30 May 2013

Commelinaceae haunts me...

Old habits die hard. During my dissertation I spent lots of time traveling all over the United States and Mexico collecting species in the plant family Commelinaceae (wandering jews, spiderworts). I've mentioned in passing my propensity to continuously stalk wandering jews maintained as ornamental plants inside buildings. Tradescantia pallida (picture to the left) is frequently planted as ground cover outside in the summer. Despite its perennial growth habit, it was replanted each summer back in Missouri as the winters were too harsh for it to survive freezing. This picture was taken recently on Duke's campus, where it seems to overwinter quite happily and persist in random patches.

I don't get much time with plants now that my research is exclusively computational, so it's nice when ornamentals remind me of how attractive my selected species appear (so pretty, in fact, that I obtained a tattoo of one such flower). Therefore, I'm veritably overflowing with glee when I stumble across a member of Commelinaceae in the wild. I visited a friend's farm this past weekend and came across a really nice population of Callisia graminea (right) growing quite happily in the middle of their property. I spent a summer collecting this species with the intention of looking at range expansion of polyploids compared to their diploid progenitors, and hope to get back to this project someday.

I'm even more tickled when I travel someplace I've never been and see plants unknown to me but clearly Commelinaceae. I came across a number of exemplars from Aneilema and Commelina in Kenya last spring. Even though I don't research those particular genera, I still insisted on pulling the van over so I could take a few photos.

Regardless of where I go, wandering jews follow me. I didn't purposely pick a plant family to research that grows in all sorts of exotic, tropical locations. That's just a bonus!

23 May 2013

Accidental irises.

My boyfriend, Matt, needed to purchase a new cell phone a few weeks back, and asked if I could accompany him to a shopping mall while we ran errands one Saturday. I agreed, careful to tamp back my utter disinterest and anxiety in patronizing that bastion of teenage angst and commercialization on the busiest day of the week.

We arrived at the mall and greeted my fears: scores of teenagers, families with young children, and the occasional lone adult wandering with a shell-shocked expression on their face. We started walking towards the store possessing new phones (indeed, the ticket to my delivery from this monstrosity and ultimate salvation) and my eyes were met with a surprising vista.

A group of tables had been set up in one of the mall's open areas, on which were displayed an amazing array of irises. The Eastern North Carolina Iris Society was showing its award winning exemplars that weekend! Tall, short, bearded, and unbearded were all represented, with a stunning array of colors to boot. Matt indulged me while I wandered through the displays, pausing to examine some particularly lovely coloration or remarking on the cultivar names (botanists are never-endingly creative, see this blog post for some examples).

Looking at irises for a few moments was a welcome reprieve from what would otherwise be a tiresome shopping trip. I was gratified to experience growing excitement in...well, growing things again, as my current job doesn't include the greenhouse and field work to which I'd become accustomed during my graduate work. I was ultimately pleased I had the opportunity to accompany Matt, and was reminded that, just in like science, it's sometimes the serendipitous encounters which yield the biggest rewards.

20 May 2013

Today's reason plants are amazing

While walking to the bus stop last week, I happened upon this lovely example of a wicked cool plant breeding system. Allium (onion) undergoes a form of vegetative apomixis (reproduction without sex) in which little plantlets form where flowers have bloomed. The picture shows an onion growing wild on a North Carolina roadside. The long squiggly line on the bottom right is the scape, or stem which supports the inflorescence (group of flowers). I'm holding the inflorescence, which has a few small and one REALLY BIG plantlet growing out of it. These can become individual plants. Remember that in the case of onion, there are bulbs growing below ground which are also producing little bulblets, which is another form of vegetative reproduction.

15 May 2013

Bladderwort revisited: Because the fun never ends in Junk DNA Land!

I've had some feedback and read additional commentary posted elsewhere about the bladderwort news I posted about earlier this week and feel compelled to post a follow-up. I also just submitted revisions to a manuscript, which means I'm validated in indulging my whims of...continued professional development via blogging?

Anyway, I particularly like Jonathan Eisen's Twisted Tree of Life award to MSNBC's coverage of the bladderwort study. His argument is compelling and his rhetoric is golden.

Next, my friend Jared astutely pointed out in a comment on my last post that I appear to have misrepresented the research from the ENCODE project. Again, here I fell victim to a common folly among transposable element researchers. I've adopted the term "junk DNA" to refer to any non-coding sequence in a genome, whereas others use the term in a functional sense (i.e., junk DNA is a sequence to which function has not been ascribed). I've since edited the previous post to reflect my viewpoint. Simply put, a large portion of the human genome is comprised of transposable elements and other non-protein coding sequence, yet contemporary research indicates many of these sequences still perform functions necessary to organism function. I appreciate the comment, Jared, and am so grateful for folks like you who help me stay on my toes!

Finally, there was also my embarrassing gaffe in mistyping "Badderwort" in my title of the original post. It's since been corrected, but will live on in the automatically generated permanent web address. It's ok, though, because the bladderwort is definitely the baddest of the worts regardless.

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

03 May 2013

Spring Fling!

Today is the day everyone at NESCent talks for three minutes and we get to throw things at them if the go over time (see pic). So exciting!