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In E.coli strain SMS35 a complete absence of CRISPR2 was detected due to a recent insertion of a sucrose operon (Figure 2).
This split easily indicates that the LTRs with the faster substitution rates are those of a more recent insertion time, namely the ERVK2, ERVK7 and ERVK9 along the Human-Chimp branch.
The first includes a regional change in GC skew suggesting either a recent insertion or inversion whereas the second includes a region with GC content significantly different from that of the surrounding sequences suggesting a recent horizontal aquisition.
Thus, waterfowl provide a unique source of information for recent insertion events of CR1 elements.
Specifically, more than half of the D. melanogaster elements have identical LTR sequences, indicating very recent insertion.
Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred.
Similar(26)
Independent, relatively recent insertions of TransibSUs, followed by fossilization of the inserted elements, apparently occurred in the genomes of green sea urchin, starfish and oyster (and possibly also in many other species).
However, if the LTR-RT elements are active or have been active in recent evolutionary time, they can only have a lower variance due to coalescence because of new or recent insertions.
Most of these putatively recent insertions (83%) are proviral, consistent with the overall pattern observed in the genome (Table S1).
In this context, we checked mutations in resident NUMTs, compared to the corresponding mitochondrial sequence (captured NUMTs, that are recent insertions, are 100% identical to the mitochondrial DNA).
For more recent insertions, this signal distinguishes retrocopies from non-processed pseudogenes.
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