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.

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.

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.

To play around with the panel of genes shown at the end of the video, click here. Note that I misspoke during the video voice over, saying the Brachypodium genome hadn’t been sequenced (obviously it has since I ran a BLAST search of it during the video), what I meant to say was that the paper describing the Brachypodum distachyon genome has not yet been published.

The video itself was more an experiment than anything else. At a bare minimum it has convinced me that I need to either invest money in better video editing software, or invest time in checking out the best open source video editors. I did the editing on an ancient version of iMovie that was choking on the high resolution videos I was trying to edit (why many of the transitions are less smooth than I would like.) Ideally I’d also like to hire voice actors to read my lines more clearly, and with fewer ‘uhhs’ than I can manage myself. Since I wasn’t able to do that, please forgive the times when my voice becomes unintelligible, the voice overs were primarily recorded between midnight and 2 am local time.

If you’re interested in using the particular aspect of CoGe I’m advertising today, check out the written tutorial on CoGepedia, or ask me any questions you have directly.

*Genes arranged in the same order in different genomes, or different parts of the same genome

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.