James and the Giant Corn Genetics: Studying the Source Code of Nature

November 9, 2010

Columbine and Foxtail Millet

Filed under: Uncategorized — James @ 4:36 am

The latest version of phytozome (v6) just came out and it includes two genomes people in my lab have been waiting on for a LONG time.

The first is Aquilegia coerulea or Blue Rock Columbine. From a comparative genomics standpoint columbine is important because its a representative of a lineage of eudicots that split off from the two biggest families in that group (the asterid and rosids), very early on. It’s also only the second plant species to be sequenced that’s known for its flowers (the first was Monkey Flower or Mimulus). Most of the ~300 megabase genome is contained within 156 large scaffolds. So not as big as whole chromosomes, but hopefully large enough for some useful syntenic analysis. The sequenced cultivar of Columbine is “Goldsmith.” You can read more details and download the genomic data here.

The second new genome is even more exciting as far as I’m concerned, but that’s because I’m a grass guy. Foxtail millet (Setaria italica) is an important crop in its own right and comes from a tribe of grasses called the Paniceae that was previously unrepresented by any sequenced genome. The Paniceae are relatives of the Andropogoneae, the tribe that contains both maize/corn and sorghum (as well as cool unsequenced species like sugarcane) and the addition of Setaria will do a lot to help balance out grass phylogenetic comparisons.* A second species of Setaria (Setaria viridis) is also being sequenced (likely using this species as a road map to assemble the genome) which is being pushed by one of my old bosses as a good genetic model to study the C4 photosynthesis that makes species in both the Paniceae and Andropogoneae so much more efficient at photosynthesis than species that still do plain old vanilla** C3 photosynthesis. Almost all of the Setaria genome is contained within 24 large scaffolds, which should definitely be big enough for the syntenic analysis my lab likes to do. More details and download links here.

Both genomes are still Fort Lauderdaled, but that only means you can’t PUBLISH on them yet, can’t stop you from looking for cool stuff. That’s what I plan to do myself after lab meeting this morning. Putting this data up on the website also means the clock has started ticking on that restriction. The version of the Fort Lauderdale accord that JGI uses gives the researchers involved in sequencing the genome 12 months to get their paper published. If they don’t manage to do that, the genome becomes fair game for anyone. Which is very useful for people like me planning future research projects. One way or another, I know that by November of 2011 I will be able to publish papers that use insight gained from the Setaria and/or Columbine genomes.***

Normally I’d dig up some pictures and interesting trivia about these species, but it 4:40 in the morning out here on the west coast, so I’m going to wrap this post up and wish you folks on the east coast good morning.

*I hope to explain what I mean by this in a followup post, but I’ve learned to be careful about promising ANY updates in advance.

**I don’t know what kind of photosynthesis vanilla plants carry out.

***I’m sure both groups will beat the deadline for getting their genomes out the door, but I can think of at least one example of a research group sitting on a completely genome indefinitely which is why having early data release and expiration dates on exclusivity is so important.


  1. Thanks for the heads up. I was just mining some data out of the Aquilegia coerulea shotgun reads. Figures the genome would get released after I’m done 🙂

    Comment by Noah Fahlgren — November 9, 2010 @ 9:43 am

  2. Tell me about it. Just finalized a “Pan Grass” gene set last week.

    Comment by James — November 9, 2010 @ 8:05 pm

  3. […] This post was mentioned on Twitter by AgBlogFeed, James. James said: The genomes of Foxtail Millet and Blue Rock Columbine now available for download. More details at J&TGC: http://bit.ly/9n1uJK […]

    Pingback by Tweets that mention Columbine and Foxtail Millet – James and the Giant Corn -- Topsy.com — November 9, 2010 @ 3:20 pm

  4. Sorry to be pedantic, but the genus is spelled “Setaria”, not “Seteria”.

    Comment by JS Hoyer — November 9, 2010 @ 9:03 pm

  5. Fixed thanks.

    Comment by James — November 9, 2010 @ 9:20 pm

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