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.

I mention all this to explain why I was so excited to learn that her post this week sings the praises of a group of species near and dear to my heart, the grasses. The whole post is definitely worth a read. Even if you don’t learn something you didn’t already know, read it as a source of inspiration for telling OTHER people how cool grasses are. And the closing is truly excellent:

We usually talk of our domestication of grasses, and the ways in which we have evolved them: we have made plants with bigger, more nutritious seeds that don’t fall to the ground, for example.But their effect on us has been far more profound. Our domestication of grasses, 10,000 years ago or so, allowed the building of the first cities, and marks the start of civilization as we know it. Grasses thus enabled the flowering of a new kind of evolution, a kind not seen before in the history of life: the evolution of human culture.

Some of the comments are heart warming to read as well, although a bunch of people have fallen prey to the maize/corn confusion. (Explained in detail here)

*Speaking of cool science that most of the general public doesn’t know about: We’ve known for more than four years that mutations of the gene talpid2 in chickens cause chicken embyros to develop teeth, something we thought birds had lost the ability to do 60-80 million years ago (around the same time grass was bursting onto the world stage.) Don’t worry too much about getting bitten by a sabertoothed turkey, the toothed embryos have other problems that mean they don’t survive.

**There’s also a three-part video series based on the book that I can best describe as … odd.

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.

Family tree of the sequenced grasses. As you can see, corn (green) and sorghum (blue) are quite closely related, and while brachypodium (red) is more closely related to rice (orange) than it is to the sorghum/corn pair, it's still pretty far away from anything else yet sequenced. Tree visualized in Mesquite ( http://mesquiteproject.org/ ) and is an approximation at best.

As I’ve said many times, both on this site and elsewhere, it is the unrivalled productivity of three grasses (grains) that underpin our civilization. Without corn/maize, rice, and wheat, it might have been that human societies would never have been able to produce enough surplus food so that farmers could support philosophers and copper workers and all that great surplus people who do things other than bring food from the ground. Of the big three grains, rice was the second genome ever sequences and the genome of maize/corn was published this past November. Wheat stands alone as a genome so complex the very though of trying to assemble it makes grown bioinformaticians cry (I’m obviously taking some dramatic license here). As you may have guessed, wheat (and its close relatives barley, rye, and oats) also belong to the Pooideae. Prior to the publication of the brachy genome, wheat geneticists would have to go all the way to rice to find the most closely related species with a sequenced genome. So while the publication of the brachypodium genome may not be of huge excitement to wheat geneticists (the relationship between brachypodium and wheat still last shared a common ancester more than 30 million years ago), it’s still an improvement from their previous situation. (Though it may be cold comfort wheat geneticists, remember the rest of us plant folks are in awe of you.)

Brachypodium Really is the Arabidopsis of the Grass World.

It can be said as an insult, implying that like Arabidopsis, brachy is small and boring, but being small really does have its advantages for research. A lot more brachypodium plants can fit into a given square foot than can corn or sorghum. And from my own experience, brachy takes much better to life in a growth chamber than any other grass species I’ve worked with, which means instead of doing genetics out in a field, with all the costs**, limitations***, and risks**** that entails. Brachy researchers can just grow their plants in growth chambers down the hall (or downstairs) from their labs, a convenience arabidopsis researchers have been enjoying for decades. Personally I think those limitations build character and encourage the development of good habits like planning out one’s research in advance (including fallbacks and alternative avenues), but I’d also be thrilled to see more labs get into grass genetics so on the balance I consider brachy’s arabidopsis-like nature to be a Good Thing.

Brachypodium has a very NICE genome.

A dotplot showing the conserved order of genes in the chromosomes of rice (Oryza sativa) and Brachypodium distachyon. The darker blue diagonal lines represent orthologous genes. The light-blue/cyan lines homeologous regions (ones that were created when the ancestor of all sequenced grasses doubled its whole genome. The regions have evolved independently since but enough duplicated copies of genes are still in the same order that they're easy to spot.) Tree generated using CoGe's Synmap tool ( synteny.cnr.berkeley.edu/CoGe/SynMap.pl ), with color coding based on synonymous substitution rates.

Brachy has only five chromosomes, and, as you can see in the dotplot comparing brachy to rice, the genes line up in long straight syntenic stretches. Even the light blue regions which result from a whole genome duplication in the ancestor of all grasses are relatively long and well defined. You’ll also notice brachypodium only has five chromosomes, to rice’s 12. (Maize/corn and sorghum both have 10)

Transposons, the “jumping genes” that make working in maize so complicated, are a much smaller proportion of the total genome in Brachypodium than in other systems weighing in at less than 27% of the total genome which in total is only 271 megabases long (less than 15% the size of the 2.3 gigabase corn genome which is 85% transposons, which … mumble…carry the one …. means corn has 26.7 TIMES more transposon sequence than brachy, and I sure want to learn more about how brachy keeps its transposons in check.)

The Author List

Publishing a good genome paper is an enormous undertaking, involving collaborations between dozens of research groups across the country or sometimes around the world. Of the, by my count, 135 names attached to the paper paper I can count old employers, current collaborators, science friends and acquaintances, one relative and (at least) one regular reader of this site.

One of those 135 names is also my own. This is from work I did back during my second rotation last winter doing manual verification and analysis of flowering time genes in the brachypodium genome sequence. A very small part of the work that in turn went into a small section of the paper, but this is the first time my name has actually been attached to a peer reviewed publication, EVER! (My undergraduate work made it onto a couple of poster abstracts but no papers, and none the projects I’ve worked on since joining my lab have made it to print yet.)

Random thought:

-Brachypodium is the first sequenced grass that hasn’t been domesticated as a crop. I would expect at least a couple of papers will eventually be published that capitalize on that distinction.

*The International Brachypodium Initiative, “Genome Sequencing and analysis of the model grass Brachypodium distachyon” DOI: 10.1038/nature08747 The genome sequence itself can be accessed at here among other places.

**Especially on urban and suburban campuses, land for a cornfield represents a substantial investment.

***No growing plants in winter unless you’ve got enough green house space (and even then they may not be happy enough to flower), or the money to run a winter field somewhere warm like Hawaii or Puerto Rico. And no way to fix it in August if you realize you didn’t plant enough plants to do get everything you need done.

****The number of people will break into a building to pull plants out of a growth chamber because they (usually mistakenly) have decided they plants are genetically engineered and need to be kills is much lower than the number who will do the same thing to an unguarded cornfield.

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.

The soybean genome has doubled twice since its last common ancestor with other published genomes like grape and arabidopsis. The genome paper dates the more recent duplication as ~13 million years old and the older as ~59 million years old. When I look at homeologous* regions in soybean from the most recent genome duplication, they look more conserved than comparable regions in corn which also underwent a whole genome duplication relatively recently (the maize genome paper estimated the date at 5-12 million years ago), when one would expect a slightly older duplication to be either less conserved, or at most indistigushable from the younger. Dating genome duplications is difficult to do precisely, it’s possible the maize duplication is older and the soybean younger than current measurements suggest. It’s also possible the difference is exaggerated because comparing homeologous maize chromosomes runs into issues with the waves of transposons that have washed over the maize genome in the past ten million years. The favorite explanation I’ve thought of so far is that the different selective pressures and/or reproductive strategies of the wild ancestors of corn and soybean favored or permitted higher loss of duplicate genes in maize or selected for the avoidance of any gene loss in soybean. No idea how to test any of these ideas though…

Comparison of four homologous regions in soybean resulting from the two tetraploidies described in the soybean genome paper. Top two and bottom two are related by the recent tetraploidy, and the top and bottom pairs are related by the older tetraploidy. To load this figure live in CoGe (where you can examine the quality of the blast hits, the identity of the genes and generally have fun) visit: http://tinyurl.com/ydh95oh

After a whole genome duplication, every single gene exists as two separate copes on two different chromosomes. Generally speaking two things can happen to a pair of genes. One possibility is that both copies will be retained for either dosage reasons** or because one copy will take on a new function a change called neofunctionalization, or because each of the new gene copies has specialized in part of the job of the original gene, a change called subfunctionalization. The other, generally more common fate of duplicated genes is that one disappears from the genome. Plant genomes are dynamic places (especially compared to animal genomes, but more on that later) and sequences that don’t provide some benefit aren’t preserved for long***. A lot of my own research has to do with how a genome sheds duplicate genes, and the biases in which kinds of genes are lost and which are preserved and I find it fascinating stuff.

Anyway, to all those involved in sequencing the soybean genome, thank you for giving me even more fascinating information to study.

Previous in depth post on soybeans.

*Homeologous regions are areas of the genome that started out as duplicate copies of the same part of the genome after a whole genome duplication, but have since been evolving on their own, usually in different directions.

**If one set of genes produces a protein that works together with many other genes, doubling all of them at once has no stong effect, but if only one gene loses its extra copy, the ratios of the different proteins could end up out of balance, harming the plant. Since it’s highly unlikely that one copy of all the genes involved would be deleted at the same time, the result is that deletions or serious mutations of any of the copies of any of the genes get selected against, and the plant keeps two copies of all the genes involved for longer than other types of genes.

Think of the genome as a restaurant where there’s one person for every job (we’ll simplify it down to just a hostess, and waitress and a cook). Though it wouldn’t in the real work, hypothetically this ratio works out perfectly, the hostess can seat people fast enough to keep the waitress busy but not overwelm her and the cook is constantly cooking but orders aren’t finished late.. If suddenly the owners decide to hire another person for every job so now there are two cooks, two hostesses, and two waiteresses, everything stays in balance. Twice as many people are seated, which is just enough to be handled by two waitresses, and two cooks exactly handle the doubling of orders. But if any one of our six hypothetical people calls in sick the system breaks down. If the hostess calls in sick not enough people are seated and the waitresses, and cooks spend a lot of time just standing around. If one of the waitresses is out, the one waitress has to try to deal with twice as many constomers as she can actually handle, customers aren’t happy because of the poor quality service, and the cooks and dishwashers are still underutilized. If one of the cooks doesn’t show up, people are seated and their orders get taken promptly, but food arrives late, the cook is stressed out, and the customers are unhappy again. If a cook, a waitress, and a hostess all didn’t show up on the same day, everything would be still be in balance, but since sick days (like knock out mutations of genes) occure independently of each other, anyone not showing up to work will be bad for the restuarant, and losing a gene that functions in a complex will be bad for a plant.

***Before anyone points out transposons as a counterexample of sequences that last a long time without, usually, providing a benefit to a plant, keep in mind that because transposons are self replicating, they generate lots of copies. Most of those copies don’t last for millions of years, and almost all those that do are mangled enough by point mutations and insertion deletions that they can no longer function. Similarly when scaning through the genome it’s common to spot pseudogenes. Bits of sequence that used to be a gene, but have been destroyed by

Humans are inadvertently manipulating bird genetics by innocently providing birds with feeders in winter, according to findings by German researchers. Over less than 30 generations, birds visiting British and European gardens in winter have evolved different-shaped wings and beaks, the scientists say.

In time, they could eventually become a distinct species. The birds breed side-by-side in the same Central European forests, but began to follow different winter migration routes after some discovered rich pickings from humans in Britain.

Eventually they divided into two reproductively separate groups. One continued to fly south for the winter, migrating to Spain to forage for olives and other fruits. The other got into the habit of flying a shorter distance north-west to Britain, where bird-lovers fed them.

If you’re interested and with journal access, here is the scientific paper the story is based on (from current biology).

The single most consumed fruit in America, yet in the tropics this bananas starchy relatives play an even more vital role in feeding whole nations.

At the Plant and Animal Genome Conference next month (which I really wish I was going to), there will be a workshop on banana genomics, but from the abstract submitted by Carine Charron (h/t to Jeremy at the Agricultural Biodiversity Weblog) I learned that:

The sequencing phase will be completed in early 2010 and automatic annotation will take place during the first semester of 2010.

Why is sequencing the banana genome important? Three reasons:

• Despite their image in western cuisine, bananas (particular starchy varieties) are a vital food source for people living throughout the tropics (especially in countries like Uganda and Rwanda where bananas supply close to a third of peoples total calories in a day)
• Because most farmed bananas are sterile breeds, crop breeding (used to great effect to increase yields and disease resistance in most crops of bananas importance) is impossible. A sequenced genome will make it easier to plan and test genetic engineering approaches to increasing the diseases and stress resistance (as well as yield) of bananas.*<– I really enjoyed writing this footnote
• Banana will be the first non-grass monocot to be sequenced. Grasses evolved from the monocots, the same way that birds evolved from dinosaurs. You can’t define a common ancestor of all dinosaurs that isn’t also the ancestor of birds.**

The ancestor of all grasses from turfgrass to corn to bamboo, probably had more in common with this dwarf banana than its wildly successful descendants

As someone who studies grass genomes, the chance to see what the genomes of monocots looked like before the big evolutionary breakthroughs that lead to grasses (one of the younger and most successful groups of plants on the face of the planet if I do say so myself***) is like a bird scientist getting a chance to sequence the genome of a dinosaur species that had somehow survived to the present day. Yes, with only one non-grass monocot genome it’ll be hard to stay which parts represent banana specific changes and which parts are unchanged from the common ancestor of all monocots, but it’ll still be way more than we know today.

The banana genome has been promised before, this story from back in 2001 claimed it would be sequenced in less than five years and been the third genome ever sequenced. But this time it’s actually happening. The sequence data is pouring in, the assembly (putting pieces of the genome together like a giant jigsaw puzzle) and annotation (figuring out which pieces of the genome are actually genes) will soon begin if they haven’t already.

My thanks and appreciation go out to the scientists involved in the complex effort sequencing the banana genome entails (and before that the possibly even more complex effort of getting funding to pay for the sequencing). I know you’re doing it for the people who depend on bananas for food, but you’re making my work as a comparative genomicist even more interesting than it already was (something that seems almost impossible).

If you’re interested in bananas check out my previous posts on the history of the banana and banana biology.

*In fact a lot of the work scientists have done studying the genetic changes that have been selected for during domestication of crops like corn could be leveraged to introduce similar changes in banana. One example is the selection for corn that doesn’t compete as much with its neighbors (reduced shade avoidance response), leaving more energy left over for producing a large ear. The same trait has been selected for in many crops that reproduce sexually. Norman Borlaug’s dwarf wheat is an extreme example of the same principle (although it that case there were also benefits to nitrogen use efficiency). If similar changes were introduced to bananas, farmers would be able to plant bananas closer together and produce more bananas per acre. That sort of change is the closest to a free lunch as you’re going to get in ag research.

**People who study how species are related to each other get very annoyed when anyone starts taking about groups of species that doesn’t have a common ancestor that isn’t the ancestor of any other species not in the same group (such bad groupings are called paraphyletic clades but don’t worry that name isn’t going to be on the midterm). To them birds ARE dinosaurs, because otherwise looking at the group of non-bird dinosaurs is defining a paraphyletic group. For the same reason grasses ARE monocots. I understand why defining groups properly is important to them, and it generally will make biology make more sense, but sometimes I do need to talk about paraphyletic groups like non-grass monocots.

***For most intents and purposes, grasses didn’t exist when dinosaurs walked the earth, yet today grasslands cover 20% of the earth’s land area, and along the way the productivity of key crops like corn, wheat, and rice (all grasses) creating the surpluses of food enabled human civilization.

Go check out MAT Kinase and John Hawks‘s posts on how human evolution has been driven by the dietary changes of our relatively recent ancestors, farmers and herders rather than hunter-gatherers. (At least in many cases, it’s quite possible someone reading this blog can trace their ancestry back to human populations that remained hunter-gatherers into the 20th century.)