biology

Why I’m so Excited About the Banana Genome

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: (more…)

Panda Genome

Dec 13th, 2009

by James.

3 comments

Can you imagine how much easier it would be to get funding if you too worked on panda biology?

Nature just released a pre-publication copy of a paper detailing the sequencing of the panda genome. The genome was sequenced and assembled using entirely 2nd generation sequencing technologies (specifically the Illumina sequencer) which produced reads that averaged only 53 basepairs long.*

The panda they chose was a three year old female, and they got such resolution (the average individual base pair was sequenced 73 times!) they were even able to identify individual changes in sequence between her two copies of each chromosome.** From this they were able to estimate a difference in the DNA sequence (called a SNP***) occur once every 740 bases which is almost twice the rate of humans. (more…)

Stalling

Dec 11th, 2009

by James.

1 comment

It was a very long day at work and I have nothing interesting to tell you.

Go check out MAT Kinase and John Hawks‘s posts on how human evolution has been driven by the dietary changes of our relatively recent ancestors, farmers and herders rather than hunter-gatherers. (At least in many cases, it’s quite possible someone reading this blog can trace their ancestry back to human populations that remained hunter-gatherers into the 20th century.)

The Domestication of Maize

Nov 23rd, 2009

by James.

2 comments

Twenty thousand years ago, not a single crop species existed in its current form. Almost* every bite of food you eat today is the result huge amounts of human artificial selection, both unconsciously and intentionally by farmers and plant breeders. Sometimes the obvious changes are minor, for example between wild and domesticated strawberries:

Wild strawberry (left) and domesticated strawberry (right)

Clearly one of the major traits early strawberry growers selected for was bigger fruits. Which makes sense since it takes about the same amount of time an effort to pick a strawberry either way, but if you’re picking the ones on the right you’ll have more pounds of fruit picked at the end of the day.

But even in this case, the similarity in form hides major changes at the genome left. Strawberries went through two whole genome duplications during domestication (looks like it’s more complicated than I made it sound see comments), so each of the cells in the strawberries on the right contain eight copies of each chromosome, while the strawberry on the left contains the more standard two copies of each chromosome.

On the other end of the spectrum is maize. (more…)

Of course plants are more genetically complex!

Nov 21st, 2009

by James.

2 comments

Let’s remember back to a time before the human genome project published it’s first draft assembly in 2001. The genome of C. elegans a tiny nematode had already been published with ~20,000 genes. The C. elegans genome is one 1/30 the size of the human genome and the tiny worms are so small that biologists have mapped the developmental fate of every single cell in their bodies (an adult C. elegans has exactly 959 or 1031 cells depending on gender), whereas the human body contains tens of trillions. How many genes would you guess humans have?

Estimates at the time ranged from 40,000 to 150,000 genes. (more…)

Maize: The Genome Sequence Itself

Nov 20th, 2009

by James.

4 comments

The corn genome is ~2.4 gigabases (2.4 billion As, Ts, Cs, and Gs) divided among ten chromosomes. The genome of sorghum, the most closely related species with a sequences genome to maize, is also divided into ten chromosomes, but it’s only less than 800 megabases long, approximately a third the size of maize.

What accounts for the size different? Well since their divergence, maize went through a whole genome duplication, doubling it’s genome to twenty chromosomes (which have since been reduced to ten again, as pieces of chromosomes broke apart and stuck to each other*). Since then a bunch of deletions have also occurred, so only sometimes like 20-30% of the genes from the ancestor of maize and sorghum can still be found in both duplicated regions. Clearly the genome duplication of maize is not responsibly (or at least not solely responsible) for the the enormous size of the maize genome. (more…)

About the Maize Genome Paper

Nov 20th, 2009

by James.

2 comments

Looking at the maize genome paper in isolation it’d be easy to wonder what all the fuss was about. The paper itself is only four pages long with (plus a page of citations), with two figures, and as awesome as figure 1 is (and it really is very, VERY awesome), it doesn’t seem like an lot for a project that represents the work of more than 150 authors over four years. But the real fruits of the maize genome project are the sequences that can be found on either maizesequence.org or maizegdb.org and additional exciting research it is already enabling. And as the result of a quirk the way genome sequence is released to the research community, we can already get a sense of some of that other research. (more…)

Corn Genome

Nov 19th, 2009

by James.

3 comments

So I was mixed up and didn’t think this could be publically mentioned until tomorrow, but the finalized corn genome has come out. Edited this link to point to the ISU coverage which seems to be more detailed than the release from Wash U. If Wash U can mention it, so can I. Expect tomorrow to be a day of corn here at Jamesandthegiantcorn (though it would have been more fun if I could had started the day of corn before this news was publically announced.)

Lots of corn … and maybe some genomics. Consider yourselves forwarned!

Genetically Engineered Crops: Canola

Nov 9th, 2009

by James.

6 comments

Field of Canola in Bloom. Photo: Joe Shlabotnik, flickr (click photo to view Joe's photostream)

Scientific name: Brassica napus

Genetically Engineered Traits: Herbicide Resistance.

Details of Genetic Engineering:

Two companies have produced canola that is resistant to different herbicides.

Monsanto sells canola (Roundup Ready canola) that is resistant to glyphosate, an herbicide monsanto sells under the brand name Roundup and lots of other companies sell under lots of other brand names since the herbicide itself recently came off patent (the resistance trait is still under patent.)

Bayer sells canola (Liberty Link canola) that resists the completely different, if similar sounding herbicide, glufosinate. Glufosinate is sold under a number of brand names (including, you guessed it, Liberty), but I wasn’t able to figure out whether or not it is still under patent.

About Canola:

Derived from the name “Canadian Oil” canola is an oilseed plant also known as rapeseed. The name change came in the 1970s when conventional breeding (this was approx. two decades before the first genetically engineered plants hit the market) created plants with healthier oil and without the bitter taste , and presumably someone to majored in advertising suggested that selling “Rape Oil” would be a good way to go bankrupt.

Two companies have produced canola that is resistant to different herbicides.

Monsanto sells canola (Roundup Ready canola) that is resistant to glyphosate, an herbicide Monsanto sells under the brand name Roundup and lots of other companies sell under lots of other brand names since the herbicide itself recently came off patent (the resistance trait is still under patent.)

About Canola:

Derived from the name “Canadian Oil” canola is breed of the oilseed crop rapeseed. The name change came in the 1970s when conventional breeding (this was approx. two decades before the first genetically engineered plants hit the market) created plants with healthier oil and without the bitter taste people associated with rapeseed oil, and presumably someone to majored in advertising suggested that selling “Rape Oil” would be a good way to go bankrupt.

Close up of Canola Flowers. Photo: Pollobarca2, flickr (click photo to see pollobarca2's photostream)

Rapeseed (the USDA doesn’t break out separate statistics for Canola) was the third biggest source of vegetable oils around the world in 2008-2009 at 20.5 million metric tons, coming in behind only soybeans and oil palms.

Canola is the main oil I use in my own cooking. Canola is apparently one of the healthier sources of vegetable oils, but the two things I most appreciate about it are the high smoke point (it’s harder to burn the oil itself*), and low cost. Last time I checked I was able to find a 48 oz bottle of canola oil for 2.99 which was better than local prices for peanut or corn oil. (Olive oil of course comes in much smaller containers that cost $10 or more, not at all suitable for graduate students.)

*Good for someone who is both as indifferent a cook, and as easily distracted as I am.

Biological Control of Western Corn Rootworms

Nov 8th, 2009

by James.

No comments yet

Face of the Enemy: Adult Western Corn Rootworm chewing on the silks of a corn ear. Picture from wikimedia, apparently in the public domain

This post discusses the paper Degenhardt, J et al. (2009) “Restoring a maize root signal that attracts insect-killing nematodes to control a major pest”

The Western Corn Rootworm (which as you can see from the picture to the right are not actually worms) is estimated to cost farmers in the US alone one billion dollars a year in lost yield and pest control measures. The newly hatched larva begin feeding on root hairs and as they get bigger start attacking the main roots of a corn plant. The damage to the roots from the feeding itself is exacerbated by the open wounds becoming infected. The loss of roots both stresses the plant and reduces yield by decreasing the plant’s supply of nutrients and water, but also makes it much more vulnerable to lodging (getting blown down by a gust of wind). Oh, and did I mention the adults like to feed on the corn plant’s reproductive tissues, decreasing yield even further?

Rootworms are one of the pests controlled by plants genetically engineered to express BT a protein taken from organic agriculture. Without it, the 1 billion dollar price tag for rootworm damage and control would be even higher. But this isn’t an article about bt, it’s an article about how some corn already knows how to call for help when rootworms attack.

Rootworm larva may feast on the roots of maize, but they are in turn eaten by some species of nematodes.* And it turns out some kinds of corn know how to attract nematodes, and when they’re under attack by rootworms they do just that. The nematodes get a delicious meal of rootworms and the corn plant gets to keep more of its roots intact.

How do corn plants attract their, unintentional, nematode defenders? (more…)

biology

Why I’m so Excited About the Banana Genome

Panda Genome

Stalling

The Domestication of Maize

Of course plants are more genetically complex!

Maize: The Genome Sequence Itself

About the Maize Genome Paper

Corn Genome

Genetically Engineered Crops: Canola

Biological Control of Western Corn Rootworms

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