COOOOOOORN!!!

All of my research in undergrad was on corn.

All of it.

For classes, for labs, every lab– corn. We were basically watching a gene become ‘irreducibly complex’ in shoot apical meristems… I mean, it was definitely cool, its just that I couldnt eat corn for years (Im over it now, but I dunno how people like Anastasia do it hehe!).

But now that we have sequenced the whole genome of a few strains of corn, I am now MADLY IN LOVE WITH CORN AGAIN!!

ITS AN EVILUTIONARY POWERHOUSE!!!

RAAAAAAAAAARW!!

The B73 Maize Genome: Complexity, Diversity, and Dynamics

Okay, there is a TON of data here, so Im going to focus on one thing: transposable elements.

When I talk about these things in humans, Im normally talking about ERVs, LINEs, SINEs, and such– These are Class I transposable elements, retrotransposons. They operate by a copy/paste mechanism.

But then there is another group– Class II, DNA transposons. They dont copy/paste, they cut/paste, leaving little nucleotide repeat ‘footprints’ after they move.

The human genome is made up of about 45% of this stuff.

Corn genome?

84.2%

WHOAAA!

A full 75.6% is Class I retrotransposons! Thats so cool!

What does all this transposable-gobbledegook mean? All these repeating nucleotides means there are lots of opportunities for the DNA to accidentally line up wrong, leading to lots and lots and lots of ways corn can duplicate, delete, and rearrange its genome!

The strain of corn they sequenced is B73 (Iowa corn, all I know). When they compared it to another strain, Missouri-17 (Missouri corn, I am a genius, ) check this out:

The researchers also uncovered evidence that maize strains are creating new genes and losing others. For example, at least 180 of B73′s genes are missing from another strain of corn known as Missouri 17 or Mo17. In fact, thousands of pieces of DNA found in one strain are completely missing from the other, Schnable and colleagues report in one of the 10 companion articles published in PLoS Genetics. This degree of structural variation is not seen in any other plant, animal or fungus studied so far, says Schnable.

AHHHHH!

Missouri inbred corn vs Iowa inbred corn and ‘thousands of pieces of DNA found in one strain are completely missing from the other’!! Could you imagine that in humans?? If you had 180 different genes doing different stuff that doesnt exist in my genome???

Thats nuts.

Cant wait to hear more from the plant bio folks (leave links in my comments, please!)!!!

Comments

#1 Mary
November 23, 2009

At James and the Giant Corn I was joking that essentially corn is essentially just a delivery mechanism for TEs. Heh.

James is all over this. Check it out.
#2 ERV
November 23, 2009

Sweeeeeeet!! Thanks!!
#3 D. C. Sessions
November 23, 2009

Could you imagine that in humans?? If you had 180 different genes doing different stuff that doesnt exist in my genome???

Sure, no problem Abbie.

Of course, I do cheat by using an entire chromosome (limited though it is) that you don’t have.
#4 James
November 23, 2009

Someone as excited about the corn genome I am! Keep in mind while there may be at least 180 genes that completely don’t exist between B73 and Mo17, from what I’ve seen there are a lot more which are present in both, but with a big frame-shift mutation bite taken out of one copy.

Maize’s tetraploidy was recent enough a lot of the genes that have been killed by deletions like still hanging around. Though I’m still not sure how we’re going to be able to differentiate between dead genes and ones that are doing completely new and awesome neofunctionalization stuff.
#5 HP
November 24, 2009

And people wonder why I drink so much bourbon.

IT’S AN ANALOGY!

For something, I’m sure.
#6 Party Cactus
November 24, 2009

Wait a minute, I thought that if you added or removed any genes (let alone 180!), than that would set off a chain reaction that would cause the plants to produce genetically modified evil rays? Do we really know the long terms effects of what we’re doing? Obviously, we need an immediate global ban on this whole reproduction thing. It’s clearly far too dangerous to eat food with these mutant genes in them created by such unnatural things as breeding or evolution.

I kid I kid. But do you think this means anything to that sort of argument on the GE side of things?
#7 IanW
November 24, 2009

“All of my research in undergrad was on corn”

And you have the corns to prove it – right?!
#8 Left_Wing_Fox
November 24, 2009

ITS AN EVILUTIONARY POWERHOUSE!!!

GOOD! THEN LET THE MATING… BEGIN!

BWAHAHAHAHAHAHAHHAHA!!!!

http://www.youtube.com/watch?v=vMkGkRw1h7Q

(Sorry, I couldn’t help it. Cool stuff though. Not being one following the research, I wonder if the number of transposons is a result of our millenia of cornbreeding, or if that was what made it easier for us to breed all those varieties of corn in he first place, prior to modern GM.)
#9 Mary
November 24, 2009

About missing human genes: at the ASHG meeting last month Vrijenhoek gave a very nice talk (that started with a hilarious sequence of conversation on facebook, actually) that was called “First map of dispensable regions in the human genome” and went on to describe that if you eliminate all the missing chunks from “normal” folks a lot of your DNA is actually dispensable. What I have in my notes (any errors of data are mine) = In total, 2.8 MB of the genome appears to be dispensable. A lot of single exon genes seem to be dispensable.

Abstract: http://www.ashg.org/2009meeting/abstracts/fulltext/f21182.htm
#10 Prometheus
November 24, 2009

Left_Wing_Fox@8

“I wonder if the number of transposons is a result of our millenia of cornbreeding, or if that was what made it easier for us to breed all those varieties of corn in he first place, prior to modern GM.”

More the latter than the former. Corn’s transposons and resulting high frequency of genetic mutation got Barbara McClintock (Who was awesome!) her Nobel Prize.

Corn bred selectively through human intervention is pretty late in the game compared to other grains. The oldest domesticated variety is popcorn. The Mohica Popcorn poppers used hot wet sand for steam popping. 300 A.D?? maybe??
#11 becca
November 24, 2009

Any idea whether what kind of sequence quality we’ve got? I know multiple copies of highly conserved bits can make it difficult to do the alignments. I’d be curious about what the copy number variation looks like.
#12 James
November 24, 2009

Becca: I’d call the sequence information good but not great. The maize genome was sequenced using a BAC tilling path with shotgun sequencing within every BAC. The ordering of the BACs is quite good. Within the BACs the shotgun sequences are aligned into contigs and sometimes the contigs aren’t in the right order or alignment within the BAC, but from the cases I can check by comparing to the sorghum genome, they got it right more of the time than they had any right to in a genome as big and complex as corn.

There’s a great open access paper on CNV in the genome here: http://dx.doi.org/10.1371/journal.pgen.1000734
#13 titmouse
November 24, 2009

In total, 2.8 MB of the genome appears to be dispensable.

My hypothesis: the useless bits serve to shield the useful bits from ionizing radiation in the folded chromosome.

What do others think?
#14 Prometheus
November 24, 2009

Is corn a Tetraploid or Hexaploid? I know my wheat but I can’t remember corn chromosomes.
#15 James
November 24, 2009

Corn is a middle aged (5-12 million years old) tetraploid. Its current haploid number of ten is the result of breaking and joining twenty chromosomes present right after the tetraploidy.
#16 D. C. Sessions
November 24, 2009

My hypothesis: the useless bits serve to shield the useful bits from ionizing radiation in the folded chromosome.

What do others think?

I think you need to sharpen Occam’s Razor.

Before assuming any kind of utility, first reject the “shop trash” hypothesis: leftover fragments of prior transpositions, fragments of previously inactive-but-present genes, ERV fragments, etc.

Not that all that isn’t useful in its own way — once upon a time I asked people who actually know what they’re talking about if these scraps ever turn into functioning genes and (IIRC) was given examples.
#17 Ian Musgrave
November 24, 2009

Abbie wrote:

What does all this transposable-gobbledegook mean?

Those are the secret instructions the Intelligent Designer put into its favoured creation, which obviously needs so much more transposon-instructions to build its exquisite form than the lowly, less complex primates
#18 386sx
November 25, 2009

Wow, Ian Musgrave’s Intelligent Designer sounds funny, but kinda “corny” though.
#19 Mobius
November 25, 2009

Happy Thanksgiving, All.
#20 David
November 25, 2009

Blatant plug alert. http://crocoduck.bch.msstate.edu/Papers/Ray_et_al_2008_-_Waves_of_bat_transposons.pdf

You mention that Class I’s are the most common in humans. That’s true of mammals in general with one big exception – the most diverse family of bats, Vespertilionidae. They have Class II’s hopping around all over the place and also are amazingly diverse – genus Myotis has over 100 species. In order for adaptation to occur, genome diversity must be there first. TEs are one of the best ways to generate it.
#21 Paul S.
November 25, 2009

Wow, next time I eat corn I’ll try to remember what a genetically remarkable plant I’m eating!

Prometheus: I think that corn (maize) was domesticated before 300 A.D., at least in Central America and Mexico, though it might not have been cultivated in any other part of the Americas until 300 A.D. or later. Still, it did not appear until considerably later than the major domesticated grains of the “Old World”, especially wheat and rice. I think that historians and anthropologists have speculated that corn might have appeared later than other grains because it took a lot more selective breeding to develop into a really useful food plant than other grains did. Apparently, domestic wheat, rice, barley, etc., are still fairly similar to their wild cousins, but domestic varieties of corn are quite different from any wild plant, both genetically and in physical appearance. The difference is so great that there is still debate over exactly what wild species or hybrid was actually the ancestor of domesticated corn.
#22 The Curmudgeon
November 25, 2009

All I know is this: I ain’t no kin to no corn!
#23 Prometheus
November 25, 2009

Paul S.@ 21

You are probably right and I should have said I was working from a conservative “before 300 A.D. in the material archeological record”.

I know reported carbon dating on the New Mexico Bat Cave popcorn was something like 5600 years old which makes me suspicious because that seems to predate the culture that lived there.

I wonder how old the oldest depiction of the Maya “God E” is.
#24 dNorrisM
November 25, 2009

Sure enough, Ian @17:

…..Cornelius Hunter deduces, completely out of thin air, that an elaborate T-urf13-designing mechanism must exist in the corn genome (presumably he thinks this design mechanism was intelligently designed into corn).
< ?blockquote>

Over at PT
#25 dNorrisM
November 25, 2009

Ouch. Link to PT post disappeared.Try again: Sorry.
#26 James
November 26, 2009

Paul: at this point it’s pretty clear corn is a domesticated form of teosinte. I guess there’s still some debate about how much of its genetic material originated from which teosinte subspecies, but given that the two happily interbreed and as well as comparisons of genetic sequences that question has been settled, although you’re absolutely right the wild ancestor of corn was a big question mark for a long time.
#27 Azkyroth
November 26, 2009

Abbie’s posting cr0ns.
#28 complex field
November 26, 2009

well, males have the Y chromosome and females have the X….I guess they really *are* different species!
#29 RBH
November 27, 2009

titmouse conjectured

the useless bits serve to shield the useful bits from ionizing radiation in the folded chromosome.

Anytime one is tempted to conjecture about functionality in dispensable DNA, first apply T. Ryan Gregory’s onion test.
#30 titmouse
November 28, 2009

Yeah I yanked that idea out mah butt.

Guess I was imagining that over time, non-coding regions would tend to get deleted faster than they’d get inserted, unless some selective pressure exists to keep the junk in there.

Deletion mutations seem more likely than insertion mutations (fewer steps). But deletion errors are probably more often fatal.