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I know jawed vertebrates have a lot of junk DNA floating around coming from ancient retroviruses. Some of the DNA is important to mammalian evolution. The DNA also provides a useful means to study the evolution of viruses.

I wonder if similar things happen for other lifeforms. I know parasitic wasps have a very interesting story even if I don't know the details.

I suppose even if viruses inserted themselves into microbes that microbes have much more pressure to have less DNA and so they may have gained genes but the evidence of junk DNA would have long ago been lost.

I suppose I'm asking: did ancient viruses insert themselves into other life in a similar manner to the endogenous retroviruses found in vertebrates and would we have evidence of it today in a similar manner?

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I would not say that they are “equivalents” of endogenous retroviruses, but there are two types of elements in bacteria that bear some similarity.

Prophages

As some bacterial virus (phages) can undergo lysogeny as well as causing lysis of the host (e.g. phage lambda) it is not surprising that there are traces of phages in almost all sequenced bacterial genomes, although it is not always easy to detect and/or identify them unequivocally. This was reviewed by Casjens in 2003 who considered its significance in terms of the evolution of both phage and bacteria.

Of course, the structure of such phages differs from that of endogenous retroviruses and is generally much more complex.

Insertion Elements (IS)

To some extent endogenous retroviruses can be considered as retrotransposons elements, and this is certainly the case for the related LINE (L1) elements. So perhaps the bacterial insertion elements — the IS transposons — are worth mentioning. The structure of one class is shown below.

Composite transposon

(Source: https://commons.wikimedia.org/wiki/File:Composite_transposon.svg)

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