Ears segregating for the colored aleurone mutant phenotype. Image courtesy of MG Neuffer via MaizeGDB.

Purple plant1's phenotype is highly variable depending on the genetic background the mutant is in. Images courtesy of MG Neuffer via MaizeGDB.

The two genes are also duplicates (homeologs) resulting from the maize whole genome duplication. From the picture below you can also see both the two genes and the regions they are in match up to single regions in rice and sorghum, two grasses that haven’t gone though a whole genome duplication since the great radiation of grass species that took place an estimated 50 million years ago (well after dinosaurs stopped walking the earth).

More interesting, at least to me, is the fact that there is NO gene equivalent to colored aleurone1 and purple plant1 in the region we’d expect to find such a gene in Brachypodium (the only other grass species with a sequenced genome)*. From all the genes that line up perfectly on either side we can predict the exact location the gene equivalent to colored aleurone1 and purple plant1 should be found in the Brachypodium genome. But the gene isn’t there…

The GEvo panel shown here can be regenerated at: http://tinyurl.com/yddlwor

The original version of this image had Pl1 mislabeled as C1. This version corrects that error.

For a couple more examples of comparisons between the four sequences grass genomes check out the Cogepedia post I spent this morning pulling together.

*The publication of which I celebrated just a little while ago.

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.

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.

I’m still feeling brain dead after the final push for submitting.

Speaking of NSF, here’s the one figure I managed to shoehorn into my research proposal.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy. As usual click the picture to see it fullsized

If you’d like you can even click here to be able to play around with the figure yourself using the CoGe interface. Now I’ve got to try to explain what this figure is about.

The definition of ortholog boils down to being the same gene in different species. Scientists (like me!) can identify orthologs not just by looking for the most similar gene in another species’ genome, but also looking at synteny, the order of genes on chromosomes. Orthologous genes are in the genomes of two species descended from a common ancestor*, and the genes themselves can both trace their history back a gene sitting on a chromosome in that ancestral species. After the two species went their separate ways, each of their genomes began to accumulate differences (mutations). Eventually it can be hard to tell which genes are most closely related to each other, but one of the things that lasts a long time is orthologous genes will has some or many of the same genes nearby on the chromosome, in a similar order to each other, since many genes are still in the same places in the genome as they were in the genome of the common ancestor of both the species being studied.

That’s a huge mouthful. And it gets even more complicated when plants start holding on to extra genomes (something that isn’t too uncommon in plants, see my discussion on the genetics of wheat). Maize (corn) went through such a genome doubling, estimated to have happened ~10 million years ago. So when we compared the genome of corn (which should be getting officially published really REALLY soon) to that of other grass species like rice and sorghum (all the grains we grow (wheat, rice, corn, sorghum, barley, rye, oats, etc) are grasses) there are actually two separate maize regions that are equally related to every sorghum or rice region.**

This figure shows a gene conserved between all four regions and the dna surrounding it. The lines connect blast hits, regions a program (called BLAST) used by lots of biologists as identified as having similar DNA sequences between the the segments from the different genomes.

*One of the reasons comparative genomics is a field that wouldn’t exists if the people who don’t believe in evolution were right.

**That doesn’t mean maize has two copies of every gene present in sorghum and wheat. Right after getting an extra genome copy (technically two extra copies, since normal diploid organisms have two, one from each of their parents to start with, and maize doubled both) it did. Over the past ten million years the extra copies of many genes were lost, either deleted from the genome or accumulating so many mutations that they stopped functioning.