The year is 2002. The first complete version of the human genome is still a year away. The genomes of two plant species have already been published (rice and arabidopsis) but in terms of shere genome size, both species are a drop in the bucket compared to the human genome, or other plant genomes like corn or wheat. But none of this is particularly important except to set the stage.

Two researchers at Rutgers University were sequencing a tiny piece of the maize genome (~0.01%) that surrounded a single gene call bronze1 — the fifth most studied gene in maize — when they found something unexpected.

They had previously 10 identified genes in a single stretch of 32-kb of the maize genome. (A similar gene density throughout the remainder of the maize genome would have resulted in a maize genome containing more than 700,000 genes!) However it was already known that the maize genome was split between small gene-rich islands and vast desolate expanses of transposons (referred to as transposon nests**), and in fact the same study identified a couple of these nests of transposons on either side of their gene rich island (see part A of the second picture in this post).

Below I'll use cartoons, but here's a real and to scale example of a gene rich island I picked at random from maize chromosome 3. Genes and intergenic spaces are to scale. Base image generated with GenomeViewer, part of the CoGe toolkit. http://www.genomevolution.org/CoGe/

Their initial sequencing used DNA from a breed of corn called McC, which I must admit I’ve only ever read about in this particular paper. However, when they decided to sequenced the same region from the genome of B73*** they made three discoveries which I’ve listed in increasing order of strangeness:

1. The giant nests of transposons on either side of the bronze1 gene island were made up of completely different transposons in the two varieties of corn. While this was surprising, transposons are generally squirrelly pieces of DNA. (Part B of the image below.)
2. An new group of transposons had split the bronze1 gene island apart in B73 (Part C of the image below).
3. The last four genes of the island were completely missing (Part D of the image below).

A cartoon summarizing the differences between the bronze1 gene island in the inbred McC (part A) and the same region in B73 (part D), the kind of corn that was used in the maize genome sequencing project. Part B shows the completely different set of transposons found in the two transposon nests bordering the bronze1 island. Part C shows the new cluster of transposons found between genes in the bronze1 island, and part D shows the disappearance of four genes from the bronze1 island. Absolutely nothing is to scale. The arrangement of transposons within clusters in this image was completely random.

The last was a finding that had enormous implications. Out of 13 genes (the ten in the island, plus three more on the far side of one of the transposon nests), four were completely absent in a comparison between two inbred lines. It was a finding that had huge implications for explaining heterosis or hybrid vigor — the observation that the offspring of dissimilar parents tend to be stronger and healthier than the offspring of closely related parents.

The Big Idea:

If you’re a corn plant that is missing a bunch of genes, it’s a good bet your relatives are missing a lot of the same genes, so if you reproduce with them, your kids will have the same missing genes (and the same problems) that you do. But when you mate with a really distantly related corn plant, even if its also missing a lot of genes, they’re not likely to be the same genes, so your children will have at least one working copy of most of the genes either of their parents were missing, and be stronger and healthier as a result.

But there’s a two part punchline to this story:

-The first part is that the lost genes reported in this paper weren’t really genes at all but fragments of genes captured by another type of transposon called helitrons. (A finding reported in a paper from the same lab that made the original discovery (2).) As helitrons move around the genome, they can copy pieces of real genes and carry them with them to their new location. Because the gene fragments are copies of actual genes, they can be dead ringers for the real thing, and the helitron and their capture gene fragments contribute significantly the the difficulty of estimating the true number of genes present in the genome of corn, even a year after the publication of the corn genome. Helitrons also have important implications for evolution, since they provide a mechanism to mix and match pieces of existing genes, potentially creating an occasional new and evolutionary beneficial gene.

-The second part of the punchline is even better. Even though the original lost genes of the bronze1 gene island turned out to not be real genes at all, the arguments made in the original paper for how the complete absence of genes from some inbreds could contribute to hybrid vigor have taken on a new life recently in the maize (corn) genetics community, after the publication of a paper this October that found more than 10% of the genes we’re most confident truly are genes are missing from the genomes of some kinds of corn (3). So even though the original data used to support the idea turned out to not support it after all, the idea that restoring copies of lost genes is at least part of the explanation for hybrid vigor may still prevail. (It has be conclusively shown that the gene content of different kinds of corn really are different, but someone still needs prove that restoring copies of these missing genes makes hybrid plants bigger and stronger).
1. Fu H, & Dooner HK (2002). Intraspecific violation of genetic colinearity and its implications in maize. Proceedings of the National Academy of Sciences of the United States of America, 99 (14), 9573-8 PMID: 12060715

2. Lai J, Li Y, Messing J, & Dooner HK (2005). Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proceedings of the National Academy of Sciences of the United States of America, 102 (25), 9068-73 PMID: 15951422

3. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, & Springer NM (2010). Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome research PMID: 21036921

*Old by my standards, since I hadn’t even begun to study biology back them.

**When some varieties of transposons jump from one location to another in the genome, they prefer to land inside DNA that codes for other transposons instead of near genes. So one transposon lands in between two genes by chance, more transposons target it as a safe place to insert, and before you know it (relatively speaking) a cluster of transposons 100 kilobases or longer has wedged itself into the genome.

***The variety of corn that would ultimately be the source of the complete maize genome seven years later.

Adding a little extra useless DNA doesn’t help an organism survive, but it also doesn’t cause serious harm. But in yesterday’s post I completely avoided one serious question:

When new copies of a transposon get inserted across the genome, what happens to the DNA they land in? For what matter, what kind of DNA do transposons land in in the first place?

The answer to the second question is that different kinds of transposons each have their favorite places to land in the genome. Some transposons like to land in centromeres. Some transposons like to land in other transposons. Some transposons like to land near genes.

Then there are transposons like Mutator. Mutator is a maize/corn transposon that really likes to insert itself into genes. Transposons that usually land in other parts of the genome are also sometimes found in genes.

When a transposon lands in a gene, whether because that’s where it likes to insert or simply by accident, the gene stops working. Depending on which gene has to misfortune to interrupted by a transposon, the effects can range from so-subtle-we-can’t-even-detect-them to so lethal the organism dies before we get a chance to study it. In between are a whole range of effects. From severe developmental mutants, to gorgeous and apparently random streaks of color in flowers, to the spotted corn kernels which were my first introduction to the world of transposons.* (**)

Transposons are always breaking genes. The deadliest mutations disappear from the population as quickly as their appear. More subtle mutations can linger on for generations given rise to all sorts of genetic disorders. And keep in mind many genes can be broken with no visible effect at all. Anything you eat from asparagus to zuccini has the potential to contain genes broken by transposons. And depending on the gene, you’d probably never even know it.

Sorry to put this post up so late (it’s technically already Thursday) and in such a poor shape. I had some craziness in lab today and was waiting (unfortunately without any luck) to hear back about some more interesting stories I could tell about the Mutator transposon.

*To be fair, the last two are actually caused by transposons jumping OUT of genes allowing them to resume their normal function. The original mutations caused by transposons inserting into genes were to break the biochemical pathways used by Dahlia’s to make red pigment in their petals and by corn to produce purple pigment (anthocyanin) in its kernels.

**I really wish there was a good source of freely usable pictures things like transposon sectors in flowers and corn kernels. I can usually find pictures of normal plants on Flickr with creative common licenses. But I really want to be able to show you guys the cool mutants that make genetics so exciting.

But the reason most of genetics-genomics people aren’t in a huge rush to discover the hidden function behind most of this “junk DNA” is because we KNOW what most of it does and where it comes from. It’s not junk, it’s selfish DNA. <– although there’s certainly lots of cool stuff remaining to be discovered in the much smaller fractions of genomes we can’t classify at all.

The difference between junk DNA, and selfish DNA is quite large. One has no apparent function, the other has as a clearly defined function, just one that doesn’t (usually) benefit the organism whose genome that selfish DNA is hanging out in.

Transposons are anything by random DNA. Some contain whole genes that produce proteins devoted to duplicating the transposon. Others don’t even go to that much effort, but instead simply contain recognition sequences to fool the proteins made by other transposons into helping them move.*

Moving around the genome (and making new copies of themselves in the process) are how transposons manage to survive, and sometimes thrive, in genomes without actually helping their host organisms to better survive and reproduce — the two ways a new gene, or new version of an old gene can spread throughout a population.

To understand how this works, imagine a useless bit of DNA that is found only in a single … platypus. Whenever that platypus reproduces, there is a 50% chance its baby will also carry the useless chunk of DNA. But assuming the total population of platypi/platypuses/platypodes isn’t expanding, the average platypus will only have two offspring that survive long enough to have babies of their own. Since only 50% of them got the useless gene in the first place only one platypus survives to pass the useless DNA to one of its two successful offspring, and so on.** That useless DNA is going nowhere fast.

But now imagine that useless DNA knows how to make lots of copies of itself, which get inserted thoughout the genome of our first platypus. Now almost all of that platypuses offspring will inherit at least once copy of of the useless DNA. And that copy will their their genomes with new copies (include the chromosomes they inherited from their other parent), so all of their offspring will inherit the — functionally useless — bit of DNA. In this scenario, the transposon will, on average, go from being found in only one platypus, to two, to 4, to 8, to 16 and so on. In only ten generations we’d expect it to be found in the genomes of more than 1000 platypodes.***

That, in a nutshell, is what transposons are, and how they came to be some common in the genomes (from corn to our own) without giving anything back**** to their host organism.

*Transposons that make all the proteins they need to move on their own are called autonomous transposons. Transposons that need proteins made by other transposons are called non-autonomous transposons.

**In reality, due to the way genetic drift works, a useless piece of DNA that’s present in only a few individuals will eventually be lost entirely. If there’s a 50% chance a given baby platypus will inherit the useless DNA, there’s a 25% chance they’ll both inherit it, and the number of copies of that particular bit of useless DNA in the population will go up. However, there’s also a chance neither of them will inherit it (also 25%) — there’s also a chance this platypus will have only 0 or 1 offspring survive long enough to reproduce. If the copy number goes up a little, it can always come back down a little, but once it hits 0, it never comes back. Even a small chance of a rare piece of useless DNA being lost from the population adds up to a high likelyhood that it will eventually disappear completely over dozens or hundreds of generations.

***If any DNA that wanted to could duplicate itself as much as it wanted, life as we know it would quickly end, the victim of a terminal case of genome bloat. Most organisms have whole systems that attempt to prevent transposons from duplicating (sometimes more successfully than others). But telling you about those defenses would demand a whole week of its own.

****Anything doing so much to reshape the genome the way transposons do is going to end up occasionally changing things for the better, and I’ll touch on a couple of possible examples of that later this week.

But there’s a lot of be happy about! I’m done teaching for a long time. As much as I enjoyed working with the kids in my class, the other responsibilities of teaching (grading, sitting through lectures without the chance to break in for the discussions and arguments that make academia so fun, grading, designing assignments, grading) were really starting to wear me down.

And I’m only three weeks (June 22nd) from either passing my qualifying exam or becoming a beaten and broken shell of a man. For three hours four professors will question me on everything I’ve learned (or should have learned but didn’t) in my education up to this point, and everything I propose to spend the next few years of my life doing. This may not sound like a good thing, but it is. Because my qualifying exam has been hanging over my head all semester,

The lab has a new paper in press, having run the sequential gauntlets of Peer Review, Editorial Evaluation, and finally (and perhaps most dreaded) Your-Figures-Aren’t-High-Resolution-Enough e-mails from the journal’s publication department. But more on the details of that whenever the paper actually shows up.

But what was the point of this entry again? Oh yeah. Transposons. I have a soft spot from transposons (I’m guessing most people who work with maize genetics do). Today we may know that transposons are found in practically every genome under the sun, but they were discovered first in maize using old school genetics (breeding plants together and counting traits in the offspring), before DNA sequencing was a gleam in its inventor’s eye.

And on top of that, some delightfully high-copy number transposons are in the middle of proving a major scientific point for me, so I figured the least I could do was devote a week to them here on the site.

If you’re not a geneticist, should you still care about transposons? Absolutely! Transposons are one of the best arguments, not for why genetic engineering is safe, but for why, if anyone worried about hypothetical unintended consequences of genetic engineering should be worried about any food with DNA in it (and as far as I know, that’s all food.) To paraphrase a seinfield character: “No food for you!”

The week’s schedule:

• Tuesday: An introduction to transposons. Selfish (not junk) DNA.
• Wednesday: Transposon mutagenesis. In which we learn what happens when selfish DNA (transposons) goes head to head with DNA that has learned to cooperate with other DNA to build whole organisms (genes).
• Thursday: Transposons and gene regulation. How tiny transposons are changing the way rice genes respond to stress and where orange cauliflower comes from.
• Friday: Franken-gene! The terrifying (actually awesome) story of a new gene stitched together from pieces of lesser genes by (you guessed it) a transposon!

1.1 pound peach from the Berkeley Farmer's market.

Here. I had no idea anyone was even considering sequencing the peach genome until I heard a single off-hand comment at the maize meeting last month, and all of the sudden here it is. And in better shape in its first release than some genomes are even after they’re published.

This is a pre-publication release, so the Fort Lauderdale Convention is still in effect,* but the peach genome looks really great from the quick and dirty analysis I have already run. They’ve already got the genome assembled into pseudomolecules (chromosomes), unlike some genomes I could mention that have already been published, and marked the locations and structures of genes in the geneome (there was a weird period last summer when there were pre-release versions of the maize genome organized into chromosomes, and pre-release versions with the genes marked, but none that had both.)

*In short, you or I can download the peach genome, play around and study it to our hearts content, but we can’t publish anything on it until the people who actually sequenced the peach genome publish a paper describing their work.

It’s too late to do me any good at the maize meeting, but I have created the figure I think I needed to explain those ideas. Too late for the maize meeting, but maybe I can squeeze it into my qualifying exam proposal. Or maybe the next time I get a chance to give a talk on campus. Let’s just not get into how much of my morning I spent putting this together, and pretend it was a good investment of my time ok?

Click for full size.

Right after its whole genome duplication, the ancestor of maize had twenty chromosomes. Through rearrangements and fusions that number has since dropped back to ten, but it’s still possible to reconstruct the twenty paleo-chromosomes of maize by comparing the order of genes on the maize chromosomes to order of genes in sorghum, a related species of grass/grain that didn’t experience the same whole genome duplication and whose overall genome probably looks a fair bit like the unduplicated ancestor of maize.

The purple lines represent orthologous genes between maize and sorghum. Notice how you can trace a line of purple all the way from top to bottom for both maize1 and maize2 (except for maybe at the bottom of the maize2-region equivalent to sorghum chromosome 6 this looks like it was actually just a bug in the analysis).

This shows, in the most graphical way I can manage, that the genome of maize is made up of two genome copies, each equivalent to the whole genome of sorghum.

Nevertheless. I, through the power of Python*, have split the maize genome in twain. In those rare moments when the excitement about the actual research I do wanes I can still enjoy the fact that I know how to do dramatic, if not scientifically impressive, things like this.

Caveats:

• That doesn’t mean every single gene in sorghum has two copies in maize. After the duplication, many duplicate genes were lost, but the conserved order of genes remains.
• This is only one possible way of arranging the duplicated chromosomes of maize. I’ve grouped the paleo-chromosomes that have lost fewer genes relative to sorghum into maize 1 and the paleo-chromosomes that have lost more genes relative to sorghum into maize 2. But there’s no proof that’s a biologically relevant way to group them. There are 2^9 possible ways to arrange the pairs of chromosomes, and only one of those will accurately reflect the relationships of the chromosomes in the the original duplicated maize genome.

*As well as CoGe’s SynMap and all the various computational tools incorporated into synmap.

Last november when the maize genome was published, one of the companion papers looked at genes where a different number of copies were found in different breds of maize (this is called Copy Number Variation) and genes found in B73 (the variety of maize that was sequenced) but completely missing from the genomes of other varietes. There’s a great post on that paper written up by Mary at OpenHelix.

A few months later, it sounds like this dataset has grown substantially. Over XXXX B73 genes (that’s X% of the filtered B73 gene set!) that appear to be lost (or have sequences so different they no longer register) in at least some varities of maize. And because the new dataset incorporates data from XX different maize breds and XX different teosinte* lines they’re able to identify some of the losses as older because they’re found in multiple comparisons, while some appear to be lost in only a single breed, and might represent more recent losses.

As you can imagine I’d love to get my hands on this dataset myself, but the next best thing will be to take furious notes when Nathan Springer talks about the project on Friday morning**, and being sure to swing by Steven Eichten’s poster soak in the awesomeness.

Ruth A. Swanson-Wagner et al. “Combined Analysis of genomic structural variation and gene expression variation between maize and teosinte populations” Talk #1 2010 Maize Meeting (Presented by Nathan Spinger)

Steven R. Eichten et al. “Extenisve Copy Number Variation Among Maize Lines” Poster #139 2010 Maize Meeting

*Teosinte is the wild species from which maize/corn was domesticated.

**And he’s talking at 8:30 AM on a day when I still plan on being heavily jet lagged.

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.

• Added an entry on Columbine, a member of an early diverging group of eudicots. As far as I can tell this sequence is currently unreleased, but from the JGI website it looks like the initial assembly is already complete, so if you know of a way for people to get ahold of that let me know.
• Added an entry on the Castor Bean. The sequencing group has released a 4x coverage genome assembly. (The castor bean is the source of the deadly toxin ricin, and is not grown in the US, we import our castor oil from other countries.)
• Split the entry on Arabidopsis into “Arabidopsis species and allies“. This gives the Arabidopsis lyrata its own heading, and will be important since there are another 7 species from the Arabidopsis genus and its close relatives in the JGI sequencing pipeline.
• Added an entry on v2 of the date palm genome generated by Weill Cornell Medical College in Qatar. This definitely should still be considered an “in progress” genome, but at least until the banana genome comes out it’s the best non-grass monocot genome available.
• Added an entry on the genome of Physcomitrella patens, which, as a moss, is the descendant of an evolutionary lineage that split from all the other genomes I’ve listed on the page around 450 million years ago.
• Added the recently announced sunflower genome project to the list of planned, in-progress, and private genome efforts. (Apparently the genome of the cultivated sunflower is more 3 gigabases. Bigger than corn!) That’ll be a cool genome to see when it comes out.
• Added information on the woodland strawberry genome project, which aims to have an assembled genome of Fragaria vesca by sometime this year. You may remember the woodland strawberry genome from the mix up back in January.
• Added the various groups that have announced they have private genome sequences of the oil palm genome to the same section.

Particular thanks to Greg, Jeff, and Eric whose suggestions where behind most of these additions.

Completely unrelated, you may have noticed I switched the RSS feed back to full length entries. I recently tried out Google Reader (I’m way behind the times I know), and it is SO MUCH nicer to see the full entries there than have to click through from a brief summary. The downside, as I know from previous experiences, is that when I send out the full entries by RSS I get a lot less traffic.

I don’t earn any income from traffic to this site, but it is a nice feeling to know people are reading and enjoying something I wrote, and I have no way of tracking how many people (if any) read an article from the RSS feed.

Anyway I’ll keep sending out full entries for at least the next week (I expect I’ll be too busy to worry about ego stroking traffic statistics until at least a week from Tuesday.)

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.