Tuesday, January 12, 2010

More evidence of genomic modularity

Regular readers know of my affinity for all things related to genome evolution and transposition, partly because of my rejection of the common creationist model of mendelian speciation and partly because my understanding of comparative genomics within baramins demands it. Recent studies are beginning to shed light on theoretical links between stress, transposition, and speciation. Over the holidays, there were two additional papers published on this subject.

First, in a paper in Nature, Horie et al. found evidence of bornavirus insertions in mammalian genomes. This is of interest because prior to this, bornaviruses were not known to integrate into genomes. This observation is related to a point I brought up in my review of Liu and Soper's endogenous retrovirus paper in ARJ, where I wrote,
Another implication would be exploring the origin of other viruses. What about DNA viruses? Could they ultimately originate as escaped genomic elements from other critters? Do we know of any other kinds of endogenous viruses? Could this idea be expanded to a general theory of viral origin?
Liu and Soper tried to interpret endogenous retrovirus sequences as the source of exogenous retroviruses (instead of the other way around). In contrast, Horie et al.'s results are far easier to explain as the result of infection by bornaviruses. For one, the bornavirus remnants found came from a single gene, not the whole bornavirus genome. Horie et al. also found evidence of chromosomal integration of that one gene during bornavirus infection. Nevertheless, their results are further evidence that viruses can alter genomic structure (and potentially genome function as well).

A recent paper by Maumus et al. in BMC Genomics looks at stress-induced genome changes in diatoms, a single-celled kind of algae. They looked at retrotransposon activity in the diatom Phaeodactylum tricornutum and found that transcription was especially high when the diatoms were grown in the nitrate-limited media or in the presence of reactive aldehydes. Their conclusion? "Based on these findings we propose that LTR-RTs [retrotransposons] may have been important for promoting genome rearrangements in diatoms." Make that "stress-induced genome rearrangements." Very nice, and nice to see something other than the standard reference organisms getting some attention for a change.

Horie et al. 2010. Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 463:84-87.

Maumus et al. 2009. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics 10:624.