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

October 22, 2010

“Without plants, we’d be in serious trouble.”

Filed under: Uncategorized — James @ 6:17 pm

No time to talk about this in depth, but here’s a link to an interesting article by Zachary Russ talking about how and why of plant genome sequencing. It’s a good read covering a fair number of fundamentals. I particularly enjoyed this passage:

A small sidebar trumpets the development of “submergence tolerance rice,” expected to greatly increase crop yields in Bangladesh and rescue many of the world’s poor from malnutrition and worse. Dig a little deeper and you’ll find that this rice was produced with precision breeding rather than genetic modification to avoid regulatory testing and public disapproval.

For all the advances in gene delivery and plant modification, these remarkable advances are being impeded by societal apprehension and regulatory hurdles. Indeed, in a recent article, researchers at Oregon State argued that onerous paperwork, excessive containment requirements, and legal liability were effectively strangling biofuel and agricultural GMO R&D.

Thanks to @idtdna for the pointer.

October 20, 2010

“How to grow corn”

Filed under: Uncategorized — James @ 8:57 am

The sort of corn information that has apparently dominated the web in my absence:

I have no words. If it wasn’t so funny I’d be so sorry.

October 19, 2010

So you want to download the apple genome

Filed under: Uncategorized — James @ 3:35 pm

Well depending on what sort of dataset you need for your research today is your lucky day (actually late last week was your lucky day but I’m buried in work and way behind).

Download links for lots of apple genome related data are now available from GDR: The Genome Database for Rosaceae.

One file you’ll be surprised not to find a a link to download the pseudomolecules. (For those reading this who don’t have to work with genomic data, pseudomolecules are continuous DNA sequences of entire chromosomes. Each chromosome is technically a single, incredibly complex, molecule, not unlike water or carbon dioxide.)  From GDR: (more…)

October 4, 2010

JGI Decides to Sequence Barley!

Filed under: Uncategorized — James @ 11:59 am

Barley with two rows of grain (left) and six rows (right). Public domain photo by Xianmin Chang via wikipedia.

After shunning the grasses in 2009 and 2010, the Joint Genome Institute of the US Department of Energy is making up for lost time with their latest set of genome sequencing announcements. There’s probably some organism that will excite anyone on that list, but let me tell you the one that excites me:

JGI is going to sequence the genome of barley (Hordeum vulgare), a reasonably close relative of wheat, an important crop in its own right, and a monster genome (though not as much of a monster as wheat itself).

Barley will be the fourth grass genome sequenced by JGI and the sixth grass genome sequenced in total (baring any secretive grass genome projects I don’t know about, a very real possibility). On the other hand, the barley genome is more than three times bigger than the combined size of all three grasses sequenced by JGI previously. Heck, at five gigabases it’s more than twice the size of the maize genome (one of two grass species, along with rice, sequenced by someone other than JGI)!

Now I assume that, like maize (or humans for that matter), a huge percentage of the barley genome is composed of transposons. I don’t know how JGI plans to handle assembling the genome, but I assume they’re be relaying heavily on the genetic maps developed by the barley community.

If you’re wondering how long it’ll be before this genome becomes available, consider this time-line of previous grass genomes sequenced by JGI:

  • Sorghum bicolor: ~700 megabases
    • Announced as part of the CSP 2006 program
    • Published January 2009
  • Brachypodium distachyon: ~275 megabases
    • Announced as part of the CSP 2007 program
    • Published February 2010
  • Setaria italica (Foxtail millet): ~515 megabases
    • Announced as part of the CSP 2008 program
    • Published: Not yet
  • Hordeum vulgare (Barley) ~5,000 megabases
    • Announced as part of the CSP 2011 program
    • Based on previous time lines expect to see a paper on this genome in early 2014*

So does this announcement have any bearing on my own research? Absolutely not. Even if the barley genome isn’t slowed down at all by representing more total sequence than all previously sequenced grass genomes to date (~4,000 megabases for rice, sorghum, maize, brachypodium, and setaria combined), it still won’t come out until after I’ve hopefully graduated. Does that fact make me any less excited to know it’s getting sequenced? (Or envious of the people who will get to play with the genome before its published?)

Not on your life!

*Estimated based on extrapolation from exactly 2 datapoints so don’t put too much faith in the estimate. If the foxtail millet genome is published early next spring, that will increase to three datapoints.

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