James and the Giant Corn Genetics: Studying the Source Code of Nature

December 19, 2022

The Paspalum Genome

Filed under: agriculture,biology,genomics,Plants — James @ 4:41 pm

A paper eight years in the making and sixteen months in review. A real credit to Guangchao. I don’t think it ever would have come out without his dedication above and beyond what anyone could expect from a postdoc – James.

A team of researchers, led by Dr. Guangchao Sun and Prof. James Schnable of the University of Nebraska just published the genome of paspalum (Paspalum vaginatum) alongside evidence that paspalum may employ some tricks that could help its relative, corn, grow better with less fertilizer. 

Illustration of a paspalum vaginatum inflorescence.
A flowering paspalum plant growing in the University of Nebraska’s Beadle
Center greenhouses.


The Nebraska team, in collaboration with researchers from the Department of Energy’s Joint Genome Institute, the University of Georgia, and the HudsonAlpha Institute for Biotechnology, wanted to use the new genome sequenced this resilient grass to understand what makes the grass so much more stress tolerant that closely related crops, including corn and sorghum.

Using comparative transcriptomic and metabolomic analyses of paspalum, corn, and sorghum under optimal and stress conditions they identified a specific metabolic pathway — trehalose — that was being produced in paspalum, but not in corn and sorghum, in response to stress. 

The team used a strategy called chemical genetics to convince corn plants to also start producing and accumulating trehalose and showed that these corn plants grew faster and larger in conditions without enough fertilizer than corn plants without extra trehalose. Finally, the team used a combination of experiments to show that the reason these corn plants were able to grow more with less fertilizer was because of a process called autophagy, essentially a recycling program within plant cells that breaks down old, damaged, and unneeded proteins into spare parts that can be used to make new proteins. 

Guangchao Sun working with Aime Valentin Nishimwe measure nitrogen stressed plants in the Schnable lab at the University of Nebraska-Lincoln
Dr. Guangchao Sun working with Aime Valentin Nishimwe to collect data from
plants grown without enough nitrogen fertilizer.

“I’m so excited to see this story come out,” said Prof. Schnable, who is currently taking leave from the University of Nebraska while working at Google. “Paspalum is vegetatively propagated which means we cannot just save seeds, we always have to keep living plants for our research. There was a period where no one remembered to water the paspalum plant for a couple of months. But the plant was completely fine. In fact it usually grows so fast it’ll try to invade the pots of neighboring plants and the greenhouse manager has to yell at me or folks in my lab to come down and trim it. With this genome sequence and all the great work Guangchao Sun and the team have done, we finally are starting to understand just what makes this plant so
resilient.”

Sun, G., Wase, N., Shu, S. et al. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nature Communications 13, 773 (2022) doi: 10.1038/s41467-022-35507-8

January 1, 2022

James and the Tiny Corn Part 3: Even Tinier

Filed under: biology,Genetics,Plants — Tags: , , — James @ 4:42 pm

Back in 2015 we were one of the first groups to get to try out Fast Flowering Mini-Maize (FFMM) [1]. The plants were about two feet tall, flowered in five weeks, and were ready to harvest only 61 days after we planted them. But what if I told you that the same genotype could be even smaller?

This past summer a technician in the lab rediscovered our carefully guarded stash of FFMM seeds and we decided it was time to increase them. While we did most of the increase in the greenhouse, the idea came up at the same time we were finalizing the plans for our summer nursery* so we decided to plant the line in the field as well.

And this was the result:

Fast Flowering Mini Maize in the field in Lincoln Nebraska in the summer of 2021.
Fast Flowering Mini Maize in the field in Lincoln Nebraska in the summer of 2021. Planted May 13th. Photo July 1st. Non-fast flowering non-mini maize in the background was planted approximately one week earlier.
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April 3, 2017

I’ve been saying it for nearly a decade: pineapples really are awesome

Filed under: genomics,Plants — James @ 9:17 am

With all these new third generation sequencing technologies coming out in 2010, hopefully someone will sequence the pineapple genome. If not, maybe the cost of sequencing will drop enough while I’m in grad school that I can sequence the genome myself ( a guy can dream).

An incredibly overused graph, but the reason it’s so overused is that it really is a remarkably useful dataset. Source: https://www.genome.gov/sequencingcostsdata/

Although I was a bit overly optimistic back in 2010 about how fast the cost of sequencing (and critically assembling) genomes would decline. Back then we are all talking about sequencing prices dropping 10x every 1-2 years. This turned out of be a quick burst of innovation brought about by second generation sequencing technologies (primarily 454 at first, then Solexa which became Illumina later on). Like many technologies, there was a lot more low hanging fruit for optimization early on, and the cost of sequencing essentially plateaued from 2011 to 2015.

Of course now we’re finally starting to get those economically viable 3rd generation sequencing technologies I though were right around the corner in 2010. And they still have lots and lots of headspace for optimization (pacbio and oxford nanopore being the two most successful ones at the moment) that maybe in another 6-7 years grad students really will be able to generate genome assemblies on a whim.

In the meantime, hey, we did get a pretty cool pineapple genome assembly a couple of years ago.

Ming R., VanBuren R., Wai C. M., Tang H., Schatz M. C., et al., 2015 The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47: 1435–1442.
Also, here’s a fun video of a 3D scan of the internal structure of a pineapple:

https://twitter.com/CygnusPlantXray/status/848882758692724736

Evidence of my ongoing obsession with pineapples.

Science is fun.

Editor’s note: Robert VanBuren, second author on the pineapple genome, and first author on at least one of dozen or so published grass genome sequences got his own research group out at MSU working on CAM photosynthesis and drought. Check it out!

March 30, 2017

Dichanthelium oligosanthes (One in a Thousand Series)

Filed under: biology,evolution,genomics,One in One Thousand — James @ 8:46 am

Inflorescence of Dichanthelium oligosanthes. Accession “Kellogg 1175”

Out of the ~12,000 known grass species, the genomes of less than one in one thousand have been sequenced. The “One in a Thousand” series focuses on these rare grass species.

Dichanthelium oligosanthes is a wild grass that grows in forest glades throughout the American midwest. It is a small plant. Doesn’t grow particularly fast. Its flowers aren’t particularly striking. And it has enough issues with seed dormancy that growing it in captivity is a major pain. Dichanthelium is a one in one-thousand grass with a sequenced reference genome.*

The reason folks are interested in Dichanthelium isn’t because of what it is, but who it’s related to. Dichanthelium occupies a spot on the grass family tree between a tribe** of grasses that includes foxtail millet and switchgrass, each one in a thousand species themselves, and another tribe of grasses that includes corn and sorghum, two more one in a thousand species. The relationship looks something like this:

Phylogenetic relationship of Dichanthelium oligosanthes to related grasses with sequenced genomes.

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March 28, 2017

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

Filed under: genomics,Plants — Tags: , , — James @ 9:15 am

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.

(more…)

May 11, 2010

Where the superpowers of superweeds come from

Filed under: agriculture,biofortified,Genetics,Plants — Tags: , , — James @ 11:53 am

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…)

April 15, 2010

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

Filed under: agriculture,Genetics,Plants — James @ 12:14 am

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.

March 13, 2010

Sequenced Plant Genomes

Filed under: genomics,Plants,research stories — James @ 7:13 pm

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.

March 8, 2010

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

Filed under: biology,Genetics,genomics,Plants — Tags: , , , , , , — James @ 12:50 pm

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…)

March 3, 2010

Oliva Judson’s Salute to Grasses

Filed under: biology,evolution,Genetics,Plants — Tags: , , , , — James @ 2:33 pm

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.

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