Some genes old, some genes new, some genes borrowed… some genes blue?: February in Genome Biology

February was an unexpectedly busy month for science. A mangy skeleton lying unceremoniously under a concrete parking lot was shown by forensic science to be no lesser a historical figure than the last Plantagenet King of England. To trump Richard III, a once-in-a-century meteor strike in Russia startled stargazers distracted by an asteroid flyby, in a coincidence that I have yet to see a p-value for. But in the genomics world, even stray royals and exploding space rocks cannot compete with the excitement of Florida's annual AGBT conference. In the words of Genome Biology's Editor Clare Garvey: "Rothberg describes a 'future-proof' machine. It's gotta be #agbt13". Yes, machines and the future, that pretty much sums it up.

But, having established that nothing short of – well, a bigfoot genome, perhaps? – could compete with AGBT’s buzz, we tried anyway. By publishing a fabulous February issue.

Some genes old
This month's issue has something of an evolutionary biology flavor to it, exemplified by Nicole King's and Brendan Loftus's studies on the origins of complex life, using the choanoflagellate Salpingoeca rosetta and the amoeba Acanthamoeba castellanii as living fossils. Of note, the A. castellanii article reports the first whole-genome assembly of a solitary free-living amoebozoan.

Some genes new
Continuing the evolution theme, transcriptomic studies in a primitive eusocial wasp and in newt regenerative tissue identified a host of genes for which homologs could not be identified in other lineages. Are these new genes part of novel molecular pathways responsible for caste determination and tissue regeneration?

Queen wasps: boring?
Interestingly, it was in worker wasps, rather than queens, that the novel genes were upregulated. This finding might seem counterintuitive, turning on its head the idea of queen supremacy in the insect world's very own Battle of Bosworth. Could it be that queen wasps are the default caste, borne of biology basics, whereas the proles are the unlikely product of evolution's most sophisticated gadgets?

The novel genes found in the newt study have some very different – and problematic – implications. Newts are the closest regenerative species to humans, and hence seen as a good model for regenerative medicine. Although many insights in the study will serve as a foundation for research in this area, the large number of lineage-specific genes up-regulated in regenerative tissue suggests that many of the key molecular tools underlying newt regeneration may not be available in human cells. However, recent innovations in genome engineering (digested in a Research Highlight by Srinivasan Chandrasegaran) may prove to be a 'Get Out Of Jail Free' card for this type of medical dead end, where the organism’s gene composition is the limiting factor.

Some genes borrowed
Horizontal gene transfer (HGT), where genes are transferred from one organism to another rather than inherited from a parent, can be a thorn in the side of phylogeneticists. Instead of nice, neat evolutionary trees, HGT pushes phylogenies in the direction of complex squiggles. But studying these 'borrowed' genes can also provide useful insights into interactions between neighboring species and into the selective pressures at work in adaptive evolution.

The form of HGT most frequently discussed in the literature is prokaryote-to-prokaryote; however, gene transfers can also take place between prokaryotes and a different type of microbe: parasitic eukaryotes. A survey of this form of HGT revealed gene acquisitions from human microbiota, as well as a preference for genes in core enzymatic pathways, perhaps due to pressures on the parasite to adapt to its host environment. A second example of HGT in eukaryotes can be found in the aforementioned A. castellanii genome, which includes many genes thought to have been transferred from other kingdoms of life.

Some genes blue?
If you read this far just to find out what I meant by "some genes blue" then, sorry, I got nothing. But you might be interested to read about SOAPfuse, the latest addition to the BGI's 'SOAP' software suite for short read analysis; or our latest RBPome study, about the global footprint of RNA binding proteins in yeast; or about how nuclear envelope proteins contribute to chromosome positioning – all also appearing in our February issue.

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