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

The plant and animal genome conference is held every January in San Diego California. This will be my first year attending and I wanted to get a sense of where the researchers I’ll be listening to and mingling with are coming from.

1. The USDA (145 attendees)
2. Iowa State University (45 attendees)
3. *Cornell University (37 attendees)
4. (3) *University of California – Davis (37 attendees)
5. University of Minnesota (25 attendees)
6. *University of Georgia (22 attendees)
7. (6) *Washington State University (22 attendees)
8. University of Illinois (21 attendees)
9. University of Florida (19 attendees)
10. Texas A&M (17 attendees)
11. *North Carolina State University (15 attendees)
12. (11) *North Dakota State University (15 attendees)
    
13. (11) *Pennsylvania State University (15 attendees)
14. 14th is also a three-way tie between Clemson, Kansas and Oregon State (all with 14 attendees)

All attendee numbers are based on hastily written regular expressions and people can find a whole bunch of different ways to write the name of the same university, so these numbers should be take, at best, as minimum estimates.

Huazhong Agricultural University deserves some special recognition as the highest ranked organization based outside of the US, sending at least 13 researchers to PAG.

Last spring I did a similar calculation for this year’s maize genetics conference. Three institutions overlap between the two lists: Iowa State (ranked #5 at the maize meetings), Cornell (ranked #1), and the University of Florida (ranked #7)

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.

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.

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…)

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.

Cacao seed pood. Source: H. Zell, wikimedia (click to see photo in its original context)

Today’s addition to the list of available plant genome sequences has been on my mental list of missing in action genome projects for quite some time: Theobroma cacao, the tree whose seeds provide the world with chocolate. The sequencing of the cacao genome was announced with great fanfare back in 2008. I distinctly remember discussing the announcement with a several grad students while on a tour to see Iowa State’s recently acquired Illumina sequencer. (That’s right I hadn’t even started grad school out here on the coast when this genome project was announced.)

The Genome:

The cocao tree has ten chromosomes. The genome project was able to assemble a little more than 92% of the genome into pseudomolecules representing those ten chromosomes.* The remainder of the genome was assembled into smaller pieces of sequence that have not yet been accurately assigned to a chromosome. The genome already has a preliminary set of genes annotated onto it (~35,000 gene models). The entire genome is estimated to be ~400 megabases, which is quite reasonable sized as genomes go and the press release mentions that the genome has been sequenced to 200-fold coverage (can this be right, it seems absurdly high?) using a mixture of 454 and Illumina sequencing. At the opposite extreme from technical stats like that, David Kuhn, one of the people involved in the genome project was quoted in the Washington Post describing it as “a very well-behaved genome” and I’m intrigued to find out what he means by that.

The genome is already released, and can be downloaded from this website. The appear to be no Fort Lauderdale restrictions, which means people can begin asking questions of the genome and publishing the answers they discover today!

The Plant: (more…)

I’m assuming most of the people who read this site also follow the posts going up on Biofortified, but in case you don’t, Kevin Folta has a great new post up on why so few horticultural crops (think fruits and vegetables) have commercial available genetically engineered varieties (at the moment the only two you have any chance of finding in the grocery store are virus resistant papayas and crook-necked squash). I found this part particularly maddening, but there’s a lot of other points he brings up that many people probably haven’t considered.

After all of the regulatory hurdles the product still may not be commercialized, mostly based on public perception. For instance, it cost nearly half a million dollars to build raspberry plants resistant to the Raspberry Bushy Dwarf Virus, a devastating disease.  While the plants work brilliantly, the industry suggested they not be commercialized due to public fears.

The other problems are from coordinated attacks by anti-GE groups.  In 2007, while ‘Honeysweet’ was in the process of deregulation, instructions on gmofreetrees.com provided details to cut-and-paste complaints into websites of federal agencies. Of the 1725 notes provided, 1708 were negative to ‘Honeysweet’ deregulation, but all followed the cut-and-paste format.

But don’t stop here, read the rest of the post!

Milkweed seed pod. Source: ms.Tea,flickr (click to see photo in its original context)

The first genome I bring news of isn’t available yet, but I’ll be very interested to see the results when it is. The species is Asclepias syriaca, but the name you’re more likely to recognize is milkweed. These plants grow all over the place back home. If you’re not familiar with them, their most distinctive trait (in my own opinion) are their seedpods (pictured on the right). The name, which I believe applies to the whole genus Asclepias, comes from the white latexy — and toxic! — sap that oozes from broken leaves or stems. The other reason to be familiar with these plants is that they serve as the sole source of food for monarch butterfly caterpillars. The caterpillars retain so much of the defensive toxins produced by milkweed plants that adult butterflies are in turn toxic to many predators.

So that’s why milkweed the species is cool. What’s interesting about milkweed the genome? (more…)

Happy labor day if you’re somewhere that celebrates it. If you’re not, consider my working from lab an act of solidarity with you, although in all honesty it’s more not-wanting-to-take-six-years-to-finish-grad-school.

I’ve been meaning to thank all of you again, August was the first time traffic on this site has come close to matching the levels seen right after the maize genome was published. And while that shouldn’t matter (most of the benefit I get from this site is practice articulating scientific concepts, and that would work almost as well if I was just talking to myself), it’s great to know people are actually reading some of it.

I’ve got a couple of new additions to our list of published and in progress plant genomes, which I’ll try to get updated tomorrow.

Until then, I leave you with this comic.

Sweet Cherry and Pear. (You have to scroll down to the bottom of the section, there are a lot of in-progress genomes out there.) Both being worked on by a group at Washington State that was also involved in the just published apple genome (although it looks like it will take a little longer for the sequence itself to come out). Pear is a close relative of apple, while sweet cherries are closely related to peaches, a species for which a truly excellent assembled genome has been released but remains unpublished (the opposite of the situation with apple at the moment).

I’d just like to add this is the first time I’ve been able to add new genomes to the list because someone involved in the genome sequencing projects pointed them out to me. This is an excellent development that I hope to see continue in the future!

More on the sweet cherry genome project.

What would people like me do without public domain images from the USDA?