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research stories

The long genome drought

Mar 15th, 2010
by James.
2 comments

Grad students graduating with PhDs right now probably entered grad school at point A, or earlier. People at the end of their first post-doc (and potentially in a position to apply for faculty positions and start training new graduate students themselves) would have entered grad school at point B or earlier.

Today there are a mere 10 published plant genomes out of the more than quarter million named plant species in the world. But even ten genomes is a huge amount of data to deal with for a plant genomics community that largely came of age during the long genome drought of 2002-2006. What is the genome drought? The rice genome was published in April 2002. It was only the second plant genome to be sequenced, and the last plant genome to be published until the poplar genome came out in September of 2006, a gap of more than four years. Two genomes, especially of species as distantly related as arabidopsis and rice doesn’t make for a lot of compelling comparative genomics (Although there was certainly some really cool stuff being discovered in this time period.)

Does that matter? Probably not, but it’s important to remember that the people earning their PhDs today probably entered grad school (and chose a lab and field of study) during that two-plant-genome era (see point A) and less opportunity for exciting research mean less grant money and less ability to attract grad students. The youngest people applying for faculty positions today (assuming they only did one, quite successful, post-doc), also entered grad school in the two genome era (see point B), if not the previous single genome era.

I’m talking about this mostly to make the point that I think comparative genomics as a field of study is getting a lot more exciting as more genomes become avaliable, which is likely to attract more graduate students in that key first year when they join a lab and begin to specialize. Which means as we move farther away from the time of the long genome drought, we will hopefully* start to see a lot more well trained people doing plant genomics.

Which is a good thing because the other point this graph should make (not that I think many people need to be reminded of it), is that the pace of sequencing plant genomes is accelerating, and SOMEONE needs to analyze the huge quantities of data that are already starting to flow through the plant biology community.

This should be the last plant genome themed post for a while, but please continue to let me know if you know/hear about more plant genome projects. jcs98 (@) jamesandthegiantcorn.com

*If the hypothetical end to the also-hypothetical-and-possibly-the-result of-wishful-thinking-on-my-part shortage of plant comparative genomicists could hold off long enough for me to be really in demand when/if I finish grad school, that would be great. ;)

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Sequenced Plant Genomes

Mar 13th, 2010
by James.
7 comments

Libe slope in Ithaca, NY. Behind you are student dorms. At the top of the hill, campus starts. Photo: foreverdigital, flickr (click to see in original context)

When I was an undergraduate, there were exactly two sequenced plant genomes, rice and arabidopsis. And sure maybe I didn’t have to walk “ten miles to school, barefoot, in the snow, uphill, both ways”* the one way I did have to walk uphill (sometimes in the snow but always with shoes), was very uphill. But where was I?

Oh yeah, plant genome sequences. Kids getting into plant genomics these days don’t realize how easy they’ve got it. By my count (which may be low but I’m getting to that) there are ten published plant genomes, with several more unpublished genomes that are available in various states of completion, and lots more on the way.

Which brings me to what I was doing yesterday instead of writing an update for this website: trying to document the published plant genomes, the unpublished genomes that are available, and which new genomes we can expect to see published in the near future.

Please, if you find mistakes or know of additional flowering plant genomes I should mention, let me know! jcs98 (@) jamesandthegiantcorn.com.

If you don’t work in biology, it might be interesting to see which plants have sequenced genomes and how they’re related to each other.

*An explanation of this phrase.

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How many maize/corn genes have actually been studied? (Not a lot)

Feb 22nd, 2010
by James.
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When the maize genome paper came out last November (see the summary of this blog’s maize day coverage) it included information on 32,690 genes within the maize genome.  These were the genes which the researchers involved in sequencing the genome were very confident really were genes. And by themselves those 30,000+ genes put the maize genome way ahead of our own. Of course EVERY plant genome ever sequenced has contained more genes than we do, so you’d think by now this wouldn’t be news any more. We’re not the most genetically complex creatures on the planet, and we’ll just have to learn to live with that fact.

But where was I? Oh yeah, gene counts. 32,690 high confidence genes*. Of those, how many have been studied individually? (more…)

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Newer Tighter CoGe-MaizeGDB demo

Feb 16th, 2010
by James.
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I invested in a new video capture program that lets me record voice overs in real time. There are a few more ums and uhhs but my voice and the action on screen are in much better sync, and I don’t find myself rushing to keep up with the movements of my own mouse or trying to fill apparently dead time while nothing happens on screen. The new video is also two minutes and fifteen seconds shorter, dropping below the psychologically important 5 minute barrier, above which watching a video starts to feel a lot more like work, and I get to show off two new features (visually flagged tandems, and predictions of where a gene would have been before it was lost) that we’re still in the process of rolling out.

Sorry to harp on the same topic a second time, this video is just SO MUCH BETTER than the previous one and I needed to show it off. ;)

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Why to Celebrate the Publication of the Brachypodium Genome

Feb 11th, 2010
by James.
10 comments

Brachypodium distachyon (photo courtesy of Devin O'Conner)

Sorry this is late going up. -James

This morning Nature officially published the paper* describing the sequence of the Brachypodium distachyon genome. This publication brings the number of grass genomes available for comparative analysis to four. In celebration I’m going to list four reasons to be excited about the publication of this genome.

The location of Brachypodium within the grass family tree.

Brachy (as I will refer to the species from here on) is a member of the Pooideae a sub-family of grasses from which no sequenced grasses have come. For the work we do in my lab this is exciting because it adds more depth to our analysis of changes in the grass genomes. The more distantly related grasses we can compare at the whole genome level, the better we can infer what the ancestral species that gave rise to all the grasses might have been like at a genome level. The most we know, or can make educated guesses about that species, the better position we are in to say what changed along the evolutionary paths leading to grasses like maize, rice, and sorghum. The choice of the Pooideae wasn’t at random, or even because of the sub-family’s distant relationship to other sequenced grasses. (more…)

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MaizeGDB and CoGe: A Beautiful Friendship

Feb 9th, 2010
by James.
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Editor’s note: I have a new shorter, better, tutorial, here.

One of the earliest fruits of my work to define relationships between syntenic genes* was a list of sorghum genes and corn genes in one or both of the two related regions of the corn genome (each region in sorghum corresponds to two in corn because the ancestors of corn completely doubled their genome in the time after the ancestors of corn and sorghum went their separate ways.)

But this is not the post where I explain my research projects. That post would be confusing and densely written at the best of times, which two AM in the morning certainly isn’t. Tonight my goal is simply to introduce the embedded video below, which explains how any researchers who want to can check out the relationships I’ve identified between genes in the two duplicate regions of maize, and the genes of the sorghum genome can do so using the MaizeGDB genome browser, and CoGe’s own GenomeViewer application. Video below. If you’re going to watch, I recommend selecting the highest resolution youtube offers you. (more…)

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How to Give an Interesting Research Talk?

Jan 20th, 2010
by James.
4 comments

Corngrass1 a dominant mutant that keeps maize from making the transition to adult growth. The stalk of a normal maize plant is shown to the left for comparison. According to George Chuck, in some genetic backgrounds where they never flower, corngrass plants are potentially immortal, as cuttings of the stalk can be transplanted to new soil and simply continue to grow. (Normally corn plants are annuals, they stop growing once the end of their stalk turns into a tassel and eventually die off even if they're grown in temp. controlled greenhouses.) Photo courtesy of MaizeGDB.org

Just got back from a great talk given by George Chuck, who works on microRNAs that control the transitions between the juvinile and adult phases of plant development in maize at the USDA’s Plant Gene Expression Center. In trying to figure out why it was such a great talks (besides the obvious, that he had exciting data to present).

The obvious ones I could spot where: (more…)

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The Newly Published Soybean Genome and Fractionation

Jan 14th, 2010
by James.
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Here’s the key statistic: The maize genome paper estimated that roughly a quarter of maize genes are currently retained as duplicate pairs from maize’s whole genome duplication, while the soybean paper estimates just over half of soybean genes are similarly retained after soybean’s (apparently slightly older) duplication. <– had it buried at the end of this, but figured it’d be more fun to start out with something cool.

But first of all, let’s do this the right way this time. Here’s the paper in Nature describing the soybean genome. Here’s one of the places you can download the entire sequence from. Hopefully that establishes, beyond a reasonable doubt, that the soybean genome has, in fact, been published. (more…)

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One of the Joys of Comparative Genomics

Dec 1st, 2009
by James.
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I was originally scheduled to fly home yesterday, but was forced to extend my stay by unfortunate chain of events that (among other things) has resulted with me swearing off contact lenses for the foreseeable future.

If I worked with arabidopsis or brachypodium, I’d probably have plants flowering this week that I’d be missing. Without the chance to make the crosses I needed to continue my research I might be set back a month or more while I waiting for new plants to grow. If I was mostly doing wet lab work, I wouldn’t fall as far behind assuming I’d gotten all my projects properly refrigerated or frozen before leaving for Thanksgiving, but the whole week I was gone would still be a complete loss.

Fortunately, I now study comparative genomics, which means, while I won’t get as much done this week as I normally would have, I’m definitely going to continue working. I’ve already shown off my workstation in the lab.

And here is where I’ll be working most of this week.

IMG_0848

I’ve been advised, by people who’ve been doing a lot longer than I have, that working on a laptop long-term is a great way to burn out your hands (carpel tunnel), but for a week it’s no big deal. I can get more work done from here, thousands of miles away, than from an apartment a few blocked from the job, because the faster internet connection means I’m better able to access my own workstation (the first computer pictured), two of the my lab’s servers, and even a Linux box I left running in my apartment, all of which was using for different parts on my work on Monday.

If you look closely you’ll also notice one other difference between the permanent and temporary digs. Just for this week, I have a window!

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Corn vs Maize

Nov 24th, 2009
by James.
2 comments

I use the words basically interchangeably on this site. I know it’s confusing and I at least attempt to pick one and use it all the way through a post (often without success, which I’ll catch, and wince at, days later). The problem is that naturally I use one word or the other depending on context.

The plant in question is studied internationally and while in America “corn” means those cool looking plants that you see me standing in front of one third of the time when you visit this blog, in british english the same word means any grain. I’ve never heard it explicitly said, but I assume the reason the geneticists who study the plant originally called it maize was to avoid confusion from those mixed definitions. It’s also possible “corn” was still considered a slang term back then, and not the sort of name a well educated scientist should be using regardless.

As a result of growing up in the midwest surrounded by corn and getting interested in comparative genomics by way of maize genetics, terms like “corn geneticist” and “corn genome” don’t sound right to my ear and ones like “maize plant” or “maize is selling for $5 a bushel” sound even worse. On the other hand, the sentence “Sequencing the maize genome is going to provide even more powerful tools to corn breeders” sounds fine, but I realize it can be confusing to people whose life experiences are different from my own.*

*An even weirder one: Back when I was still doing science that required writing with pen and paper instead of doing everything on the computer, without thinking about it I’d either cross my sevens or not depending on whether I was writing a number in a scientific context.

A crossed 7. Theoretically this is easier to distinguish from a 1, especially on tassel bags and row stakes that are going to be outside, exposed to the elements for months.

A crossed 7.

Theoretically a crossed 7 is easier to distinguish from a 1, especially on tassel bags and row stakes that are going to be outside, exposed to the elements for months. (And where a mistake has the potential to ruin a year or years of work. It’s not like maize geneticists can run down to Walmart and buy more seeds carrying the genotypes they’ve spent years putting together.)

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