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The formation of multi-replicon genomes, in which the basic genomic information is split between various replicons, seems to be beneficial to bacteria.
This observation was recently extended to vertebrate genomes, in which the above three genomic features are anticorrelated with the chromosomal length [ 46].
For many years, TEs were thought to be genomic parasites that did not contribute functionally relevant sequences to the genomes in which they reside [ 2, 3].
These "non-conserved" miRNAs are most often represented by single genes in the genomes in which they are found.
The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions.
Importantly, CatSperβ is present in genomes in which CatSpers are identified, but is missing in genomes that lack CatSpers.
Alternatively, genomes in which particular rearrangements have not taken place might be destroyed by R activity (Figure 1B (i)).
These genomes were used to create model genomes in which the position and origin of each horizontal transfer is known.
It is not clear whether these changes indeed represent true recurrent mutations or whether this portion of the Mus genome has evolved with a very different history than the genomes in which it resides.
This is sufficient for highly curated genomes in which pseudogenes have already been annotated.
Because myosins are large proteins we only used those genomes in which we could unambiguously reconstruct all myosins.
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