13 May 2013

Bladderwort: tiny plant, tiny genome, weird name. So what?

My dad emailed me a link this morning. Then a NESCent coworker passed along another. Then my boyfriend tagged me in a post linking a similar article on Facebook.

All those news articles refer to a recent paper (Ibarra-Laclette et al., 2013, Nature) which reports on a newly sequenced plant genome (Utricularia gibba). YAWN, we all say, it's a silly little plant and we can't even eat! What makes it news worthy?

Turns out there are a few reasons why. First, it's called badderwort, and that's just funny. Second, bladderworts are a wickedly awesome type of carnivorous plant which capture prey by rapidly sucking them into bladder-like traps (complete with a trapdoor!).

Then there are a whole slew of other (more "publishable-in-Nature") type reasons to care about bladderworts. This species has a remarkably small genome but still possesses the same number of genes as other plants surveyed. Most of the news articles linked above talk about the implications of the research for our understanding of "junk DNA," or portions of the genome which do not code for protein sequences. It's admittedly a hot topic in science news right now, following heavy on the heels of research in human genomics suggesting that a large portion of the human genome is junk (EDIT: but still functional). The repercussions of the bladderwort genome research is that junk DNA isn't really necessary for "healthy organisms," as we now have an example of one species which has managed to "throw out" junk DNA.

I find the bladderwort research interesting for a few reasons. First, my professional research interests revolve around junk DNA and how changes in genome size affect organisms. The main focus of my research here at NESCent is comparative genomics of a group of plants called Asparagales (includes agave, onion, iris, orchid, asparagus). Species in Asparagales have genomes which range from very small (i.e., a few times larger than bladderwort) to ginormous (200,000 times larger); the variation in genome size is like due at least in part to junk DNA. The conclusions from the bladderwort news articles are kind of no-brainers: OF COURSE plants can persist quite happily without tons of junk DNA. There are fungal species which entirely lack junk DNA, too.

I'm also pretty tired of the semantics surrounding the "Is junk DNA important?" argument, which has been very well described elsewhere (and there's concomitant throwback from the creationist community as well, but that's for another day). To me, junk DNA is just another source of mutation. In the context of evolutionary biology, junk DNA provides more opportunity for evolutionary innovation. That's a hypothesis which is better tested with a broad sampling of species' genomes to infer changes over time. A snapshot of a single genome at a single point in time can't tell you as much as broad comparisons. Asking about the relevance of junk DNA to an organism living today is like asking whether money is required for humans to survive. In a strict sense, currency ISN'T required for humans to persist. It IS a means to an end, though, and a mechanism through which contemporary humans purchase food, shelter, and other resources required to survive. That might be a crappy analogy.

A better question to ask from the bladderwort research is what pathways allow for regulation of junk DNA and other mechanisms of genome downsizing. It's not just about the ability of the bladderwort genome to remove sequences already present. It's also about the ability of the genome to prevent other sequences from incorporating themselves into extant sequences, since some junk DNA is derived from viruses and the genome can be continually invaded. There is also evidence the bladderwort genome has undergone whole genome duplications at least three times, but has managed to remove most of the extra genetic material (including extra genes!) after each event. Now THAT'S some cool science.

Architecture and evolution of a minute plant genome, Ibarra-Laclette et al., Nature (2013) doi:10.1038/nature12132


Jared Decker said...

I think the human ENCODE project concluded (with much criticized hype) that there is not "junk" DNA in the genome. http://www.sciencemag.org/content/337/6099/1159.full

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