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Entries in genomics (4)


Whale Sharks on Mother Nature Network

Our whale shark genome project is featured in this short video on Mother Nature Network this week.  It’s got some sound bites from the Georgia Aquarium president David Kimmel, as well as Emory University research scientist Ryan Weil and yours truly.


Whale shark genome schwag has been unbridled!

This is so cool!  To raise funds for the whale shark genomics research on which I am one of the lead investigators, Georgia Aquarium has had a limited run of custom Silly Bands made - that latest of wildly popular kids fashion accessories.  In each pack is a band for each letter of the genetic code (for the non-biologists among you, that’s A, C, T and G), as well as a first-of-its-kind whale shark and the Aquarium’s spiffy G-fish logo.  With these bad-boys your kids can be fashionable and learn about genetics and marine biology at the same time.  Its not just for kids; heck, I am wearing them right now (and I feel cooler already!)

 The exclusive whale shark genome Silly Bands. Go on, you know you want them.

They’re exclusive to the aquarium and you can bask in the glow of their rubbery goodness for just $3 a pack, with all proceeds going to the whale shark genome project.  The best way to get them is to visit the aquarium in downtown Atlanta, but if you’re not in the ATL, don’t despair; if you buy five or more packs (i.e. $15), you can send a check directly to Stephanie at the address below and she’ll send them right to you.  PLUS you get to say you helped scientists at the Aquarium and Emory University to sequence the genome of the world’s largest fish, as well as participating in the craziest bit of crowd-sourced science funding ever.  SCIENCE - love it!


Stephanie Brown

Assistant Manager

Georgia Aquarium

225 Baker Street

Atlanta, GA 30313

(please make checks out to “Georgia Aquarium”)

Georgia Aquarium is a 501(c)3 not-for-profit institution


While we're talking genomes...'s something distinctly more marine. 

ResearchBlogging.orgA little while ago I drew attention to Andrea Marshall's paper showing that there's not one but possibly three species of manta ray (see Whats A Manta Do?).  In the preamble for that post, I drew analogy between mantas and killer whales as monotypic species; that is, the only members of their genus, a taxonomic one-of-a-kind.  Well blow me down if some new genomics work with killer whales doesn't suggest that there's more than one species of those, too!  Morin and colleagues used a different approach than Marshall, whose work was mostly based on colors and patterns and tooth shape.  Instead, they used "massively parallel pyrosequencing" (try saying that with a mouth full of marbles) to show genetic differences in the mitochondrial genome.  So what the heck does that mean?  Well, lets just say its sequencing a whole bunch of DNA at once, using DNA not from the nucleus of the cell, but from its engine room: the mitochondrion.  The technology is actually a really, fantastic example of miniaturisation; perhaps I'll write about it one day.  But, I digress...  Morin and friends recommend three species of Orcinus orca, with two more subspecies as well.  Subspecies are not required by the taxonomic code, but they are eligible for separate protections under the Endangered Species Act, so its a meaningful result for conservation biologists too; they'll now have to make assessments of each species and subspecies to see which, if any, require additional protections.

To the experts, its not a total surprise that there are multiple species in either of these groups.  You can bet your bum that they set out to confirm a hunch that there are more than one, leaving the surprise for the rest of us less familiar with these beasties and who never saw the subtle differences.  That's OK, I like surprises, especially when they involve new and unexplored diversity, right under our noses.  Maybe we should take a harder look at a few more monotypics, for the inevitable species flocks hiding in the details or the DNA.  Whale sharks, basking sharks, Mola, anyone?

Morin, P., Archer, F., Foote, A., Vilstrup, J., Allen, E., Wade, P., Durban, J., Parsons, K., Pitman, R., Li, L., Bouffard, P., Abel Nielsen, S., Rasmussen, M., Willerslev, E., Gilbert, M., & Harkins, T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species Genome Research DOI: 10.1101/gr.102954.109


Complete genome from a single cell - well, yes, *technically*

ResearchBlogging.orgIts not quite marine science (hey, its my blog, so nerrr), but there's a paper in PLoS One this week where the authors describe the assembly of a genome sequence (all the DNA from beginning to end) from a single cell of a bacterium.  Normally it would take a whole bunch of cultured cells to do this, which limits genome sequencing to those bacteria that can be cultured and right now that isn't many (probably less than 10%).

Having announced this great achievement (and it is) in their abstract, the authors go on to point out that this particular bacterium, a symbiont from the gut of an insect, is polyploid.  In other words, it has multiple copies of the whole genome per cell - in fact, up to 900 copies!  So, while its technically correct that they sequenced a genome based on a single cell, you'll forgive me for thinking they're gilding the lily a bit.

While we're at it, who is proofing manuscripts at PLoS One these days?  The last sentence of the abstract reads: "This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes."  Huh?

Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., Lapidus, A., Wu, D., McCutcheon, J., McDonald, B., Moran, N., Bristow, J., & Cheng, J. (2010). One Bacterial Cell, One Complete Genome PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010314