What regulates such differences in the assembly pathways?
Differences in the assembly of macromolecular signaling complexes may explain the distinct biological outcomes.
In Figure 5, we see significant differences in the assembly of eleven genomes due to variance in the number of total contigs and repeat contigs.
We focused on differences between the two strains that are supported by reciprocal mapping of raw reads and are therefore independent of differences in the assembly and/or the annotation procedures.
Despite these profound differences in mitochondrial appearance, we observed no obvious alterations in the composition of the various cytochrome complexes, nor were there obvious differences in the assembly of individual electron transfer components using Blue Native Gel analysis.
The prediction of unique genes based on the mapping of reads from the other strain (Additional file 1: Table S2) is independent of differences in the assembly or gene prediction quality and thus should be considered to be more accurate.
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