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STAG-CNS: Finding smaller conserved promoter regions by throwing more genomes at the problem

Functionless DNA changes more rapidly, functional DNA more slowly. This is one of the fundamental principles of comparative genomics. It’s why people look at the ratio of synonymous nucleotide changes to nonsynonymous nucleotide changes within the coding sequence of genes. It’s why the exons of two related genes will still have strikingly similar sequences after the sequence of the introns have diverged to the point where it’s impossible to even detect homology. It’s also a way to identify which parts of the noncoding sequence surrounding a set of exons are functionally constrained. The bits of noncoding sequence that determine where, and when, and how much, a gene is expressed are by definition, functional, and should diverge more slowly between even related species than the big soup of functionless noncoding sequence that the functional bits of a genome float in. These conserved, functional, noncoding sequences are called, unimaginatively, conserved noncoding sequences (CNS).*

Comparison of a single syntenic orthologous gene pair in the genomes of peach and chocolate. Coding sequence marked in yellow, introns in gray, annotated UTRs in blue. Red boxes are regions of detectably similar sequence between the same genomic region in these two species. Taken from CoGePedia.

I’ve been playing with CNS since I first opened a command line window back as a first year grad student. The smallest CNS we’d consider “real” were 15 base pair exact matches between the same gene in two species. On the one hand, this seemed a bit too big, because I know lots of transcription factors bound to motifs as short as 6-10 base pairs long. On the other hand this seemed a bit too short because I’d see 15 base pair exact matches that couldn’t be real a bit too often (for example a match between a sequence in the intron of one gene, and the sequence after the 3′ UTR of another).

15 bp represented a compromise between the two concerns pushing in opposite directions. Then, in the fall of 2014, a computer science PhD student walked into my office and asked if I had any interesting bioinformatics problems he could work on. The result was a new algorithm (STAG-CNS) which was both more stringent at identifying conserved noncoding sequences and able identify shorter conserved sequences than was previously possible. It achieved both of these goals through the expedient of throwing genomes from more and more species at the problem.


Where the superpowers of superweeds come from

Superman had the yellow sun of earth, spiderman had a radioactive spider-bite, but what about superweeds, where does their super power (surviving application of Round-up/glyphosate) come from?

To understand how superweeds survive, we first have to understand why normal weeds (the Jimmy Olsens and Lois Lanes of the plant world) die. <– last superhero reference of this post I promise. (more…)

Don’t judge the genetic diversity of a species by its cover

Photo: ekpatterson, flickr (click photo to see in original context)

There are more differences in the genomes of two unrelated corn plants than between the genomes of a human and a chimpanzee (two species separated by 3.5 million years of evolution).

On the other hand, two unrelated human beings, members of the same species, have more than four times as many genetic differences as two unrelated heirloom tomatoes.

Genetic Diversity:

Corn vs. Corn > Human vs. Chimpanzee >> Human vs. Human >> Heirloom Tomato vs. Heirloom Tomato

Now the fact that any two human beings are more closely related to each other than either is to a chimpanzee should be obvious to anyone who gives it a moments thought.

I plan to poll my sections tomorrow to see how many of them would put corn and heirloom tomatoes in the opposite positions, but many have figured out my feelings about corn, so they’ll probably guess it’s a trap.

Sequenced Plant Genomes

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.

Two classical maize genes, synteny, and the mystery of the missing gene

Colored aleurone1 and Purple plant1 are both genes with long histories in maize research and are involved in the regulation of anthocyanin biosynthesis.The mutant version of purple plant1 does exactly what it sounds like. (In the proper genetic background) it has plants producing anthocyanin (a purple plant pigment) everywhere, resulting in purple plants. The mutant form of colored aleurone1 was identified from a mutant that changed the color of individual corn kernels. Guess which of these two classic maize mutants made it into the top 15 most published on genes in maize, and which fell barely short.

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…)

Oliva Judson’s Salute to Grasses

People who can actually get the general public interested in science are almost as rare as hen’s teeth.* One of those gifted scientist-communicators is Olivia Judson, an english evolutionary biologist who sometimes writes a column for the nytimes and published an interesting/hilarious pop-science book titled: Dr. Tatiana’s Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex.**

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.

The Most Studied Genes of Maize (and why we love kernel phenotypes)

Unique citations determined from papered linked to from MaizeGDB gene locus pages. Images of c1 and y1 segregating years by Gerald Neuffer and made available through MaizeGDB.

* = tied for number of citations

** = some mutant alleles have kernel phenotypes.

If you want to become one of the famous mutant corn genes, it helps if you have an effect that is visible in corn kernels instead of only from fully grown plants.

And here is why:

  • A geneticist could determine that the version of c1 that creates yellow kernels is recessive to the version that creates purple kernels just from looking at the ear of corn on left.
  • Furthermore, they could tell you that both the male parent (the plant that provided the pollen) and the female parent (the plant on which the ear of corn grew) were both heteryzygous for the c1 genes (they each had one dominant version of the genes and one recessive version), and therefore the corn kernels the parent plants were grown from were both purple.
  • They would know with certainty that all of the yellow kernels contain two recessive versions of the c1 gene.
  • While they couldn’t predict with absolute certainty whether a specific purple corn kernel on that ear carried two dominant versions of the c1 gene or one dominant and one recessive version, they would know there was a 1/3 chance that kernel has two dominant copies, and a 2/3 chance it had one dominant and one recessive copy.
  • That geneticist could make all sorts of predictions about what ears would look like in future generations depending on what colors of corn kernels were planted and which plants were mated with each other.

All this from a single picture of an ear of corn. For a phenotype seen in corn plants but not in kernels (like Knotted1), a geneticist would have to plant a row or more of corn seeds from an ear and examine the growing plants to get the same quantity of information.

And that is why mutations with kernel phenotypes have been so popular over a century of maize genetics research.

Corn Smut

Corn Smut photo: oceandesetoiles, flickr (click to see photo in its original context)

And no that doesn’t mean corn pornography*. Corn smut, or Ustilago maydis, is a fungus that infects corn plants. It’s an old acquantance from my days working in the field. We always used to tell the new hires that corn smut was a rare delicacy in some countries (as we’d been told ourselves), but this was in the days before iPhones so until recently I never actually checked on this bit of received wisdom.

Turns out this particular bit of knowledge was true:

The immature galls, gathered two to three weeks after an ear of corn is infected, still retain moisture and, when cooked, have a flavor described as mushroom-like, sweet, savory, woody, and earthy.

More corn smut. Photo: moskatexugo, flickr (click to see photo in its original context)

I haven’t been able to figure out what the trade off in nutrition is between the ear of corn that is produced by a normal plant and the fungal galls that can be harvested from a plant infected with corn smut. I’d imagine corn smut provides more (and more complete) protein than an ear of corn (assuming corn smut is nutritionally similar to mushrooms.) But what’s the comparison in number of calories? The fungus is certainly sold at a higher price pound for pound.

My renewed interest in corn smut comes courtesy of a new paper** that came out in PLoS Biology describing how the fungus steals energy from infected corn plants without triggering the corn’s usual anti-fungal defenses. It’s an interesting read, you can check out the paper itself since PLoS Biology is open access, or Diane Kelley’s summary at “Science Made Cool.”

I’d seen a number of talks recently about another fungal parasite, powdery mildew in Arabidopsis, but somehow it’s much easier to focus on this stuff now that I can connect it back to corn. Even mammalian systems can be interesting*** once the make that connection.

*Please PLEASE don’t let that phrase start showing up in the search terms people use to find my site!

**Wahl R, Wippel K, Goos S, Kämper J, Sauer N (2010) A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis. PLoS Biol 8(2): e1000303. doi:10.1371/journal.pbio.1000303

***The talk I’m practicing for Monday actually uses an example of a pheromone receptor in new world monkeys that was lost 23 million years ago in old world monkeys (including us humans).

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

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…)

Plant Links of the Day: Diverse Citrus, Extinct Cucurbits, and more

When I woke up (which yes, was only a couple hours ago, but remember I’m on pacific time) I found a whole bunch of interesting plant links waiting in my RSS reader, and I thought I’d pass along a few to you guys.

Keith Robinson writing over at Omics! Omics! posted Celebrating Citrus where he catelogs some of the diversity available to him from local grocery stores before pointing out a citrus review article that suggests all that diversity can be traced back to only three wild species and wraps it up by pointing out the project to sequence the sweet orange genome.

Imagine if you could have a whole series of clementine-like fruits, with the size & easy peeling characteristics but with the whole range of other citrus flavors and colors genetically grafted in — cara cara clementines and blood clementines and ruby red clementines and perhaps even sweet lemontines and key clemenlimes.

Highly recommended.

The Biogeography of Darwin’s Gourd is a post I discovered through research blogging (speaking of which I should really write another entry that meets their standards some day). The gourd of the title is Sicyos villosus, a cucurbit (the group of plants that includes squashes, melons, and pumpkins) collected by Darwin from one of the islands in the Galapagos the better part of two centuries ago … and never again recorded by science. At this point the dried sample collected by Darwin may be the only existence the species ever lived:

The analysis of the cucurbit’s DNA, extracted from the seed samples taken by Darwin, revealed that S. villosus is closest in relation to cucurbits in North America and Mexico. The species probably diverged roughly 4 mya, when the Galapagos were still geologically young. Dispersal was not human in origin, meaning long distance from the mainland, potentially from its spiny fruits stuck to birds, the authors suggest.

How cool is it that we can learn so much from a single sample of a species that has otherwise vanished from the earth?

Finally, by way of DailyKos, comes a pointer to this valentine’s day themed article, clearly written for the non-scientist, where a summary written by me seems superfluous given the title: Sex, Drugs, and Paleo-botany! And yes, the exclamation point is in the original title as well.